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@@ -111,3 +111,17 @@ token_classification/v_2.0.2/roles_small_mol/test.jsonl filter=lfs diff=lfs merg
 token_classification/v_2.0.2/roles_small_mol/train.jsonl filter=lfs diff=lfs merge=lfs -text
 token_classification/v_2.0.2/roles_small_mol/validation.jsonl filter=lfs diff=lfs merge=lfs -text
 neo_dumps/sourcedata_v2-0-2.db.dump.2023-09-25-08.45.40 filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/ner/test.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/ner/train.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/ner/validation.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/panelization/train.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/panelization/validation.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/roles_gene/test.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/roles_gene/train.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/roles_gene/validation.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/roles_multi/test.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/roles_multi/train.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/roles_multi/validation.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/roles_small_mol/test.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/roles_small_mol/train.jsonl filter=lfs diff=lfs merge=lfs -text
+token_classification/v_2.0.3/roles_small_mol/validation.jsonl filter=lfs diff=lfs merge=lfs -text

token_classification/10-1002_eji-200323730.xml

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+<?xml version='1.0' encoding='UTF-8'?>
+<article doi="10.1002/eji.200323730" abstract="Biochemical and functional studies have demonstrated major histocompatibility complex (MHC) class II-restricted presentation of peptides derived from cytosolic proteins, but the underlying processing and presentation pathways have remained elusive. Here we show that endogenous presentation of an epitope derived from the cytosolic protein neomycin phosphotransferase II (NeoR) on MHC class II is mediated by autophagy. This presentation pathway involves the sequestration of NeoR into autophagosomes, and subsequent delivery into the lytic compartment. These results identify endosomes/lysosomes as the processing compartment for cytosolic antigens and furthermore link endogenous antigen presentation on MHC class II with the process of cellular protein turnover by autophagy."><fig id="710"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=710"/><sd-panel panel_id="980"><p><strong>(A)</strong> The <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="cell_type" role="component" text="T cell" ext_ids="CL:0000084" norm_text="" ext_dbs="CL" in_caption="True" ext_names="T cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">T cell</sd-tag> clone <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="cell_type" role="component" text="20–4/A4" ext_ids="CL:0000084" norm_text="" ext_dbs="CL" in_caption="True" ext_names="T cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">20-4/A4</sd-tag> recognizes an epitope derived from the <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> protein in the context of <sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="subcellular" role="component" text="HLA‐DP3" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐DP3</sd-tag>. <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="subcellular" role="component" text="MHC class II" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MHC class II</sd-tag> expression on <sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="cell" role="experiment" text="RCC1.24" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RCC1.24</sd-tag>‐<sd-tag id="sdTag270" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> cells following <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="protein" role="intervention" text="IFN‐γ" ext_ids="P01579" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IFNG" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IFN‐γ</sd-tag> treatment confers recognition by <sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="cell_type" role="component" text="20–4/A4" ext_ids="CL:0000084" norm_text="" ext_dbs="CL" in_caption="True" ext_names="T cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">20-4/A4</sd-tag>. This recognition is almost completely blocked by the <sd-tag id="sdTag272" source="sdapi" category="entity" entity_type="subcellular" role="component" text="HLA‐DP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐DP</sd-tag>‐specific antibody <sd-tag id="sdTag550">B7/21</sd-tag>. <sd-tag id="sdTag50">EBV‐B</sd-tag> cells transfected with <sd-tag id="sdTag51">pINCO</sd-tag>‐<sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> are able to present endogenous <sd-tag id="sdTag273" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> on <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="subcellular" role="component" text="MHC class II" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MHC class II</sd-tag>. As exemplified by the cell lines <sd-tag id="sdTag52">EBV‐B1.11</sd-tag> (<sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="subcellular" role="component" text="HLA‐DP3" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐DP3</sd-tag>) and <sd-tag id="sdTag53">EBV‐B1.25</sd-tag> (HLA‐DP4), recognition by <sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="cell_type" role="component" text="20–4/A4" ext_ids="CL:0000084" norm_text="" ext_dbs="CL" in_caption="True" ext_names="T cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">20-4/A4</sd-tag> is dependent on <sd-tag id="sdTag276" source="sdapi" category="entity" entity_type="subcellular" role="component" text="HLA‐DP3" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐DP3</sd-tag> expression. Bacterially expressed <sd-tag id="sdTag274" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> protein and a synthetic peptide encompassing amino acids <sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag><sub>216-229</sub> served as controls.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=980"/></sd-panel><sd-panel panel_id="981"><b>(B)</b> <sd-tag id="sdTag55" source="sdapi" category="assay" entity_type="" role="" text="Cross-presentation experiments" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cross-presentation experiments</sd-tag> to exclude release of <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> and re‐uptake as exogenous protein. <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="cell_type" role="component" text="EBV‐B1.25" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.25</sd-tag> cells transfected with the <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="gene" role="intervention" text="neoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><i>neoR</i></sd-tag> expression plasmid <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>‐<sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag>, were co‐cultured for 24 h with the same number of untransfected <sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="cell_type" role="component" text="EBV‐B1.11" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.11</sd-tag> cells, or vice versa. Then, <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="cell_type" role="component" text="T cells" ext_ids="CL:0000084" norm_text="" ext_dbs="CL" in_caption="True" ext_names="T cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">T cells</sd-tag> were added and co‐cultured with the cells for additional 24 h. To test for <sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> release by <i><sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="gene" role="intervention" text="neoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">neoR</sd-tag></i>‐transfected <sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="cell_type" role="component" text="EBV‐B1.11" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.11</sd-tag> cells, total <sd-pretag id="sdPretag14253982055630" parent-tag-id="147" class="component subcellular">supernatant</sd-pretag> (200 μl) of 1×10<sup>5</sup> <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="cell_type" role="component" text="EBV‐B1.11" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.11</sd-tag> cells was harvested 48 h post transfection by centrifugation, and was used as culture media for 1×10<sup>5</sup> untransfected <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="cell_type" role="component" text="EBV‐B1.11" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.11</sd-tag> cells. After 48 h, 1×10<sup>5</sup> <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="cell_type" role="component" text="20–4/A4" ext_ids="CL:0000084" norm_text="" ext_dbs="CL" in_caption="True" ext_names="T cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">20-4/A4</sd-tag> <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="cell_type" role="component" text="T cells" ext_ids="CL:0000084" norm_text="" ext_dbs="CL" in_caption="True" ext_names="T cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">T cells</sd-tag> were added and <sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GM‐CSF" ext_ids="P04141" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CSF2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GM‐CSF</sd-tag> concentration determined after additional 24 h.<graphic href="https://api.sourcedata.io/file.php?panel_id=981"/></sd-panel></fig><fig id="711"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=711"/><sd-panel panel_id="982"><p>(A), <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>‐<sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> transfected <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="EBV‐B1.11" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.11</sd-tag> cells (B), and as control <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>‐<sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="gene" role="component" text="Tyrosinase" ext_ids="7299" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TYR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Tyrosinase</sd-tag>‐transfected <sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="EBV‐B1.11" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.11</sd-tag> cells (C), were either left untreated or treated with 5 μM <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="lactacystin" ext_ids="CHEBI:52722" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lactacystin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">lactacystin</sd-tag> or 50 μM <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="AAF‐CMK" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">AAF‐CMK</sd-tag> for 20 h. Following fixation with 0.5% paraformaldehyde, cells were incubated with <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="cell_type" role="component" text="T cells" ext_ids="CL:0000084" norm_text="" ext_dbs="CL" in_caption="True" ext_names="T cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">T cells</sd-tag>, and 24 h later <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GM‐CSF" ext_ids="P04141" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CSF2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GM‐CSF</sd-tag> release was determined by <sd-tag id="sdTag72" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=982"/></sd-panel><sd-panel panel_id="983"><p>(D) <sd-tag id="sdTag84" source="sdapi" category="assay" entity_type="" role="" text="FACS analysis" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FACS analysis</sd-tag> of <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="cell_type" role="component" text="EBV‐B1.11" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.11</sd-tag> cells (open histograms) and <sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="cell_type" role="component" text="EBV‐B1.11" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.11</sd-tag> cells stably transfected with the <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ICP47" ext_ids="1487353" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="US12" ext_tax_ids="10310" ext_tax_names="Human alphaherpesvirus 2" ext_urls="http://www.ncbi.nlm.nih.gov/gene/"><i>ICP47</i></sd-tag> gene (shaded histograms). Inhibition of <sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="protein" role="component" text="TAP" ext_ids="Q03518" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TAP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TAP</sd-tag> by <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ICP47" ext_ids="1487353" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="US12" ext_tax_ids="10310" ext_tax_names="Human alphaherpesvirus 2" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ICP47</sd-tag> down‐regulates <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="HLA class I" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA class I</sd-tag> but not <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="HLA‐DP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐DP</sd-tag> expression. An isotype‐matched antibody was used as control (thin‐lined histogram). <sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="cell_type" role="component" text="EBV‐B1.11" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.11</sd-tag>‐<sd-tag id="sdTag282" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ICP47" ext_ids="1487353" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="US12" ext_tax_ids="10310" ext_tax_names="Human alphaherpesvirus 2" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ICP47</sd-tag> cells were transfected with <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>‐<sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> (E), <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>‐<sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Tyrosinase" ext_ids="7299" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TYR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Tyrosinase</sd-tag> (F), or mock transfected (<sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>) and <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="MHC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MHC</sd-tag>‐restricted presentation monitored with <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="cell_type" role="component" text="T cells" ext_ids="CL:0000084" norm_text="" ext_dbs="CL" in_caption="True" ext_names="T cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">T cells</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=983"/></sd-panel></fig><fig id="712"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=712"/><sd-panel panel_id="984"><p>(A) <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="cell" role="experiment" text="RCC1.24" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RCC1.24</sd-tag>‐<sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> incubated with <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="protein" role="component" text="IFN‐γ" ext_ids="P01579" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IFNG" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IFN‐γ</sd-tag> were either left untreated (w/o) or treated with <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="chloroquine" ext_ids="CHEBI:3638" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="chloroquine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">chloroquine</sd-tag> or <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="leupeptin" ext_ids="CHEBI:6426" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Leupeptin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">leupeptin</sd-tag> for 24 h to block lysosomal processing. Subsequently cells were fixed with 0.5% paraformaldehyde and tested with <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="cell_type" role="component" text="20–4/A4" ext_ids="CL:0000084" norm_text="" ext_dbs="CL" in_caption="True" ext_names="T cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">20-4/A4</sd-tag> in a <sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GM‐CSF" ext_ids="P04141" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CSF2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GM‐CSF</sd-tag> release assay. <sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="EBV‐B1.11" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.11</sd-tag> cells transfected with <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>‐<sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> (B) or <sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>‐<sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="gene" role="component" text="Tyrosinase" ext_ids="7299" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TYR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Tyrosinase</sd-tag> (C) were tested likewise. Both substances abrogated recognition of <sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="gene" role="intervention" text="neoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">neoR</sd-tag>‐transfected cells, while <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="subcellular" role="component" text="HLA‐A2" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐A2</sd-tag>‐restricted presentation of the <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="protein" role="component" text="tyrosinase" ext_ids="P14679" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TYR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">tyrosinase</sd-tag> peptide was not affected</p><graphic href="https://api.sourcedata.io/file.php?panel_id=984"/></sd-panel><sd-panel panel_id="985"><p><strong>(D)</strong> ) <sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="cell_type" role="component" text="EBV‐B1.11" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.11</sd-tag> cells were incubated with 200 ng/ml of recombinant <sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="protein" role="component" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> protein and treated with <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="leupeptin" ext_ids="CHEBI:6426" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Leupeptin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">leupeptin</sd-tag> or <sd-tag id="sdTag115" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="chloroquine" ext_ids="CHEBI:3638" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="chloroquine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">chloroquine</sd-tag> as described in (A). Presentation of exogenous <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="protein" role="component" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> on <sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="subcellular" role="component" text="HLA‐DP3" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐DP3</sd-tag> is blocked by both substances as well, indicating that <sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="protein" role="component" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> presentation is dependent on lysosomal processing.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=985"/></sd-panel></fig><fig id="713"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=713"/><sd-panel panel_id="986"><p><strong>(A)</strong> <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293T" ext_ids="CVCL_0063" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293T" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">293T</sd-tag> cells transfected with <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>‐<sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> were harvested 6 and 96 h post transfection and <sd-tag id="sdTag286" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> localization within various cell fractions determined by <sd-tag id="sdTag137" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag>. In addition, <sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="undefined" role="experiment" text="supernatant" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">supernatant</sd-tag> of <sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag>‐<sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag> transfected <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293T" ext_ids="CVCL_0063" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293T" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">293T</sd-tag> cells (96 h post transfection) was included to test for release of <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> into the culture <sd-tag id="sdTag289" source="sdapi" category="entity" entity_type="undefined" role="experiment" text="supernatant" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">supernatant</sd-tag>. At 6 h post transfection, <sd-tag id="sdTag287" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> protein becomes detectable in the <sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="cytoplasm" ext_ids="GO:0005737" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="cytoplasm" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">cytoplasm</sd-tag>, while at 96 h post transfection a substantial amount of <sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> protein is also localized in the <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="endosomal/lysosomal" ext_ids="GO:0005764///GO:0005768" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="lysosome///endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">endosomal/lysosomal</sd-tag> fraction. For further characterization of the various fractions, blots were stripped and re‐probed with antibodies specific for the <sd-pretag id="sdPretag14253998394220" parent-tag-id="206" class="component subcellular">cytoplasmic</sd-pretag> protein <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LDH</sd-tag>, the nuclear protein <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="protein" role="assayed" text="c‐myc" ext_ids="P01106" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MYC" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">c‐myc</sd-tag>, early endosomes (<sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Rab‐5" ext_ids="P61020///P20339" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="RAB5B///RAB5A" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Rab‐5</sd-tag>), late endosomes and lysosomes (<sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Lamp‐1" ext_ids="P11279" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Lamp‐1</sd-tag>) and <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> (<sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cytochrome c" ext_ids="P99999" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CYCS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">cytochrome c</sd-tag>), which co‐purify with <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="endosomes/lysosomes" ext_ids="GO:0005764///GO:0005768" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="lysosome///endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">endosomes/lysosomes</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=986"/></sd-panel><sd-panel panel_id="987"><b>(B)</b> <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Endosomal/lysosomal" ext_ids="GO:0005764///GO:0005768" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="lysosome///endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">Endosomal/lysosomal</sd-tag> fractions were prepared from <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>‐<sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag>‐transfected cells 96 h post transfection as in (A). To prevent lysosomal degradation of <sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag>, half of the cells were treated with <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="leupeptin" ext_ids="CHEBI:6426" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Leupeptin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">leupeptin</sd-tag> for the last 48 h. These fractions were separated on a 27% Percoll gradient and eight different fractions collected. Successful separation into fractions with increasing density was verified by <sd-tag id="sdTag158" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis with antibodies directed against <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Lamp‐1" ext_ids="P11279" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Lamp‐1</sd-tag>, <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Rab‐5" ext_ids="P61020///P20339" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="RAB5B///RAB5A" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Rab‐5</sd-tag> and <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cytochrome c" ext_ids="P99999" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CYCS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">cytochrome c</sd-tag>. Inhibition of <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> degradation by <sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="leupeptin" ext_ids="CHEBI:6426" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Leupeptin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">leupeptin</sd-tag> causes accumulation of <sd-tag id="sdTag291" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> protein in the late <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="subcellular" role="component" text="endosomal/lysosomal" ext_ids="GO:0005764///GO:0005768" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="lysosome///endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">endosomal/lysosomal</sd-tag> fractions 7 and 8.<graphic href="https://api.sourcedata.io/file.php?panel_id=987"/></sd-panel><sd-panel panel_id="988"><b>(C)</b> To determine where <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> gains access to the vacuolar system, <sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293T" ext_ids="CVCL_0063" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293T" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">293T</sd-tag> cells were transfected with <sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>‐<sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag>, treated with <sd-tag id="sdTag171" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="leupeptin" ext_ids="CHEBI:6426" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Leupeptin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">leupeptin</sd-tag> to prevent <sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> degradation, and the <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="subcellular" role="component" text="endosomal/lysosomal" ext_ids="GO:0005764///GO:0005768" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="lysosome///endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">endosomal/lysosomal</sd-tag> fractions prepared at various time points post transfection and separated by <sd-tag id="sdTag179" source="sdapi" category="assay" entity_type="" role="" text="Percoll gradient centrifugation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Percoll gradient centrifugation</sd-tag>. Starting at 16 h post transfection, <sd-tag id="sdTag292" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> becomes detectable in the Rab‐5‐positive fraction 5, and then spreads into late <sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="subcellular" role="component" text="endosomal/lysosomal" ext_ids="GO:0005764///GO:0005768" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="lysosome///endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">endosomal/lysosomal</sd-tag> fractions. At 26 h post transfection an almost identical <sd-tag id="sdTag177" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> distribution pattern is observed in cells treated with or without BfA.<graphic href="https://api.sourcedata.io/file.php?panel_id=988"/></sd-panel></fig><fig id="714"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=714"/><sd-panel panel_id="989"><b>(A)</b> <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="cell" role="component" text="RCC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RCC</sd-tag> were transfected with the <sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag>‐<sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> expression construct and subcellular localization of the fusion protein monitored by <sd-tag id="sdTag187" source="sdapi" category="assay" entity_type="" role="" text="UV fluorescence" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UV fluorescence</sd-tag>. As compared to untreated cells, cells treated with <sd-pretag id="sdPretag14253992910590" parent-tag-id="191" class="component molecule">3‐MA</sd-pretag> show a much brighter <sd-tag id="sdTag293" source="sdapi" category="assay" entity_type="" role="" text="UV fluorescence" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UV fluorescence</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=989"/></sd-panel><sd-panel panel_id="990"><b>(B)</b> Semiquantitative analysis of fluorescence intensity of cells transfected with the <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag>‐<sd-tag id="sdTag189" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> fusion construct. Compared to untreated cells, cells treated for 24 h with 7.5 mM <sd-tag id="sdTag191" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635///CHEBI:25272" norm_text="" ext_dbs="ChEBI///ChEBI" in_caption="True" ext_names="3-methyladenine///methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=///http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> show an about threefold increase in mean fluorescence intensity.<graphic href="https://api.sourcedata.io/file.php?panel_id=990"/></sd-panel><sd-panel panel_id="991"><b>(C)</b> <sd-tag id="sdTag195" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis of <i><sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="gene" role="component" text="neoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">neoR</sd-tag></i>‐transfected cells. Treatment of cells with 7.5 mM <sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635///CHEBI:25272" norm_text="" ext_dbs="ChEBI///ChEBI" in_caption="True" ext_names="3-methyladenine///methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=///http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> causes a dramatic increase in <sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> protein levels in only 12 h. The ER‐resident protein <sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="BiP" ext_ids="P11021" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HSPA5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BiP</sd-tag> was used as gel loading control.<graphic href="https://api.sourcedata.io/file.php?panel_id=991"/></sd-panel><sd-panel panel_id="992"><b>(D)</b> This increase in total <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> protein in <sd-tag id="sdTag203" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635///CHEBI:25272" norm_text="" ext_dbs="ChEBI///ChEBI" in_caption="True" ext_names="3-methyladenine///methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=///http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag>‐treated cells is associated with an increase in <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="subcellular" role="component" text="cytoplasmic" ext_ids="GO:0005737" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="cytoplasm" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">cytoplasmic</sd-tag>, and a decrease in <sd-tag id="sdTag204" source="sdapi" category="entity" entity_type="subcellular" role="component" text="endosomal/lysosomal" ext_ids="GO:0005764///GO:0005768" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="lysosome///endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">endosomal/lysosomal</sd-tag> <sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> protein levels.<graphic href="https://api.sourcedata.io/file.php?panel_id=992"/></sd-panel><sd-panel panel_id="993"><b>(E)</b> <sd-tag id="sdTag212" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis of whole cell lysates prepared from <i><sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="gene" role="component" text="neoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">neoR</sd-tag></i>‐transfected cells. Inhibition of protein synthesis by cycloheximide treatment leads to a rapid decrease in <sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> protein levels. Simultaneous treatment of cells with <sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635///CHEBI:25272" norm_text="" ext_dbs="ChEBI///ChEBI" in_caption="True" ext_names="3-methyladenine///methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=///http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> prevents <sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> degradation. <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="BiP" ext_ids="P11021" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HSPA5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BiP</sd-tag> was again used as a gel loading control.<graphic href="https://api.sourcedata.io/file.php?panel_id=993"/></sd-panel></fig><fig id="715"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=715"/><sd-panel panel_id="994"><b>(A)</b> <sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="cell" role="component" text="RCC1.24" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RCC1.24</sd-tag>‐<sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> (endogenous), and <sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="cell" role="component" text="RCC1.24" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RCC1.24</sd-tag> cells to which <sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> protein had been added (exogenous), were treated with different concentrations of <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635///CHEBI:25272" norm_text="" ext_dbs="ChEBI///ChEBI" in_caption="True" ext_names="3-methyladenine///methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=///http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> and cell surface presentation of the <sd-tag id="sdTag296" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag>‐derived peptide on <sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="HLA‐DP3" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐DP3</sd-tag> monitored with the <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="cell_type" role="component" text="T cell clone 20–4/A4" ext_ids="CL:0000084" norm_text="" ext_dbs="CL" in_caption="True" ext_names="T cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">T cell clone 20-4/A4</sd-tag>‐specific <sd-tag id="sdTag297" source="sdapi" category="entity" entity_type="cell_type" role="component" text="T cell clone 20–4/A4" ext_ids="CL:0000084" norm_text="" ext_dbs="CL" in_caption="True" ext_names="T cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">T cell clone 20-4/A4</sd-tag>. Inhibition of autophagy by <sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635///CHEBI:25272" norm_text="" ext_dbs="ChEBI///ChEBI" in_caption="True" ext_names="3-methyladenine///methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=///http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> causes an almost complete inhibition of endogenous antigen presentation, while presentation of exogenous <sd-tag id="sdTag232" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> is not affected.<graphic href="https://api.sourcedata.io/file.php?panel_id=994"/></sd-panel><sd-panel panel_id="995"><b>(B)</b> <sd-tag id="sdTag233" source="sdapi" category="entity" entity_type="cell_type" role="component" text="EBV‐B1.11" ext_ids="CL:0000236" norm_text="" ext_dbs="CL" in_caption="True" ext_names="B cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">EBV‐B1.11</sd-tag> cells transfected with <sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>‐<sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="protein" role="component" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> (endogenous), or incubated with recombinant <sd-tag id="sdTag298" source="sdapi" category="entity" entity_type="protein" role="component" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag> protein (exogenous), were treated with the inhibitors of autophagy, <sd-tag id="sdTag241" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="wortmannin" ext_ids="CHEBI:52289" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="wortmannin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">wortmannin</sd-tag> and <sd-tag id="sdTag237" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635///CHEBI:25272" norm_text="" ext_dbs="ChEBI///ChEBI" in_caption="True" ext_names="3-methyladenine///methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=///http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag>, and <sd-tag id="sdTag238" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="HLA‐DP3" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐DP3</sd-tag>‐restricted presentation of the <sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="Q76MW8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="neoR" ext_tax_ids="474004" ext_tax_names="Dual-tagging gene trap vector pGT1" ext_urls="https://www.uniprot.org/uniprot/">NeoR</sd-tag>‐derived peptide determined. Inhibition of antigen presentation by <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="molecule" role="component" text="leupeptin" ext_ids="CHEBI:6426" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Leupeptin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">leupeptin</sd-tag> served as control.<graphic href="https://api.sourcedata.io/file.php?panel_id=995"/></sd-panel><sd-panel panel_id="996"><b>(C)</b> Presentation of the <sd-tag id="sdTag258" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="HLA‐A2" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐A2</sd-tag>‐restricted <sd-tag id="sdTag257" source="sdapi" category="entity" entity_type="protein" role="assayed" text="tyrosinase" ext_ids="P14679" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TYR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">tyrosinase</sd-tag> peptide in <sd-pretag id="sdPretag14253685948180" parent-tag-id="22" class="component cell">EBV‐B1.11</sd-pretag> cells transfected with <sd-tag id="sdTag260" source="sdapi" category="entity" entity_type="gene" role="component" text="pINCO" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pINCO</sd-tag>‐<sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="gene" role="component" text="Tyrosinase" ext_ids="7299" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TYR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Tyrosinase</sd-tag> is not affected by these inhibitors of autophagy.<graphic href="https://api.sourcedata.io/file.php?panel_id=996"/></sd-panel><sd-panel panel_id="997"><p><sd-pretag id="sdPretag14253716979410" parent-tag-id="84" class="assay">FACS analysis</sd-pretag> of <sd-pretag id="sdPretag14255455279520" parent-tag-id="266">HLA‐class I</sd-pretag> and <sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="HLA‐DP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐DP</sd-tag> expression on <sd-pretag id="sdPretag14253684415850" parent-tag-id="10" class="component cell">RCC1.24</sd-pretag> (D) and <sd-pretag id="sdPretag14253685958140" parent-tag-id="22" class="component cell">EBV‐B1.11</sd-pretag> cells (E) As compared to untreated cells (thick‐lined histogram), treatment of cells with 7.5 mM <sd-pretag id="sdPretag14253993005410" parent-tag-id="191" class="component molecule">3‐MA</sd-pretag> (shaded histogram) does not cause down‐regulation of <sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="HLA‐class I" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐class I</sd-tag> or <sd-pretag id="sdPretag14255456018070" parent-tag-id="265" class="assayed subcellular">HLA‐DP</sd-pretag>. Isotype control is shown as thin‐lined histogram.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=997"/></sd-panel></fig></article>

token_classification/10-1002_eji-200737900.xml

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+<article doi="10.1002/eji.200737900" abstract="Accumulating evidence suggests that intracellular antigens are endogenously presented on MHC class II, but it is still unknown whether antigens within different subcellular compartments are presented with similar efficiency, and via the same or different pathways. We have previously shown that endogenous MHC class II presentation of the cytosolic bacterial antigen neomycin phosphotransferase II (NeoR) is mediated by autophagy. Here, we addressed whether secluding NeoR from this cytoplasmic pathway by directing the protein into the cell nucleus (NucNeoR) would affect antigen presentation. Unexpectedly, NucNeoR was presented at least as efficiently as the cytosolic version of the antigen. Furthermore, presentation of NucNeoR was also dependent on autophagocytosis and lysosomal processing, indicating that both antigens were presented via the same pathway. Inhibition of CRM1-mediated nuclear export did not impede antigen presentation, indicating that NucNeoR gained access to this autophagy-dependent MHC class II presentation pathway by a CRM1-independent route. Thus, this endogenous presentation pathway broadens the spectrum of intracellular antigens surveyed by CD4(+) T cells by efficiently sampling cytoplasmic as well as nuclear antigens."><fig id="716"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=716"/><sd-panel panel_id="998"><p>Subcellular localization of <sd-pretag id="sdPretag14237289255650" parent-tag-id="7" class="intervention protein">NeoR</sd-pretag> and NucNeoR and T cell recognition of <sd-pretag id="sdPretag14237289255651" parent-tag-id="7" class="intervention protein">NeoR</sd-pretag>‐ and NucNeoR‐expressing cells. <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="cell" role="component" text="RCC1.24 cells" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RCC1.24 cells</sd-tag> were transfected with the <sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> (A) and NucNeoR (B) expression constructs. After 2 days, the subcellular localization of the proteins was analyzed by <sd-tag id="sdTag16" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunofluorescence</sd-tag> using the anti <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="protein" role="reporter" text="c‐myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">c‐myc</sd-tag> antibody 9E10. While <sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> was evenly distributed in <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="nucleus" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nucleus</sd-tag> and <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="cytoplasm" ext_ids="GO:0005737" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="cytoplasm" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">cytoplasm</sd-tag> (a), NucNeoR was confined to the cell <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="nucleus" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nucleus</sd-tag> (b). <sd-tag id="sdTag15" source="sdapi" category="assay" entity_type="" role="" text="Daylight photographs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Daylight photographs</sd-tag> of the stained cells are shown in (a') and (b').</p><graphic href="https://api.sourcedata.io/file.php?panel_id=998"/></sd-panel><sd-panel panel_id="999"><b>(C)</b> <sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag>‐ and NucNeoR‐transfected <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="cell" role="component" text="RCC1.24 cells" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14236671549170" parent-tag-id="57" class="component cell">RCC1.24</sd-pretag> cells</sd-tag> were treated with 100 U/mL <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="protein" role="intervention" text="IFN‐γ" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">IFN‐γ</sd-tag> for 48 h to induce <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="protein" role="component" text="MHC class II" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MHC class II</sd-tag> expression. Subsequently, the cells were washed and co‐cultured with the <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="cell" role="component" text="CD4 clone 20‐4/A4" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CD4 clone 20‐4/A4</sd-tag>, which recognizes a peptide derived from <sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> on <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="protein" role="component" text="HLA‐DP3" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HLA‐DP3</sd-tag>. <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GM‐CSF" ext_ids="P04141" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CSF2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GM‐CSF</sd-tag> secretion by the <sd-pretag id="sdPretag14236688669000" parent-tag-id="149">T cells</sd-pretag> was measured 20 h later by <sd-tag id="sdTag27" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag>. Both transfectants were recognized after <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="protein" role="intervention" text="IFN‐γ" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">IFN‐γ</sd-tag> treatment, indicating that directing <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> into the cell nucleus does not abrogate antigen presentation.<graphic href="https://api.sourcedata.io/file.php?panel_id=999"/></sd-panel><sd-panel panel_id="1000"><b>(D)</b> <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="cell" role="component" text="LCL1.11 cells" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LCL1.11 cells</sd-tag> were transfected with <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> or NucNeoR expression plasmids and antigen presentation was assessed 48 h later with the <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag>‐specific <sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="cell" role="component" text="T cell clone 20‐4/A4" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">T cell clone 20‐4/A4</sd-tag>. Antigen‐transfected <sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="cell" role="component" text="LCL1.11 cells" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LCL1.11 cells</sd-tag> were recognized irrespectively of <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> localization, while untransfected cells or cells transfected with a <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐expressing control plasmid were not recognized.<graphic href="https://api.sourcedata.io/file.php?panel_id=1000"/></sd-panel></fig><fig id="717"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=717"/><sd-panel panel_id="1001"><b>(A)</b> <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="cell" role="component" text="RCC1.24" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RCC1.24</sd-tag>‐<sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> and ‐NucNeoR cells were incubated for 48 h with <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="protein" role="intervention" text="IFN‐γ" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">IFN‐γ</sd-tag> and in addition with 7.5 mM <sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> or 200 µM <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="leupeptin" ext_ids="CHEBI:6426" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Leupeptin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">leupeptin</sd-tag> or 100 µM <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="chloroquine" ext_ids="CHEBI:3638" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="chloroquine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">chloroquine</sd-tag> for the last 20 h. Subsequently, the cells were fixed with 0.5% paraformaldehyde and tested with <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="cell" role="component" text="20‐4/A4 cells" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">20‐4/A4 cells</sd-tag> in a <sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GM‐CSF" ext_ids="P04141" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CSF2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GM‐CSF</sd-tag> release assay. Both <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> and NucNeoR were presented by a pathway that involves autophagy and lysosomal processing.<graphic href="https://api.sourcedata.io/file.php?panel_id=1001"/></sd-panel><sd-panel panel_id="1002"><b>(B)</b> <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="cell" role="component" text="LCL1.11 cells" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LCL1.11 cells</sd-tag> transfected with <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> or NucNeoR expression plasmids were tested likewise. Presentation of endogenous <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> and NucNeoR was blocked by all inhibitors, indicating that <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> and NucNeoR presentation is dependent on autophagy and lysosomal processing.<graphic href="https://api.sourcedata.io/file.php?panel_id=1002"/></sd-panel><sd-panel panel_id="1003"><b>(C)</b> To exclude toxic side effects of the inhibitors, <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="cell" role="component" text="LCL1.11 cells" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LCL1.11 cells</sd-tag> were incubated for 20 h with 200 ng/mL recombinant <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> protein in the presence or absence of the inhibitors. Afterwards, residual protein and inhibitors were removed by washing and the cells were co‐cultured with the <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag>‐specific <sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="cell" role="component" text="CD4+ T cell clone 20‐4/A4" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CD4<sup>+</sup> T cell clone 20‐4/A4</sd-tag>. The presentation of exogenous <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> on <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="protein" role="component" text="MHC class II" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MHC class II</sd-tag> was not affected by <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag>, but was impaired when lysosomal processing was blocked with chloroquine or leupeptin.<graphic href="https://api.sourcedata.io/file.php?panel_id=1003"/></sd-panel><sd-panel panel_id="1004"><b>(D)</b> <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="cell" role="component" text="LCL1.11 cells" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LCL1.11 cells</sd-tag> were transfected with siRNA specific for <sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg12" ext_ids="9140" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg12</sd-tag> or <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>, and <sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="gene" role="assayed" text="Atg12" ext_ids="9140" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg12</sd-tag> mRNA levels were determined 24 h later by <sd-tag id="sdTag115" source="sdapi" category="assay" entity_type="" role="" text="qPCR" ext_ids="BAO_0002084" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="real-time PCR " ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">qPCR</sd-tag>. The relative amount of <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg12" ext_ids="9140" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg12</sd-tag> mRNA was reduced approximately fourfold.<graphic href="https://api.sourcedata.io/file.php?panel_id=1004"/></sd-panel><sd-panel panel_id="1005"><b>(E)</b> At 24 h after siRNA transfection, <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> and NucNeoR were expressed in these cells and antigen presentation was assessed 36 h later. In cells transfected with <sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg12" ext_ids="9140" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg12</sd-tag> siRNA, but not in mock‐transfected cells or cells transfected with <sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> siRNA, antigen presentation of both <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> and NucNeoR was greatly reduced.<graphic href="https://api.sourcedata.io/file.php?panel_id=1005"/></sd-panel></fig><fig id="718"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=718"/><sd-panel panel_id="1006"><b>(A)</b> <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="cell" role="component" text="RCC1.24 cells" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RCC1.24 cells</sd-tag> were transfected with the NES‐<sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag>‐<sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐NLS expression construct and subcellular localization of the fusion protein was monitored by UV fluorescence. As compared to untreated cells (a), cells treated with 8 nM <sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LMB" ext_ids="CHEBI:52646" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="leptomycin B" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LMB</sd-tag> for 20 h (b) showed a strong accumulation of the protein in the <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="subcellular" role="component" text="nucleus" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nucleus</sd-tag>. (a') and (b') are the corresponding <sd-tag id="sdTag139" source="sdapi" category="assay" entity_type="" role="" text="daylight photograph" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">daylight photograph</sd-tag>s of the transfected cells.<graphic href="https://api.sourcedata.io/file.php?panel_id=1006"/></sd-panel><sd-panel panel_id="1007"><b>(B)</b> <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag>‐ and NucNeoR‐transfected <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="cell" role="component" text="LCL1.11 cells" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LCL1.11 cells</sd-tag> were either left untreated or incubated for 20 h with 8 nM <sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LMB" ext_ids="CHEBI:52646" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="leptomycin B" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LMB</sd-tag>. Subsequently, the cells were fixed with 0.5% paraformaldehyde and probed with the <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="cell" role="component" text="NeoR‐specific T cells" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR‐specific T cells</sd-tag>. <sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LMB" ext_ids="CHEBI:52646" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="leptomycin B" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LMB</sd-tag> treatment had no significant effect on the presentation of <sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="protein" role="intervention" text="NeoR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NeoR</sd-tag> or NucNeoR on <sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="protein" role="component" text="MHC class II" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MHC class II</sd-tag>, indicating that <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="protein" role="component" text="CRM1" ext_ids="O14980" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="XPO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CRM1</sd-tag>‐dependent nuclear export is not involved in the presentation of this nuclear antigen on MHC class II.<graphic href="https://api.sourcedata.io/file.php?panel_id=1007"/></sd-panel></fig></article>

token_classification/10-1002_eji-200940025.xml

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+<article doi="10.1002/eji.200940025" abstract="The induction of the autophagy machinery, a process for the catabolism of cytosolic proteins and organelles, constitutes a crucial mechanism in innate immunity. However, the involvement of autophagy in human neutrophils and the possible inducers of this process have not been completely elucidated. In this study, the induction of autophagy was examined in human neutrophils treated with various activators and detected by the formation of acidified autophagosomes through monodansylcadaverine staining and via LC-3B conversion screened by immunoblotting and immunofluorescence confocal microscopy. In addition, the expression of the ATG genes was assessed by real-time RT-PCR. We provide evidence that autophagy is implicated in human neutrophils in both a phagocytosis-independent (rapamycin, TLR agonists, PMA) and phagocytosis (Escherichia coli)-dependent initiation manner. ROS activation is a positive mechanism for autophagy induction in the case of PMA, TLR activation and phagocytosis. Furthermore, LC3B gene expression was uniformly upregulated, indicating a transcriptional level of regulation for the autophagic machinery. This study provides a stepping stone toward further investigation of autophagy in neutrophil-driven inflammatory disorders."><fig id="723"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=723"/><sd-panel panel_id="1008"><b>(A)</b> Assessment of <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vacuole" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuole</sd-tag> (arrows) formation in <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> after stimulation with <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> (II) and <sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (III), compared with control cells (I: treated with <sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="undefined" role="component" text="PBS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">PBS</sd-tag> and <sd-tag id="sdTag303" source="sdapi" category="entity" entity_type="tissue" role="component" text="serum" ext_ids="UBERON:0001977" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="serum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">serum</sd-tag>) (magnification 1000×).<graphic href="https://api.sourcedata.io/file.php?panel_id=1008"/></sd-panel><sd-panel panel_id="1009"><b>(B)</b> (I) Presence of late <sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0044754" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> as observed with <sd-tag id="sdTag20" source="sdapi" category="assay" entity_type="" role="" text="MDC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MDC</sd-tag> staining in cells treated with <sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> and <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (RAP) compared with control cells (<sd-tag id="sdTag304" source="sdapi" category="entity" entity_type="undefined" role="component" text="PBS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">PBS</sd-tag>) and cells treated with <sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> and <sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> (magnification 400 and 1000×). (II) Percentage of <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="cell_type" role="component" text="PMN" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">PMN</sd-tag> with acidified <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vacuoles" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuoles</sd-tag> as detected by <sd-tag id="sdTag21" source="sdapi" category="assay" entity_type="" role="" text="MDC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MDC</sd-tag> staining. Data are representative of six independent experiments and are presented as mean±SD; Wilcoxon matched‐pairs test, <sup>*</sup><i>p</i>&lt;0.05: <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> (bar 2: 86.16±6.49%), <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (bar 3: 65.83±8.47%) treated cells, cells treated with <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> and <sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> (bar 4: 9.17±0.75%) and cells treated with <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> and <sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> (bar 5: 8.5±1.87%) compared with control conditions (bar 1: 15.67±3.50%). The percentage of cells with acidified <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0044754" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> in <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="cell_type" role="component" text="PMN" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">PMN</sd-tag> treated with <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> and <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> (bar 4) or <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> and <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> (bar 5) was significantly lower (<i>p</i>&lt;0.05) compared with cells treated with <sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> (bar 2) and <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (bar 3), respectively.<graphic href="https://api.sourcedata.io/file.php?panel_id=1009"/></sd-panel><sd-panel panel_id="1010"><b>(C)</b> Analysis of <sd-tag id="sdTag317" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag>‐I to <sd-tag id="sdTag318" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag>‐II conversion in cells treated with <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> (lane IV) and <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (lane II), as observed by <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> <sd-tag id="sdTag137" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. Effect of <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> in both <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> (lane V) and <sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (lane I)‐treated cells. Lane III: control cells, and lane VI: cells treated only with <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag>. One representative out of six independent experiments is shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=1010"/></sd-panel><sd-panel panel_id="1011"><b>(D)</b> Impact of PI‐3K inhibition using <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LY294002" ext_ids="CHEBI:65329" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="LY294002" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LY294002</sd-tag> on <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> conversion after <sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> challenge (lane III), (lane I: control cells, lane II: <sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag>, lane IV: <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LY294002" ext_ids="CHEBI:65329" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="LY294002" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LY294002</sd-tag> only). One representative out of four independent experiments is shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=1011"/></sd-panel><sd-panel panel_id="1012"><b>(E)</b> <sd-tag id="sdTag66" source="sdapi" category="assay" entity_type="" role="" text="Immunofluorescence confocal microscopy" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Immunofluorescence confocal microscopy</sd-tag> staining of <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag>. (I) Control cells treated with <sd-tag id="sdTag305" source="sdapi" category="entity" entity_type="undefined" role="component" text="PBS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">PBS</sd-tag> and <sd-tag id="sdTag306" source="sdapi" category="entity" entity_type="tissue" role="component" text="serum" ext_ids="UBERON:0001977" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="serum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">serum</sd-tag>, (II) <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag>‐treated cells. 1. <sd-tag id="sdTag54" source="sdapi" category="assay" entity_type="" role="" text="DAPI" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAPI</sd-tag>: blue, 2. <sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag>: red and 3. merge. (III) Percentage of <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="cell_type" role="component" text="PMN" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">PMN</sd-tag> with <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> aggregates. Control conditions (bar 1: 17.7±2.4%), <sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> (bar 2: 3±1.01%), <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> (bar 3: 69±2.1%), PMA and <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> (bar 4: 4±1.9%), <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (bar 5: 56±1.6%). Data are representative of five independent experiments and presented as mean±SD; Student's <i>t</i>‐test, <sup>*</sup><i>p</i>&lt;0.01 compared to the control (bar 1) or the indicated comparision (bar 3 vs 4).<graphic href="https://api.sourcedata.io/file.php?panel_id=1012"/></sd-panel></fig><fig id="724"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=724"/><sd-panel panel_id="3008"><p><em><sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG3" ext_ids="64422" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG3</sd-tag></em> and <em><sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3B</sd-tag></em> gene expression pattern in <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> after stimulation with <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> or <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag>. <em><sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG3" ext_ids="64422" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG3</sd-tag></em> mRNA expression analysis (fold) after <sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> (2.44±0.78) and <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (RAP: 1.81±0.41) stimulation. <em><sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3B</sd-tag></em> gene alterations (<sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag>: 4.98±0.59) and <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (RAP: 1.7±0.55). Effect of <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> pre‐treatment, for both stimuli, was also assessed (<sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag>+<sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag>: <em><sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG3" ext_ids="64422" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG3</sd-tag></em>: 1.36±0.64, <sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3B</sd-tag>: 1.5±0.49 and <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag>+<sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag>: <em><sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG3" ext_ids="64422" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG3</sd-tag></em>: 1.28±0.46, <em><sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3B</sd-tag></em>: 1.24±0.57). No other significant alteration in ATG genes mRNA levels was detected. Representative data of <em><sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG7" ext_ids="10533" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG7</sd-tag></em> mRNA expression analysis after treatment with <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> (1.21±0.42) and <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (0.94±0.64). Data are representative of six independent experiments and presented as mean relative expression±SD. Wilcoxon matched‐pairs test, <sup>*</sup><em>p</em>&lt;0.05 and n.s.=not significant compared with control conditions (dot line) as indicated in the figure. Relative expression (folds) of each gene is derived from substitution of DC<sub>T</sub> values (normalized by <sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="GAPDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAPDH</sd-tag> DC<sub>T</sub> value) in 2<sup>DDCT</sup> equation 36.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3008"/></sd-panel></fig><fig id="725"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=725"/><sd-panel panel_id="1013"><b>(A)</b> (I) <sd-tag id="sdTag93" source="sdapi" category="assay" entity_type="" role="" text="MDC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MDC</sd-tag> staining in <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> treated with <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LPS" ext_ids="CHEBI:16412" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag>, <sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LTA" ext_ids="CHEBI:28640" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipoteichoic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LTA</sd-tag>, <sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="protein" role="intervention" text="peptidoglycan" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">peptidoglycan</sd-tag> (PGN), <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="loxorubin" ext_ids="60737" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="LOXORIBINE" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">loxorubin</sd-tag> (LOX) and <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="R848" ext_ids="CHEBI:36706" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="resiquimod" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">R848</sd-tag> (400×). (II) Percentage of <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="cell_type" role="component" text="PMN" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">PMN</sd-tag> with acidified <sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vacuoles" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuoles</sd-tag> as detected by <sd-tag id="sdTag97" source="sdapi" category="assay" entity_type="" role="" text="MDC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MDC</sd-tag> staining. <sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LPS" ext_ids="CHEBI:16412" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> (50 ng/mL) (bar 2: 69.67±8.21%), <sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LTA" ext_ids="CHEBI:28640" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipoteichoic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LTA</sd-tag> (bar 3: 75.17±9.80%), <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="protein" role="intervention" text="peptidoglycan" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">peptidoglycan</sd-tag> (bar 4: 77±6.96%), <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="loxorubin" ext_ids="60737" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="LOXORIBINE" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">loxorubin</sd-tag> (bar 5: 66.67±5.61%), <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="R848" ext_ids="CHEBI:36706" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="resiquimod" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">R848</sd-tag> (bar 6: 69.5±7.45%), <sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="poly I:C" ext_ids="CHEBI:84491" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="poly(I:C)" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">poly I:C</sd-tag> (bar 7: 16.33±3.14%) and <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="intervention" text="flagellin" ext_ids="P02968" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="hag" ext_tax_ids="224308" ext_tax_names="Bacillus subtilis subsp. subtilis str. 168" ext_urls="https://www.uniprot.org/uniprot/">flagellin</sd-tag> (bar 8: 19.83±5.16%)−treated cells compared with control conditions (bar 1: 14.5±4.97%). Data are representative of six independent experiments and presented as mean±SD; Wilcoxon matched−pairs test, <sup>*</sup><i>p</i><span>&lt;0.05, n.s.=not significant.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=1013"/></sd-panel><sd-panel panel_id="1014"><b>(B)</b> <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> lipidation status of cells treated with <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LPS" ext_ids="CHEBI:16412" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> (lane I), <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LTA" ext_ids="CHEBI:28640" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipoteichoic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LTA</sd-tag> (lane II), <sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="protein" role="intervention" text="peptidoglycan" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">peptidoglycan</sd-tag> (lane III), <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="loxoribin" ext_ids="60737" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="LOXORIBINE" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">loxoribin</sd-tag> (lane IV) and <sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="R848" ext_ids="CHEBI:36706" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="resiquimod" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">R848</sd-tag> (lane V), detected by <sd-tag id="sdTag115" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. One representative out of six independent experiments is shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=1014"/></sd-panel><sd-panel panel_id="1015"><b>(C)</b> <sd-tag id="sdTag309" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag>−II/<sd-tag id="sdTag310" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag>-I ratio as obtained from integrated optical density measurements. <sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LTA" ext_ids="CHEBI:28640" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipoteichoic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LTA</sd-tag> (bar 2: 1.75±0.84), <sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="protein" role="intervention" text="peptidoglycan" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">peptidoglycan</sd-tag> (bar 3: 1.82±1.17), <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LPS" ext_ids="CHEBI:16412" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> (bar 4: 1.9±1.7), <sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="loxorubin" ext_ids="60737" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="LOXORIBINE" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">loxorubin</sd-tag> (bar 5: 1.32±0.49) and <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="R848" ext_ids="CHEBI:36706" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="resiquimod" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">R848</sd-tag> (bar 6: 1.4±0.77) compared with control <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> (bar 1: 0.76±0.30). Data are representative of six independent experiments and are presented as mean±SD. Wilcoxon matched−pairs test, <sup>*</sup><i>p</i><span>&lt;0.05.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=1015"/></sd-panel><sd-panel panel_id="1016"><b>(D)</b> Analysis of <i><sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3B</sd-tag></i> gene expression levels in <sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> treated with TLR agonists. <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LPS" ext_ids="CHEBI:16412" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> (bar 1: 2.27±0.43), <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="protein" role="intervention" text="peptidoglycan" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">peptidoglycan</sd-tag> (bar 2: 2.07±0.42), <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LTA" ext_ids="CHEBI:28640" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipoteichoic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LTA</sd-tag> (bar 3: 2.1±0.49) and <sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="R848" ext_ids="CHEBI:36706" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="resiquimod" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">R848</sd-tag> (bar 4: 1.89±0.35) compared with medium−treated control cells. Dotted line represents <i><sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3B</sd-tag></i> mRNA levels of medium-treated control cells. Data are representative of six independent experiments and are presented as mean relative expression±SD. Wilcoxon matched−pairs test, <sup>*</sup><i>p</i><span>&lt;0.05.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=1016"/></sd-panel><sd-panel panel_id="1017"><b>(E)</b> Assessment of <i>ATG</i> gene expression levels in <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="cell_type" role="component" text="PMN" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">PMN</sd-tag> after <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LPS" ext_ids="CHEBI:16412" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> stimulation (50 ng/mL). <i><sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG3" ext_ids="64422" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG3</sd-tag></i> (bar 1: 2.94±0.52), <sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG4" ext_ids="23192///115201" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="ATG4B///ATG4A" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/"><i>ATG4</i></sd-tag> (bar 2: 1.72±0.42), <i><sd-tag id="sdTag147" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG5" ext_ids="9474" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG5</sd-tag></i> (bar 3: 1.84±0.34), <i><sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG6" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG6</sd-tag></i> (bar 4: 1.8±0.3), <i><sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG7" ext_ids="10533" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG7</sd-tag></i> (bar 5: 3.13±0.64) and <i><sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3B</sd-tag></i> (bar 6: 2.27±0.43) compared with control cells. Dotted line represents mRNA levels of medium-treated cells. Data are representative of six independent experiments and are presented as mean relative expression±SD. Wilcoxon matched−pairs test, <sup>*</sup><i>p</i><span>&lt;0.05.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=1017"/></sd-panel></fig><fig id="726"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=726"/><sd-panel panel_id="1018"><b>(A)</b> (I) Formation of acidified <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0044754///GO:0032009" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="autolysosome///early phagosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> after stimulation with 10 ng/mL of <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="protein" role="intervention" text="IL‐1β" ext_ids="P01584" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IL1B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag>, compared with medium‐treated control cells. (II) Percentage of <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="cell_type" role="component" text="PMN" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">PMN</sd-tag> with acidified <sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vacuoles" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuoles</sd-tag> as detected by <sd-tag id="sdTag154" source="sdapi" category="assay" entity_type="" role="" text="MDC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MDC</sd-tag> staining. <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="protein" role="intervention" text="IL‐1β" ext_ids="P01584" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IL1B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag>‐treated cells (bar 2: 65.17±10.23%) compared with control conditions (bar 1: 15.83±6.08%). Data are representative of six independent experiments and presented as mean±SD; Wilcoxon matched‐pairs test, <sup>*</sup><i>p</i>&lt;0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=1018"/></sd-panel><sd-panel panel_id="1019"><b>(B)</b> <sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> conversion in <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> treated with 10 ng/mL (lane II) and 100 ng/mL (lane III) of <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="protein" role="intervention" text="IL‐1β" ext_ids="P01584" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IL1B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag>. (lane I: medium‐treated control cells). One representative out of five independent experiments is shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=1019"/></sd-panel></fig><fig id="727"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=727"/><sd-panel panel_id="1020"><b>(A)</b> Effect of <sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> on neutrophil phagocytic capacity of opsonized <i><sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i> as observed by <sd-tag id="sdTag171" source="sdapi" category="assay" entity_type="" role="" text="flow cytometry" ext_ids="BAO_0000005" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="flow cytometry" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">flow cytometry</sd-tag>. Percentage of phagocytosing <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> after <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> pretreatment (III) compared with cells incubated with opsonized bacteria (II). Data are representative of six independent experiments and are presented as mean±SD, (I: control unstimulated group), (IV) MFI representation (bar 1: control: 1±1.9, bar 2: <i><sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>: 387.7±33.3, bar 3: <i><sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>+<sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag>: 25.13±18, Wilcoxon matched‐pairs test, <sup>*</sup><i>p</i>&lt;0.05; bar 2 compared with bar 1 and bar 3 compared to bar 2).<graphic href="https://api.sourcedata.io/file.php?panel_id=1020"/></sd-panel><sd-panel panel_id="1021"><p><span>(B) (I) Presence of acidified structures in</span> <em><sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></em>‐<span>phagocytosing neutrophils and medium‐treated control cells. (II) Percentage of <sd-tag id="sdTag298" source="sdapi" category="entity" entity_type="cell_type" role="component" text="PMN" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">PMN</sd-tag> with acidified <sd-tag id="sdTag296" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vacuoles" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuoles</sd-tag> as detected by <sd-tag id="sdTag297" source="sdapi" category="assay" entity_type="" role="" text="MDC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MDC</sd-tag> staining.</span> <em><sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="organism" role="assayed" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></em><span>‐phagocytosing cells (bar 2: 79.33±7.15%) compared with control conditions (bar 1: 14.17±4.79%). Data are representative of six independent experiments and presented as mean±SD; Wilcoxon matched‐pairs test,</span> <span>*</span><em>p</em><span>&lt;0.05. (</span></p><graphic href="https://api.sourcedata.io/file.php?panel_id=1021"/></sd-panel><sd-panel panel_id="1022"><b>(C)</b> <sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8///A6NCE7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3B2" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3B</sd-tag> conversion analysis in <i><sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>‐phagocytosing <sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> (lane II), control <sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> (lane I) and <i><sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>‐phagocytosing <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> after <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> pretreatment (lane III). One representative out of six independent experiments is shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=1022"/></sd-panel><sd-panel panel_id="1023"><b>(D)</b> Effect of <sd-tag id="sdTag191" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> administration to <i><sd-tag id="sdTag192" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>‐phagocytosing <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> 15 min after the initiation of phagocytosis (lane III) as detected by <sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> conversion analysis. Lane II represents <i><sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>‐phagocytosing <sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> and lane I control <sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag>. One representative out of four independent experiments is shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=1023"/></sd-panel><sd-panel panel_id="1024"><b>(E)</b> (I) Percentage of <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> with <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> punctuated structures. <i><sd-tag id="sdTag203" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i> (bar 1: 84±2.2%) compared with <i><sd-tag id="sdTag204" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>+<sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> (bar 2: 4±1.95%). Data are representative of six independent experiments and presented as mean±SD. Wilcoxon matched‐pairs test, <i><sup>*</sup>p</i><span>&lt;0.05. (II) Formation of</span> <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> puncta in phagocytosing <sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> and (III) in cells treated with <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> before incubation with opsonized <i><sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>, as observed by <sd-tag id="sdTag215" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence confocal microscopy" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">immunofluorescence confocal microscopy</sd-tag> (1. <sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag>: red; 2. <sd-tag id="sdTag216" source="sdapi" category="assay" entity_type="" role="" text="FITC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FITC</sd-tag> conjugated <i><sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="organism" role="assayed" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>: green; 3. <sd-tag id="sdTag212" source="sdapi" category="assay" entity_type="" role="" text="DAPI" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAPI</sd-tag>: blue; and 4. merge). Solid line arrows point the colocalization of <sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> puncta with <i>E</i>. <i>coli</i> bacteria. Dashed line arrows point <sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> aggregates that are not colocalized with <i>E</i>. <i>coli</i>.<graphic href="https://api.sourcedata.io/file.php?panel_id=1024"/></sd-panel></fig><fig id="728"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=728"/><sd-panel panel_id="3010"><p>Alterations in <em>ATG</em> gene expression after phagocytosis of opsonized <em><sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></em>. <em><sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG3" ext_ids="64422" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG3</sd-tag></em> (2.05±0.27), <em><sd-tag id="sdTag286" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG4" ext_ids="23192///115201" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="ATG4B///ATG4A" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">ATG4</sd-tag></em> (2.20±0.27), <em><sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG5" ext_ids="9474" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG5</sd-tag></em> (2.89±0.42), <em><sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG6" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG6</sd-tag></em> (2.04±0.40), <em><sd-tag id="sdTag282" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG7" ext_ids="10533" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG7</sd-tag></em> (1.98±0.30) and <em><sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3B</sd-tag></em> (2.46±0.39) gene expression (fold) in <em><sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></em>‐phagocytosing <sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> compared with control cells. Dotted line represents mRNA expression levels of control cells. Data are representative of six independent experiments and are presented as mean relative expression±SD Wilcoxon matched‐pairs test, <sup>*</sup><em>p</em>&lt;0.05.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3010"/></sd-panel></fig><fig id="729"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=729"/><sd-panel panel_id="1025"><b>(A)</b> <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> conversion status after pretreatment with the <sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="molecule" role="component" text="ROS" ext_ids="CHEBI:26523" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="reactive oxygen species" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ROS</sd-tag> scavenger <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BHA" ext_ids="CHEBI:76359" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="butylated hydroxyanisole" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BHA</sd-tag> prior to <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> or <i><sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i> stimulation (lane I: <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag>, lane II: <sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag>+<sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BHA" ext_ids="CHEBI:76359" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="butylated hydroxyanisole" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BHA</sd-tag>, lane III: <i><sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>, lane IV: <i>E</i>. <i>coli</i>+<sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BHA" ext_ids="CHEBI:76359" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="butylated hydroxyanisole" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BHA</sd-tag>, lane V: control cells). One representative out of four independent experiments is shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=1025"/></sd-panel><sd-panel panel_id="1026"><b>(B)</b> <sd-tag id="sdTag230" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> conversion status after pretreatment with the <sd-tag id="sdTag235" source="sdapi" category="entity" entity_type="subcellular" role="component" text="NADPH oxidase" ext_ids="GO:0043020" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="NADPH oxidase complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">NADPH oxidase</sd-tag> inhibitor <span><sd-tag id="sdTag320" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DPI" ext_ids="CHEBI:77986" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dibenziodolium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DPI</sd-tag></span> in <sd-tag id="sdTag299" source="sdapi" category="entity" entity_type="organism" role="intervention" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/"><i>E</i>. <i>coli</i></sd-tag>−phagocytosing <sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> (lane I: <sd-tag id="sdTag313" source="sdapi" category="entity" entity_type="undefined" role="component" text="PBS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">PBS</sd-tag>, lane II: <i>E</i>. <i>coli</i>, lane III: <i><sd-tag id="sdTag232" source="sdapi" category="entity" entity_type="organism" role="component" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>+<sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DPI" ext_ids="CHEBI:77986" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dibenziodolium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DPI</sd-tag>). One representative out of four independent experiments is shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=1026"/></sd-panel><sd-panel panel_id="1027"><b>(C)</b> (I) Effect of <sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="subcellular" role="component" text="NADPH‐oxidase" ext_ids="GO:0043020" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="NADPH oxidase complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">NADPH‐oxidase</sd-tag> inhibition with <sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DPI" ext_ids="CHEBI:77986" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dibenziodolium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DPI</sd-tag> in the formation of acidified <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0044754///GO:0032009" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="autolysosome///early phagosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> in <i><sd-tag id="sdTag241" source="sdapi" category="entity" entity_type="organism" role="component" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>‐phagocytosing <sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag>. (II) Percentage of <sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="cell_type" role="component" text="PMN" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">PMN</sd-tag> with acidified <sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vacuoles" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuoles</sd-tag> as detected by <sd-tag id="sdTag245" source="sdapi" category="assay" entity_type="" role="" text="MDC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MDC</sd-tag> staining. <i><sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="organism" role="component" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i>−phagocytosing <sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="cell_type" role="component" text="PMN" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">PMN</sd-tag> (77.17±8.33%) and <sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="cell_type" role="component" text="PMN" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">PMN</sd-tag> treated with <sd-tag id="sdTag249" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DPI" ext_ids="CHEBI:77986" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dibenziodolium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DPI</sd-tag> before incubation with opsonized <i><sd-tag id="sdTag250" source="sdapi" category="entity" entity_type="organism" role="component" text="E. coli" ext_ids="562" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Escherichia coli" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">E. coli</sd-tag></i> (21.67±4.37%). Data are representative of six independent experiments and presented as mean±SD; Wilcoxon matched‐pairs test, <sup>*</sup><i>p</i><span>&lt;0.05</span><graphic href="https://api.sourcedata.io/file.php?panel_id=1027"/></sd-panel><sd-panel panel_id="1028"><b>(D)</b> (I) Assessment of formation of acidified <sd-tag id="sdTag253" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0044754///GO:0032009" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="autolysosome///early phagosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> in <sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> pretreated with <sd-tag id="sdTag261" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BNP" ext_ids="CHEBI:77433" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="alpha-(4-hydroxyphenyl)-N-tert-butylnitrone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BNP</sd-tag> before stimulation with <sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="protein" role="intervention" text="peptidoglycan" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">peptidoglycan</sd-tag> (PGN), compared with cells treated with PGN. (II) Percentage of <sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="cell_type" role="component" text="PMN" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">PMN</sd-tag> with acidified <sd-tag id="sdTag257" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vacuoles" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuoles</sd-tag> as detected by <sd-tag id="sdTag258" source="sdapi" category="assay" entity_type="" role="" text="MDC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MDC</sd-tag> staining. PGN‐treated <sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> (74.83±9.09%) and <sd-tag id="sdTag260" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> pretreated with <sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BNP" ext_ids="CHEBI:77433" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="alpha-(4-hydroxyphenyl)-N-tert-butylnitrone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BNP</sd-tag> before the addition of PGN (17.33±2.07%) compared with control conditions (14.67±3.20%). Data are representative of six independent experiments and presented as mean±SD; Wilcoxon matched‐pairs test, <sup>*</sup><i>p</i>&lt;0.05, n.s.=not significant:<graphic href="https://api.sourcedata.io/file.php?panel_id=1028"/></sd-panel><sd-panel panel_id="1029"><b>(E)</b> Alterations in <sd-tag id="sdTag264" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> conversion in <sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BNP" ext_ids="CHEBI:77433" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="alpha-(4-hydroxyphenyl)-N-tert-butylnitrone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BNP</sd-tag> pretreated, <sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="protein" role="intervention" text="peptidoglycan" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">peptidoglycan</sd-tag>‐stimulated <sd-tag id="sdTag267" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neutrophils" ext_ids="CL:0000775" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neutrophil" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neutrophils</sd-tag> (lane III), (lane I: medium‐treated cells, lane II: <sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="protein" role="intervention" text="peptidoglycan" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">peptidoglycan</sd-tag>‐treated cells). One representative out of four independent experiments is shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=1029"/></sd-panel><sd-panel panel_id="1030"><b>(F)</b> Effect of PI3K inhibition with <sd-tag id="sdTag271" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> in the percentage of <sd-tag id="sdTag272" source="sdapi" category="entity" entity_type="molecule" role="component" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag>‐induced oxidizing cells. <sd-tag id="sdTag273" source="sdapi" category="entity" entity_type="molecule" role="component" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag> (99.41±0.33%) and <sd-tag id="sdTag274" source="sdapi" category="entity" entity_type="molecule" role="component" text="PMA" ext_ids="CHEBI:37537" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phorbol 13-acetate 12-myristate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMA</sd-tag>+<sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> (15.82±3.97%). Data are representative of six independent experiments and presented as mean±SD; Wilcoxon matched‐pairs test, <sup>*</sup><i>p</i>&lt;0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=1030"/></sd-panel></fig></article>

token_classification/10-1002_eji-201142105.xml

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+<article doi="10.1002/eji.201142105" abstract="A role for the nucleotide-binding oligomerization domain 2 (NOD2) receptor in pulmonary innate immune responses has recently been explored. In the present study, we investigated the role that NOD2 plays in human alveolar macrophage innate responses and determined its involvement in the response to infection with virulent Mycobacterium tuberculosis. Our results showed that NOD2 was expressed in human alveolar macrophages, and significant amounts of IL-1β, IL-6, and TNF-α were produced upon ligand recognition with muramyldipeptide (MDP). NOD2 ligation induced the transcription and protein expression of the antimicrobial peptide LL37 and the autophagy enzyme IRGM in alveolar macrophages, demonstrating a novel function for this receptor in these cells. MDP treatment of alveolar macrophages improved the intracellular growth control of virulent M. tuberculosis; this was associated with a significant release of TNF-α and IL-6 and overexpression of bactericidal LL37. In addition, the autophagy proteins IRGM, LC3 and ATG16L1 were recruited to the bacteria-containing autophagosome after treatment with MDP. In conclusion, our results suggest that NOD2 can modulate the innate immune response of alveolar macrophages and play a role in the initial control of respiratory M. tuberculosis infections."><fig id="2401"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2401"/><sd-panel panel_id="6733"><div><b>(A)</b> Intracellular detection of <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NOD2" ext_ids="Q9HC29" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NOD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NOD2</sd-tag> (bold line in the histogram plot) was performed by <sd-tag id="sdTag2" source="sdapi" category="assay" entity_type="" role="" text="flow cytometry" ext_ids="BAO_0000005" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="flow cytometry" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">flow cytometry</sd-tag> using freshly isolated <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="alveolar macrophages" ext_ids="CL:0000583" norm_text="" ext_dbs="CL" in_caption="True" ext_names="alveolar macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">alveolar macrophages</sd-tag> selected from a gate set on <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="cell" role="component" text="large granular bronchoalveolar cells" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">large granular bronchoalveolar cells</sd-tag> (R1, dot plot). One representative experiment out of three experiments is presented.</div><graphic href="https://api.sourcedata.io/file.php?panel_id=6733"/></sd-panel><sd-panel panel_id="6734"><b>(B)</b> Cells were stimulated with 10 μg/mL of <sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MDP" ext_ids="CHEBI:59414" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="muramyl dipeptide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MDP</sd-tag> for 24 h, and <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NOD2" ext_ids="Q9HC29" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NOD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NOD2</sd-tag> and <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IκBα" ext_ids="P25963" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NFKBIA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IκBα</sd-tag> proteins were measured in the <span><sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="subcellular" role="component" text="cytosolic" ext_ids="GO:0005829" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="cytosol" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">cytosolic</sd-tag> fractions</span> by <sd-tag id="sdTag10" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> analysis. The fold increase relative to unstimulated cells and normalized to <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="tubulin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">tubulin</sd-tag> of one representative experiment out of three is reported.<graphic href="https://api.sourcedata.io/file.php?panel_id=6734"/></sd-panel><sd-panel panel_id="6735"><b>(C)</b> The upregulation of <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="gene" role="assayed" text="NOD2" ext_ids="64127" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="NOD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NOD2</sd-tag> gene expression was assessed by <sd-tag id="sdTag13" source="sdapi" category="assay" entity_type="" role="" text="quantitative PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">quantitative PCR</sd-tag>. The results are depicted as the mean fold change in <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="gene" role="assayed" text="NOD2" ext_ids="64127" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="NOD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NOD2</sd-tag> gene expression relative to unstimulated cells (<i>n</i> = 11).<graphic href="https://api.sourcedata.io/file.php?panel_id=6735"/></sd-panel><sd-panel panel_id="6736"><b>(D)</b> Subcellular localization of <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NOD2" ext_ids="Q9HC29" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NOD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NOD2</sd-tag> was ascertained in unstimulated (left, ×80,000) and <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MDP" ext_ids="CHEBI:59414" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="muramyl dipeptide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MDP</sd-tag>‐stimulated cells (right, ×63,000) using an anti‐<sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NOD2" ext_ids="Q9HC29" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NOD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NOD2</sd-tag> antibody and detected with a secondary antibody coupled to 5‐nm gold particles, indicated with arrowheads. Bar represents 150 nm. Micrographs were obtained from one experiment.<graphic href="https://api.sourcedata.io/file.php?panel_id=6736"/></sd-panel></fig><fig id="2402"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2402"/><sd-panel panel_id="6750"><p><sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="protein" role="component" text="NOD2" ext_ids="Q9HC29" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NOD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NOD2</sd-tag> ligation in <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="cell_type" role="component" text="alveolar macrophages" ext_ids="CL:0000583" norm_text="" ext_dbs="CL" in_caption="True" ext_names="alveolar macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">alveolar macrophages</sd-tag> induces pro‐inflammatory cytokine release. Cells were incubated for <sd-pretag id="sdPretag14389508068870" parent-tag-id="155">24 h</sd-pretag> in the presence of 10 μg/mL of <sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MDP" ext_ids="CHEBI:59414" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="muramyl dipeptide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MDP</sd-tag> or 100 ng/mL of <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LPS" ext_ids="CHEBI:16412" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag>. Production of <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P01584" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IL1B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag>, <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐6" ext_ids="P05231" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IL6" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IL‐6</sd-tag>, <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TNF‐α" ext_ids="P01375" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNF" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TNF‐α</sd-tag>, and <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐10" ext_ids="P22301" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IL10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IL‐10</sd-tag> was measured in culture supernatants using Milliplex technology. Depicted are box plots with median values and quartiles for each cytokine. The data are representative of two independent experiments (<em>n</em> = 11); *<em>p</em> 0.05 and **<em>p</em> 0.01 using the two‐tailed Wilcoxon signed‐rank test.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=6750"/></sd-panel></fig><fig id="2403"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2403"/><sd-panel panel_id="6737"><p><sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LL37" ext_ids="820" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CAMP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LL37</sd-tag> and <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="gene" role="assayed" text="IRGM" ext_ids="345611" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="IRGM" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">IRGM</sd-tag> gene expression is upregulated following <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="gene" role="component" text="NOD2" ext_ids="64127" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="NOD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NOD2</sd-tag> activation (A‐D). <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="cell_type" role="component" text="Alveolar macrophages" ext_ids="CL:0000583" norm_text="" ext_dbs="CL" in_caption="True" ext_names="alveolar macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">Alveolar macrophages</sd-tag> were incubated in the presence of 10 μg/mL of <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MDP" ext_ids="CHEBI:59414" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="muramyl dipeptide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MDP</sd-tag> or 100 ng/mL of <sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LPS" ext_ids="CHEBI:16412" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> for 24 h. Upregulation of (A) <sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LL37" ext_ids="820" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CAMP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LL37</sd-tag> and (D) <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="gene" role="assayed" text="IRGM" ext_ids="345611" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="IRGM" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">IRGM</sd-tag> gene expression was assessed after specific ligand recognition by <sd-tag id="sdTag38" source="sdapi" category="assay" entity_type="" role="" text="quantitative PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">quantitative PCR</sd-tag> using the Taqman system and the ΔΔCT method for relative quantification. The fold change in gene expression relative to unstimulated cells is depicted. Data are representative of two independent experiments (<i>n</i> = 7-12). Bold lines indicate median values.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=6737"/></sd-panel><sd-panel panel_id="6738"><b>(B, E)</b> <sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LL37" ext_ids="P49913" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CAMP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LL37</sd-tag> and <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IRGM" ext_ids="A1A4Y4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IRGM" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IRGM</sd-tag> protein levels were measured in <sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="subcellular" role="component" text="cytosolic" ext_ids="GO:0005829" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="cytosol" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">cytosolic</sd-tag> fractions by <sd-tag id="sdTag46" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> analysis.<graphic href="https://api.sourcedata.io/file.php?panel_id=6738"/></sd-panel><sd-panel panel_id="6739"><b>(C, F)</b> Data are expressed as the protein fold increases relative to unstimulated cells and normalized to <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="tubulin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">tubulin</sd-tag> calculated by densitometry and are shown as means ± SEM. One representative experiment out of three experiments is presented.<graphic href="https://api.sourcedata.io/file.php?panel_id=6739"/></sd-panel></fig><fig id="2404"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2404"/><sd-panel panel_id="6740"><b>(A)</b> Intracellular bacterial burden was measured by quantifying <sd-tag id="sdTag66" source="sdapi" category="assay" entity_type="" role="" text="CFU" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CFU</sd-tag>, and the intracellular growth index was calculated after 1 and 4 days post infection relative to phagocytosed bacteria at day 0. Data are shown as medians and quartiles and are representative of <i>n</i> = 7 experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=6740"/></sd-panel><sd-panel panel_id="6741"><p>The production of (B) <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TNF‐α" ext_ids="P01375" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNF" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TNF‐α</sd-tag>, (C) <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐6" ext_ids="P05231" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IL6" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IL‐6</sd-tag> and (D) <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P01584" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IL1B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> was measured in culture supernatants using Milliplex technology. Box plots depicting median values and quartiles are representative of <i>n</i> = 9 experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=6741"/></sd-panel><sd-panel panel_id="6742"><p>(E) <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LL37" ext_ids="820" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CAMP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LL37</sd-tag> and (F) <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="gene" role="assayed" text="IRGM" ext_ids="345611" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="IRGM" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">IRGM</sd-tag> gene expression was assessed by <sd-tag id="sdTag77" source="sdapi" category="assay" entity_type="" role="" text="quantitative PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">quantitative PCR</sd-tag> using the Taqman system and the ΔΔCT method for relative quantification. Fold changes in gene expression relative to unstimulated cells are reported. Bold lines indicate median values of <i>n</i> = 9. *<i>p</i> 0.05 and **<i>p</i> 0.01 using the two‐tailed Wilcoxon signed‐rank test.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=6742"/></sd-panel><sd-panel panel_id="6743"><b>(G)</b> <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LL37" ext_ids="P49913" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CAMP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LL37</sd-tag> and <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IRGM" ext_ids="A1A4Y4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IRGM" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IRGM</sd-tag> protein was assessed by <sd-tag id="sdTag83" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag>. One representative experiment out of three experiments is presented.<graphic href="https://api.sourcedata.io/file.php?panel_id=6743"/></sd-panel><sd-panel panel_id="6744"><b>(H)</b> The amount of protein normalized to <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="tubulin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">tubulin</sd-tag> relative to infected‐only cells was calculated by densitometry. Data are depicted as the means ± SEM and are representative of <i>n</i> = 3 experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=6744"/></sd-panel></fig><fig id="2405"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2405"/><sd-panel panel_id="6745"><b>(A, B, D, E, G, H)</b> The subcellular localization of autophagy proteins was ascertained in untreated and <sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MDP" ext_ids="CHEBI:59414" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="muramyl dipeptide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MDP</sd-tag>‐treated cells using (A, B) anti‐<sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IRGM" ext_ids="A1A4Y4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IRGM" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IRGM</sd-tag>, (D, E) anti‐<sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>, and (G, H) anti‐<sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG16L1" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG16L1</sd-tag> antibodies and detected with a secondary antibody coupled to 5‐nm gold particles indicated with arrowheads; bar represents 150 nm.<graphic href="https://api.sourcedata.io/file.php?panel_id=6745"/></sd-panel><sd-panel panel_id="6746"><b>(C, F, I)</b> <span><sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="Gold" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Gold</sd-tag> particles co‐localizing with bacteria were manually counted in ten macrophages of each condition. Means ± SEM are depicted and differences between treatments are indicated, *</span><i>p</i> 0.05 using a two‐tailed paired <i>t</i>‐test. (B) <sd-tag id="sdTag113" source="sdapi" category="assay" entity_type="" role="" text="Transmission electron microscopy (TEM)" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Transmission electron microscopy (<sd-pretag id="sdPretag14389508715350" parent-tag-id="158">TEM</sd-pretag>)</sd-tag> magnification ×50,000; the rest of the micrographs are <span><sd-pretag id="sdPretag14389508935300" parent-tag-id="158">TEM</sd-pretag></span> magnification ×80,000. Data were generated from one experiment.<graphic href="https://api.sourcedata.io/file.php?panel_id=6746"/></sd-panel></fig><fig id="2406"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2406"/><sd-panel panel_id="6747"><p><span><sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="cell_type" role="component" text="Macrophages" ext_ids="CL:0000235" norm_text="" ext_dbs="CL" in_caption="True" ext_names="macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">Macrophages</sd-tag> treated with <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="molecule" role="component" text="MDP" ext_ids="CHEBI:59414" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="muramyl dipeptide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MDP</sd-tag> after</span> <em><sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="organism" role="component" text="M. tuberculosis" ext_ids="1773" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mycobacterium tuberculosis" ext_tax_ids="1773" ext_tax_names="Mycobacterium tuberculosis" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">M. tuberculosis</sd-tag></em> <span>infection develop <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagy vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagy vacuoles</sd-tag>. <sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="cell_type" role="component" text="Alveolar macrophages" ext_ids="CL:0000583" norm_text="" ext_dbs="CL" in_caption="True" ext_names="alveolar macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">Alveolar macrophages</sd-tag> were infected with</span> <em><sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="organism" role="component" text="M. tuberculosis" ext_ids="1773" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mycobacterium tuberculosis" ext_tax_ids="1773" ext_tax_names="Mycobacterium tuberculosis" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">M. tuberculosis</sd-tag></em> <span>H37Rv at an MOI of 5 for 1 h. Nonphagocytosed bacteria were washed away, and the macrophages were incubated for an additional hour. The cells were then treated with 10 μg/mL of <sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="molecule" role="component" text="MDP" ext_ids="CHEBI:59414" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="muramyl dipeptide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MDP</sd-tag> for 24 h. Autophagy indicators (arrowheads) such as (A) <sd-tag id="sdTag147" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> containing organelles (<sd-tag id="sdTag158" source="sdapi" category="assay" entity_type="" role="" text="TEM" ext_ids="BAO_0000455" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="transmission electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">TEM</sd-tag> magnification ×20,000) and (B) onion skin‐like lamellar <sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="multivesicular bodies" ext_ids="GO:0005771" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="multivesicular body" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">multivesicular bodies</sd-tag> (<sd-pretag id="sdPretag14389508107000" parent-tag-id="158">TEM</sd-pretag> magnification ×16,000) were identified by ultrastructural analysis.</span>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=6747"/></sd-panel><sd-panel panel_id="6748"><b>(C, D)</b> <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosomes</sd-tag> containing <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mycobacteria (Mtb)" ext_ids="1763" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mycobacterium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mycobacteria (Mtb)</sd-tag> are indicated with arrows (C, <sd-tag id="sdTag128" source="sdapi" category="assay" entity_type="" role="" text="TEM" ext_ids="BAO_0000455" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="transmission electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">TEM</sd-tag> magnification ×40,000; D, <sd-tag id="sdTag129" source="sdapi" category="assay" entity_type="" role="" text="TEM" ext_ids="BAO_0000455" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="transmission electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">TEM</sd-tag> magnification ×12,000). Micrographs were obtained from one experiment. Bar represents 300 nm.<graphic href="https://api.sourcedata.io/file.php?panel_id=6748"/></sd-panel></fig></article>

token_classification/10-1002_eji-201242835.xml

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+<article doi="10.1002/eji.201242835" abstract="Legionella pneumophila (L. pneumophila) is an intracellular bacterium of human alveolar macrophages that causes Legionnaires' disease. In contrast to humans, most inbred mouse strains are restrictive to L. pneumophila replication. We demonstrate that autophagy targets L. pneumophila vacuoles to lysosomes and that this process requires ubiquitination of L. pneumophila vacuoles and the subsequent binding of the autophagic adaptor p62/SQSTM1 to ubiquitinated vacuoles. The L. pneumophila legA9 encodes for an ankyrin-containing protein with unknown role. We show that the legA9 mutant replicate in WT mice and their bone marrow-derived macrophages. This is the first L. pneumophila mutant to be found to replicate in WT bone marrow-derived macrophages other than the Fla mutant. Less legA9 mutant-containing vacuoles acquired ubiquitin labeling and p62/SQSTM1 staining, evading autophagy uptake and avoiding lysosomal fusion. Thus, we describe a bacterial protein that targets the L. pneumophila-containing vacuole for autophagy uptake."><fig id="1091"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1091"/><sd-panel panel_id="2125"><div><span><strong>(A)</strong> <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag> were infected with</span> <em><sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></em> <span><sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or the</span> <em><sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></em> <span>mutant with MOI of 0.5. CFUs were scored at 1, 24, 48, and 72 h. <strong>(B)</strong> <sd-tag id="sdTag330" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag> were infected with <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or the</span> <em><sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></em> <span>mutant harboring empty PL, or</span> <em><sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></em><span>+</span> <em><sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></em> <span>pBC‐KS</span><span>+</span> <span>PL. (A, B) Data are presented as means ± SD of at least three independent experiments. Asterisks indicate significant differences, (*</span><em>p</em> <span>&lt; 0.05, **</span><em>p</em> <span>&lt; 0.01, ***</span><em>p</em> <span>&lt; 0.001; two‐tailed</span> <em>t</em><span>‐test).</span></div><graphic href="https://api.sourcedata.io/file.php?panel_id=2125"/></sd-panel><sd-panel panel_id="2127"><p>Four female <sd-tag id="sdTag310" source="sdapi" category="entity" entity_type="organism" role="component" text="C57BL/6 mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">C57BL/6 mice</sd-tag>/group received 1 × 10<sup>6</sup> of <sd-tag id="sdTag309" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or <em><sd-tag id="sdTag312" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></em> mutant bacteria intratracheally. <sd-tag id="sdTag311" source="sdapi" category="entity" entity_type="tissue" role="component" text="Lungs" ext_ids="UBERON:0002048" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="lung" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Lungs</sd-tag> were homogenized and plated for <sd-tag id="sdTag308" source="sdapi" category="assay" entity_type="" role="" text="CFU" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CFU</sd-tag>s counting at (C) 4 or (D) 48 h postinfection. (C, D) Data are shown as mean + SD of <em>n</em> = 4 and are representative as one of two independent experiments. Asterisks indicate significant differences (**<em>p</em> &lt; 0.01 two‐tailed <em>t</em>‐test)</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2127"/></sd-panel></fig><fig id="1092"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1092"/><sd-panel panel_id="2128"><b>(A)</b> Representative images from 6 h infected WT <span><sd-tag id="sdTag331" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag></span> with <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or <i><sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></i> mutant bacteria. <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Nuclei</sd-tag> were stained blue with <sd-tag id="sdTag273" source="sdapi" category="assay" entity_type="" role="" text="DAPI" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAPI</sd-tag> and <i><sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> stained green with <i><sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> antibody. <sd-tag id="sdTag274" source="sdapi" category="assay" entity_type="" role="" text="Lyso−tracker" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Lyso−tracker</sd-tag> red was used to stain acidified <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag>. White arrows show <i><sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> colocalization with lysotracker.<graphic href="https://api.sourcedata.io/file.php?panel_id=2128"/></sd-panel><sd-panel panel_id="2129"><b>(B)</b> Percent colocalization of <i><sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> with <sd-tag id="sdTag275" source="sdapi" category="assay" entity_type="" role="" text="lyso‐tracker" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">lyso‐tracker</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2129"/></sd-panel><sd-panel panel_id="2130"><b>(C)</b> Representative images from 6 h infected WT <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag> with <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or <i><sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></i> mutant bacteria. <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> is stained red with <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> antibody. White arrows show <sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/"><i>L. pneumophila</i></sd-tag> colocalization with <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2130"/></sd-panel><sd-panel panel_id="2131"><b>(D)</b> Percent colocalization of <i><sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> with <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>. Hundred bacteria were scored from each coverslips. Images were captured with the 60× objective and magnified 3×, scale bar = 10 μm. (A-D) Data are presented as mean + SD of <i>n</i> = 3 and are representative of three independent experiments. Asterisks indicate significant differences (**<i>p</i> &lt; 0.01, ***<i>p</i> &lt; 0.001; two‐tailed <i>t</i>‐test).<graphic href="https://api.sourcedata.io/file.php?panel_id=2131"/></sd-panel></fig><fig id="1093"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1093"/><sd-panel panel_id="2132"><p>Induction of autophagy in <sd-pretag id="sdPretag14449969399060" parent-tag-id="339">macrophages</sd-pretag> restricts <em><sd-tag id="sdTag304" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></em> mutant replication, and rescues colocalization with <sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="protein" role="component" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and fusion with <sd-tag id="sdTag303" source="sdapi" category="entity" entity_type="subcellular" role="component" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag>. <sd-tag id="sdTag332" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag> were untreated or pretreated with <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin (Rap)" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin (Rap)</sd-tag> for 1 h and kept throughout the infection. <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag> were infected with <em><sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></em> <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or the <em><sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="gene" role="experiment" text="leg A9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">leg A9</sd-tag></em> mutant for (A) 1 or (B) 24 h with an MOI of 0.5. <sd-tag id="sdTag66" source="sdapi" category="assay" entity_type="" role="" text="CFUs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CFUs</sd-tag> were scored at these time points.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2132"/></sd-panel><sd-panel panel_id="2133"><b>(C, D)</b> Percent colocalization of <i><sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> with (C) <sd-tag id="sdTag281" source="sdapi" category="assay" entity_type="" role="" text="lyso‐tracker" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">lyso‐tracker</sd-tag> and (D) <sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>. Hundred bacteria were scored from each coverslips. (A-D) Data are presented as mean + SD of <i>n</i> = 3 and are representative of three independent experiments. Asterisks indicate significant differences (**<i>p</i> &lt; 0.01; two‐tailed <i>t</i>‐test).<graphic href="https://api.sourcedata.io/file.php?panel_id=2133"/></sd-panel></fig><fig id="1094"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1094"/><sd-panel panel_id="2134"><b>(A)</b> <span><sd-tag id="sdTag333" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag> derived from WT and</span> <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag><sup>−/−</sup> <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> were infected with <i><sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> <sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or <i><sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></i> mutant at an MOI of 0.5. Data are shown as mean ± SD of <i>n</i> = 3 and are representative of two independent experiments. Asterisks indicate significant differences (*<i>p</i> <span>&lt; 0.05; two−tailed</span> <i>t</i>−test.<graphic href="https://api.sourcedata.io/file.php?panel_id=2134"/></sd-panel><sd-panel panel_id="2135"><b>(B)</b> <sd-tag id="sdTag109" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> showing the absence of <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg 5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg 5</sd-tag> in the knockout. Data are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=2135"/></sd-panel></fig><fig id="1095"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1095"/><sd-panel panel_id="2136"><b>(A)</b> Representative images from 6 h infected <span><sd-tag id="sdTag334" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag></span> with <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or <i><sd-tag id="sdTag115" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></i> mutant bacteria. <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Polyubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Polyubiquitin</sd-tag> is stained red. White arrows show <i><sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> colocalization with <sd-tag id="sdTag318" source="sdapi" category="entity" entity_type="protein" role="assayed" text="polyubiquitin" ext_ids="P0CG50///P0CG49///Q6ZWU9///P62984" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Ubc///Ubb///Rps27///Uba52" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">polyubiquitin</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2136"/></sd-panel><sd-panel panel_id="2137"><b>(B)</b> Percent colocalization of <i><sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> with <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="protein" role="assayed" text="polyubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">polyubiquitin</sd-tag>. Hundred bacteria were scored from each coverslips. Images were captured with the 60× objective and magnified 3×, scale bar = 10 μm. Data are presented as means + SD of <i>n</i> = 3 and are representative of two independent experiments. Asterisks indicate significant differences (*<i>p</i> &lt; 0.05, **<i>p</i> &lt; 0.01, ***<i>p</i> &lt; 0.01; two‐tailed <i>t</i>‐test).<graphic href="https://api.sourcedata.io/file.php?panel_id=2137"/></sd-panel></fig><fig id="1096"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1096"/><sd-panel panel_id="2138"><b>(A)</b> Representative images from 6 h <span>infected <sd-tag id="sdTag335" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag> with</span> <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or <i><sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></i> mutant bacteria. <sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="protein" role="assayed" text="P62" ext_ids="Q64337" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sqstm1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">P62</sd-tag> is stained red with <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q64337" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sqstm1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> antibody. White arrows show <i><sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> colocalization with <sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q64337" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sqstm1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2138"/></sd-panel><sd-panel panel_id="2139"><b>(B)</b> Percent colocalization of <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/"><i>L. pneumophila</i></sd-tag> with <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q64337" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sqstm1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag>. Hundred bacteria were scored from each coverslips. Images were captured with the 60× objective and magnified 3×, scale bar = 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=2139"/></sd-panel><sd-panel panel_id="2140"><p><strong>(C)</strong><sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0000235///CL:0002476" norm_text="" ext_dbs="CL///CL" in_caption="True" ext_names="macrophage///bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org//// https://identifiers.org/">BMDMs</sd-tag> were infected with <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or the <em><sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></em> mutant for 6 h and the level of <sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q64337" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sqstm1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> protein was quantified in cell lysates by <sd-tag id="sdTag157" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag> (performed in triplicate and the SD are too small to detect).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2140"/></sd-panel><sd-panel panel_id="2141"><p><span><sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0000235///CL:0002476" norm_text="" ext_dbs="CL///CL" in_caption="True" ext_names="macrophage///bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org//// https://identifiers.org/">BMDMs</sd-tag> were nucleofected with scrambled control (sictrl) or siRNA against <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="gene" role="intervention" text="p62" ext_ids="18412" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sqstm1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">p62</sd-tag> (sip 62). Twenty‐four hours after nucleofection, murine <sd-tag id="sdTag340" source="sdapi" category="entity" entity_type="cell_type" role="component" text="macrophages" ext_ids="CL:0000235" norm_text="" ext_dbs="CL" in_caption="True" ext_names="macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">macrophages</sd-tag> were infected with <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or</span> <em><sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></em> <span>mutant with an MOI of 0.5 for 1 h (D and F) or 24 h (E and G).</span></p><graphic href="https://api.sourcedata.io/file.php?panel_id=2141"/></sd-panel><sd-panel panel_id="2142"><b>(H)</b> <sd-tag id="sdTag166" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis showing the downregulation of <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="gene" role="intervention" text="p62" ext_ids="18412" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sqstm1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">p62</sd-tag> at 24 and 48 h postnucleofection. (A-B and D-H) Data are shown as mean + SD of <i>n</i> = 3 and are representative of three independent experiments. (C) Data are representative of one experiment <i>n</i> = 3. Asterisks indicate significant differences (*<i>p</i> <span>&lt; 0.05, **</span><i>p</i> <span>&lt; 0.01; two−tailed</span> <i>t</i>−test).<graphic href="https://api.sourcedata.io/file.php?panel_id=2142"/></sd-panel></fig><fig id="1097"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1097"/><sd-panel panel_id="2143"><b>(A)</b> <sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="gene" role="component" text="Caspase−1" ext_ids="12362" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Casp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Caspase−1</sd-tag> KO (casp−1<sup>−/−</sup>) <span><sd-tag id="sdTag339" source="sdapi" category="entity" entity_type="cell_type" role="component" text="macrophages" ext_ids="CL:0000235" norm_text="" ext_dbs="CL" in_caption="True" ext_names="macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">macrophages</sd-tag></span> were infected with <i><sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="organism" role="assayed" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or <i><sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></i> with an MOI of 0.5 for 1, 24, 48, and 72 h.<graphic href="https://api.sourcedata.io/file.php?panel_id=2143"/></sd-panel><sd-panel panel_id="2144"><p><strong>(B)</strong> <sd-tag id="sdTag182" source="sdapi" category="assay" entity_type="" role="" text="CFUs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CFUs</sd-tag> were measured at the indicated time points. Levels of <sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> were detected in supernatants of WT or <sd-tag id="sdTag189" source="sdapi" category="entity" entity_type="gene" role="intervention" text="casp‐1" ext_ids="12362" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Casp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">casp‐1</sd-tag><sup>−/−</sup> <sd-tag id="sdTag336" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag> infected with <sd-tag id="sdTag192" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or the <em><sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></em> mutant after 24 h. WT <sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0000235///CL:0002476" norm_text="" ext_dbs="CL///CL" in_caption="True" ext_names="macrophage///bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org//// https://identifiers.org/">BMDMs</sd-tag> were either not treated (NT) or infected with <em><sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="organism" role="intervention" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></em> <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or <em><sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></em> mutant bacteria for 2 h.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2144"/></sd-panel><sd-panel panel_id="2145"><p>Activation of <sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="protein" role="assayed" text="casp‐1" ext_ids="P29452" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Casp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">casp‐1</sd-tag> or <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="protein" role="assayed" text="casp‐7" ext_ids="P97864" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Casp7" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">casp‐7</sd-tag> was detected in cell extracts using (C) <sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="protein" role="assayed" text="casp‐1" ext_ids="P29452" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Casp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">casp‐1</sd-tag> or (D) <sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="protein" role="assayed" text="casp‐7" ext_ids="P97864" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Casp7" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">casp‐7</sd-tag> antibodies, respectively. (A-D) Data are shown as mean ± SD of <i>n</i> = 3 and are representative of three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2145"/></sd-panel></fig><fig id="1098"><title></title><label>Figure 8</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1098"/><sd-panel panel_id="2146"><b>(A)</b> <span><sd-tag id="sdTag337" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag></span> were not infected (NT) or infected with <i><sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="organism" role="intervention" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> <sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or the <i><sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></i> mutant at an MOI of 0.5, 1 or 5 for 24 h. Apoptosis was quantified by Photometric enzyme immunoassay analysis of cytoplasmic (apoptosis) histone−associated−DNA fragments (<sd-tag id="sdTag209" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag>).<graphic href="https://api.sourcedata.io/file.php?panel_id=2146"/></sd-panel><sd-panel panel_id="2147"><b>(B)</b> <span><sd-tag id="sdTag338" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag></span> were either not treated (NT) or treated with <i><sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="organism" role="intervention" text="L. pneumophila" ext_ids="446" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Legionella pneumophila" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L. pneumophila</sd-tag></i> <sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="gene" role="experiment" text="JR32" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">JR32</sd-tag> or the <i><sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="gene" role="experiment" text="legA9" ext_ids="19831968" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="legA9" ext_tax_ids="272624" ext_tax_names="Legionella pneumophila subsp. pneumophila str. Philadelphia 1" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">legA9</sd-tag></i> mutant at an MOI of 0.5 or 5 for 24 h. The fold change in <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LDH" ext_ids="P00342///P16125///P06151" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Ldhc///Ldhb///Ldha" ext_tax_ids="10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LDH</sd-tag> release was measured from the overall population of <span><sd-tag id="sdTag341" source="sdapi" category="entity" entity_type="cell_type" role="component" text="macrophages" ext_ids="CL:0000235" norm_text="" ext_dbs="CL" in_caption="True" ext_names="macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">macrophages</sd-tag></span>. (A-B) Data are shown as mean ± SD of <i>n</i> = 3 and are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=2147"/></sd-panel></fig></article>

token_classification/10-1002_embr-201337995.xml

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+<article doi="10.1002/embr.201337995" abstract="The RabGAP protein TBC1D5 controls cellular endomembrane trafficking processes and binds the retromer subunit VPS29 and the ubiquitin-like protein ATG8 (LC3). Here, we describe that TBC1D5 also associates with ATG9 and the active ULK1 complex during autophagy. Moreover, ATG9 and TBC1D5 interact with clathrin and the AP2 complex. Depletion of TBC1D5 leads to missorting of ATG9 to late endosomes upon activation of autophagy, whereas inhibition of clathrin-mediated endocytosis or AP2 depletion alters ATG9 trafficking and its association with TBC1D5. Taken together, our data show that TBC1D5 and the AP2 complex are important novel regulators of the rerouting of ATG9-containing vesicular carriers toward sites of autophagosome formation."><fig id="744"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=744"/><sd-panel panel_id="1075"><b>A</b> Co‐localization of endogenous <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag> and <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag> with <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag>, in steady state and autophagy induced by <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="subcellular" role="component" text="mTOR" ext_ids="GO:0031932///GO:0031931" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="TORC2 complex///TORC1 complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">mTOR</sd-tag> inhibitor <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> (6 h).<graphic href="https://api.sourcedata.io/file.php?panel_id=1075"/></sd-panel><sd-panel panel_id="1076"><b>B, C</b> Quantification of co‐localization experiments presented in (A).<graphic href="https://api.sourcedata.io/file.php?panel_id=1076"/></sd-panel><sd-panel panel_id="1077"><b>D</b> <sd-tag id="sdTag14" source="sdapi" category="assay" entity_type="" role="" text="Co‐immunoprecipitation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co‐immunoprecipitation</sd-tag> <span>of <sd-tag id="sdTag271" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag272" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐</span><sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag> with <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="protein" role="reporter" text="myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">myc</sd-tag>‐<sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS29" ext_ids="Q9UBQ0" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS29" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS29</sd-tag>, transiently overexpressed in <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293T cells" ext_ids="CVCL_0063" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293T" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">293T cells</sd-tag><span>, <sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> or</span> <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> (6 h) treated.<graphic href="https://api.sourcedata.io/file.php?panel_id=1077"/></sd-panel><sd-panel panel_id="1078"><p><strong>E, F</strong> <sd-tag id="sdTag29" source="sdapi" category="assay" entity_type="" role="" text="Co‐immunoprecipitation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co‐immunoprecipitation</sd-tag> of endogenous <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag> and <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag> with <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="protein" role="reporter" text="myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">myc</sd-tag>‐<sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="gene" role="intervention" text="VPS29" ext_ids="51699" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VPS29" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">VPS29</sd-tag></p><p>(E) transiently overexpressed in <sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293T cells" ext_ids="CVCL_0063" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293T" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">293T cells</sd-tag> or with <sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag> (F) transiently overexpressed in <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293T cells" ext_ids="CVCL_0063" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293T" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">293T cells</sd-tag>, treated with <sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> or <sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> (6 h).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=1078"/></sd-panel><sd-panel panel_id="1079"><p><strong>G</strong> <sd-tag id="sdTag37" source="sdapi" category="assay" entity_type="" role="" text="Co‐immunoprecipitation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co‐immunoprecipitation</sd-tag> of endogenous <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS29" ext_ids="Q9UBQ0" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS29" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS29</sd-tag> and <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag> with <sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag282" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag></p><p>stably expressed in <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293T cells" ext_ids="CVCL_0063" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293T" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">293T cells</sd-tag>, treated with <sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> or <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> (6 h).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=1079"/></sd-panel><sd-panel panel_id="1080"><b>H</b> <sd-tag id="sdTag45" source="sdapi" category="assay" entity_type="" role="" text="Co‐immunoprecipitation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co‐immunoprecipitation</sd-tag> of endogenous <sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O75385" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> and p<sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG13" ext_ids="O75143" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG13" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG13</sd-tag> (Ser318) with <sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag286" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag>, stably expressed in <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="cell_line" role="component" text="T‐REx 293T" ext_ids="CVCL_D585" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="T-REx-293" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">T‐REx 293T</sd-tag> cells, induced by <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="molecule" role="component" text="doxycycline" ext_ids="CHEBI:50845" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="doxycycline" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">doxycycline</sd-tag> (50 ng/ml) for 20 h prior to <sd-tag id="sdTag287" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> or <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> (6 h) treatment.<graphic href="https://api.sourcedata.io/file.php?panel_id=1080"/></sd-panel><sd-panel panel_id="1081"><p><strong>I</strong> Magnified still images extracted from Supplementary Movie S2. <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag> co‐localizes with <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="gene" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9</sd-tag> upon autophagy induction by <sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="subcellular" role="component" text="mTOR" ext_ids="GO:0031932///GO:0031931" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="TORC2 complex///TORC1 complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">mTOR</sd-tag> inhibitor, <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=1081"/></sd-panel><sd-panel panel_id="15074"><strong>H</strong> <span><sd-tag id="sdTag392" source="sdapi" category="assay" entity_type="" role="" text="Co-immunoprecipitation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co-immunoprecipitation</sd-tag> of endogenous</span> <sd-tag id="sdTag393" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O75385" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> <span>and p<sd-tag id="sdTag391" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG13" ext_ids="O75143" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG13" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG13</sd-tag> (Ser318) with</span> <sd-tag id="sdTag394" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-<sd-tag id="sdTag395" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>-<sd-tag id="sdTag396" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag>, stably expressed in <sd-tag id="sdTag390" source="sdapi" category="entity" entity_type="cell_line" role="component" text="T-REx 293T" ext_ids="CVCL_D585" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="T-REx-293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">T-REx 293T</sd-tag> cells, induced by <sd-tag id="sdTag397" source="sdapi" category="entity" entity_type="molecule" role="component" text="doxycycline" ext_ids="CHEBI:50845" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="doxycycline" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">doxycycline</sd-tag> (50 ng/ml) for 20 h prior to <sd-tag id="sdTag398" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> or <sd-tag id="sdTag399" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> (6 h) treatment.<graphic href="https://api.sourcedata.io/file.php?panel_id=15074"/></sd-panel></fig><fig id="745"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=745"/><sd-panel panel_id="1082"><b>A</b> Lysates of <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing control shRNA or shRNA targeting <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="gene" role="intervention" text="VPS29" ext_ids="51699" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VPS29" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">VPS29</sd-tag> or <sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TBC1D5" ext_ids="9779" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TBC1D5</sd-tag>. Cells were treated with <sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> or <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> (6 h), lysed in RIPA buffer (1% SDS) and lysates were subjected to <sd-tag id="sdTag64" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-PAGE</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=1082"/></sd-panel><sd-panel panel_id="1083"><b>B</b> <sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9</sd-tag> were depleted of <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="gene" role="intervention" text="VPS29" ext_ids="51699" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VPS29" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">VPS29</sd-tag> and <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TBC1D5" ext_ids="9779" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TBC1D5</sd-tag> using shRNAs, treated with <sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> or <sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> (6 h), fixed with 2% PFA, and <sd-tag id="sdTag118" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> with anti‐<sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11279" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> antibody.<graphic href="https://api.sourcedata.io/file.php?panel_id=1083"/></sd-panel><sd-panel panel_id="1084"><b>C</b> Quantification of <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9</sd-tag> vesicular structures in cells from (B) under non‐stimulated conditions.<graphic href="https://api.sourcedata.io/file.php?panel_id=1084"/></sd-panel><sd-panel panel_id="1085"><b>D</b> Quantification of <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9</sd-tag> and <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11279" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> co‐localization in cells presented in (B).<graphic href="https://api.sourcedata.io/file.php?panel_id=1085"/></sd-panel><sd-panel panel_id="1086"><b>E</b> Quantification of <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9</sd-tag> and <sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11279" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> co−localization in cells stably depleted for <sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TBC1D5" ext_ids="9779" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TBC1D5</sd-tag> (shRNA#1) or VPS29 (shRNA#2), transiently transfected with <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="protein" role="reporter" text="myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">myc</sd-tag>−<sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TBC1D5" ext_ids="9779" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TBC1D5</sd-tag> plasmid resistant to <span><sd-pretag id="sdPretag14393827884870" parent-tag-id="95">TBC1D5</sd-pretag></span> shRNA#1. Cells were treated with <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> (6 h), 20 h post−transfection, fixed, and <span><sd-tag id="sdTag302" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag></span> with anti−LAMP1 and anti−myc antibodies.<graphic href="https://api.sourcedata.io/file.php?panel_id=1086"/></sd-panel><sd-panel panel_id="1087"><b>F</b> Control shRNA and <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cell lysates depleted for <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag> (shRNA#1), transfected with empty plasmid or with shRNA‐resistant <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="protein" role="reporter" text="myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">myc</sd-tag>‐<sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TBC1D5" ext_ids="9779" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TBC1D5</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=1087"/></sd-panel><sd-panel panel_id="1088"><b>G</b> <sd-tag id="sdTag115" source="sdapi" category="assay" entity_type="" role="" text="Immunofluorescence" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunofluorescence</sd-tag> of <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="gene" role="component" text="TBC1D5" ext_ids="9779" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TBC1D5</sd-tag> (shRNA#1) cells transiently transfected with shRNA‐resistant <sd-tag id="sdTag306" source="sdapi" category="entity" entity_type="protein" role="reporter" text="myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">myc</sd-tag>‐<sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag>, treated with <sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="molecule" role="component" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> (6 h). 20 h post‐transfection cells were treated, subsequently fixed, and <sd-tag id="sdTag307" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> with anti‐<sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="protein" role="reporter" text="myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">myc</sd-tag> and anti‐<sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP1" ext_ids="P11279" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP1</sd-tag> antibodies.<graphic href="https://api.sourcedata.io/file.php?panel_id=1088"/></sd-panel></fig><fig id="746"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=746"/><sd-panel panel_id="1089"><b>A</b> <sd-tag id="sdTag313" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag314" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag315" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag> expression was induced in <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="cell_line" role="component" text="T‐REx HeLa" ext_ids="CVCL_D587" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="T-REx-HeLa" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">T‐REx HeLa</sd-tag> <span>cells for 20 h, lysates were subjected to <sd-tag id="sdTag319" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag><sd-tag id="sdTag318" source="sdapi" category="assay" entity_type="" role="" text="pull‐down" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pull‐down</sd-tag>, −</span><sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="protein" role="assayed" text="AP2M1" ext_ids="Q96CW1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="AP2M1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">AP2M1</sd-tag>. <sd-tag id="sdTag114" source="sdapi" category="assay" entity_type="" role="" text="Co‐precipitated" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co‐precipitated</sd-tag><sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag> was detected with anti−<sd-tag id="sdTag316" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag> antibody.<graphic href="https://api.sourcedata.io/file.php?panel_id=1089"/></sd-panel><sd-panel panel_id="1090"><b>B</b> Control cells and <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TBC1D5" ext_ids="9779" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TBC1D5</sd-tag> (shRNA#1) <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cell lysates subjected to <sd-tag id="sdTag111" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-PAGE</sd-tag>, subsequently blotted with endogenous antibodies for <sd-tag id="sdTag322" source="sdapi" category="entity" entity_type="subcellular" role="component" text="AP2" ext_ids="GO:0030122" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="AP-2 adaptor complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AP2</sd-tag> subunits <sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="protein" role="assayed" text="AP2A1" ext_ids="O95782" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="AP2A1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">AP2A1</sd-tag> and <sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="protein" role="assayed" text="AP2M1" ext_ids="Q96CW1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="AP2M1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">AP2M1</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=1090"/></sd-panel><sd-panel panel_id="1091"><b>C</b> <sd-tag id="sdTag119" source="sdapi" category="assay" entity_type="" role="" text="Immunofluorescent staining" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Immunofluorescent staining</sd-tag> of <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="protein" role="assayed" text="AP2A1" ext_ids="O95782" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="AP2A1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">AP2A1</sd-tag> in <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> shRNA control, or shRNA#1 <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TBC1D5" ext_ids="9779" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TBC1D5</sd-tag> cells treated with <sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063974" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063974</sd-tag> <span>or <sd-tag id="sdTag324" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> (6 h).</span><graphic href="https://api.sourcedata.io/file.php?panel_id=1091"/></sd-panel><sd-panel panel_id="1092"><b>D</b> <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing <sd-tag id="sdTag326" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag327" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag> were fixed and stained for endogenous <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="protein" role="assayed" text="AP2A1" ext_ids="O95782" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="AP2A1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">AP2A1</sd-tag> and <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag>. Regions of co‐localization are indicated with arrows.<graphic href="https://api.sourcedata.io/file.php?panel_id=1092"/></sd-panel><sd-panel panel_id="1093"><b>E</b> <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing <sd-tag id="sdTag329" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag330" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag> were starved in <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> (4 h) or treated with <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> (6 h), subsequently fixed and stained with anti‐<sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="protein" role="assayed" text="AP2A1" ext_ids="O95782" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="AP2A1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">AP2A1</sd-tag> antibody.<graphic href="https://api.sourcedata.io/file.php?panel_id=1093"/></sd-panel><sd-panel panel_id="1094"><b>F</b> <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing <sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag> were treated with <sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> (6 h), lysed in <sd-tag id="sdTag146" source="sdapi" category="assay" entity_type="" role="" text="co‐immunoprecipitation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">co‐immunoprecipitation</sd-tag> buffer. Lysates from <sd-tag id="sdTag335" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag>‐ or <sd-tag id="sdTag336" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag>‐treated cells were split and equal volumes were incubated with <sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="protein" role="reporter" text="RFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RFP</sd-tag>‐Trap beads or GFP‐Trap beads, or agarose as a negative control, overnight at 4°C. Precipitated proteins were analyzed by <sd-tag id="sdTag337" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-PAGE</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=1094"/></sd-panel></fig><fig id="747"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=747"/><sd-panel panel_id="1095"><b>A</b> <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing <sd-tag id="sdTag340" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag341" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag> transfected with siRNA targeting <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="gene" role="intervention" text="AP2A1" ext_ids="160" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="AP2A1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">AP2A1</sd-tag> (40 nM), or siRNA AllStar control (40 nM) were treated with <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="KU0063794" ext_ids="CHEBI:85572" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Ku-0063794" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">KU0063794</sd-tag> or <sd-tag id="sdTag342" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> (6 h) 4 days post‐transfection, fixed, and stained with anti‐<sd-tag id="sdTag343" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> antibody.<graphic href="https://api.sourcedata.io/file.php?panel_id=1095"/></sd-panel><sd-panel panel_id="1096"><b>B</b> Co‐localization of <sd-tag id="sdTag346" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag347" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag> with <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TGN46" ext_ids="O43493" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TGOLN2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TGN46</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=1096"/></sd-panel><sd-panel panel_id="1097"><b>C</b> Lysates of <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells transfected with siRNA targeting <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="gene" role="intervention" text="AP2A1" ext_ids="160" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="AP2A1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">AP2A1</sd-tag>, or siRNA control AllStars analyzed by <sd-tag id="sdTag167" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-PAGE</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=1097"/></sd-panel><sd-panel panel_id="1098"><b>D</b> <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing <sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>−<sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9</sd-tag> were transiently transfected with <sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>−<sd-tag id="sdTag177" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Dynamin 2" ext_ids="P50570" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="DNM2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Dynamin 2</sd-tag> or GFP−<span><sd-tag id="sdTag352" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Dynamin 2" ext_ids="1785" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="DNM2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Dynamin 2</sd-tag></span> (K44A), 20 h post−transfection cells were fixed and with anti−<sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag> antibody. <span><sd-tag id="sdTag354" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag></span> and <span><sd-tag id="sdTag355" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Dynamin 2" ext_ids="P50570" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="DNM2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Dynamin 2</sd-tag>co−localization</span> is indicated by arrows.<graphic href="https://api.sourcedata.io/file.php?panel_id=1098"/></sd-panel></fig><fig id="748"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=748"/><sd-panel panel_id="1099"><b>A</b> <sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing <sd-tag id="sdTag356" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>−<sd-tag id="sdTag357" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>−<sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag> treated with <sd-tag id="sdTag358" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> or <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Dynasore" ext_ids="5717066" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="Dynasore" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">Dynasore</sd-tag> (100 μM) 15 min, fixed and <span><sd-tag id="sdTag360" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag></span> with anti−<sd-tag id="sdTag359" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> and anti−<sd-tag id="sdTag189" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag> antibodies.<graphic href="https://api.sourcedata.io/file.php?panel_id=1099"/></sd-panel><sd-panel panel_id="1100"><p><strong>B</strong> Quantification of <sd-tag id="sdTag192" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag></p>and <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="protein" role="assayed" text="AP2A1" ext_ids="O95782" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="AP2A1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">AP2A1</sd-tag>co‐localization from experiment in (A), pictures from 3 independent experiments were analyzed and co‐localization quantified, statistics is calculated as described in Supplementary Materials and Methods.<graphic href="https://api.sourcedata.io/file.php?panel_id=1100"/></sd-panel><sd-panel panel_id="1101"><p><strong>C</strong> RGB‐line profile across the vesicle indicated with arrow in (B); red-<sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="protein" role="assayed" text="AP2A1" ext_ids="O95782" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="AP2A1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">AP2A1</sd-tag>; green-<sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag>; blue-<sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=1101"/></sd-panel><sd-panel panel_id="1102"><p><strong>D</strong> Quantification of <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag> and <sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="AP2" ext_ids="GO:0030122" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="AP-2 adaptor complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AP2</sd-tag> co‐localization. Cells were starved in <sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> media (45 min) or pretreated with <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Dynasore" ext_ids="5717066" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="Dynasore" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">Dynasore</sd-tag> (15 min) and subsequently starved for 45 min in combination with <sd-tag id="sdTag370" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Dynasore" ext_ids="5717066" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="Dynasore" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">Dynasore</sd-tag>. Control cells were treated with <sd-tag id="sdTag371" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=1102"/></sd-panel><sd-panel panel_id="1103"><b>E</b> Quantification of <sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta in cells stably expressing <sd-tag id="sdTag373" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag374" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="protein" role="component" text="ATG9A" ext_ids="Q7Z3C6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG9A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG9A</sd-tag>, treated and presented as in (D). 100 cells were quantified in 3 independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=1103"/></sd-panel><sd-panel panel_id="1104"><b>F</b> <sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="cell_line" role="component" text="T‐REx HeLa" ext_ids="CVCL_D587" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="T-REx-HeLa" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">T‐REx HeLa</sd-tag> cells were transfected with siRNA Control oligo or siRNA oligo#1 targeting (40 nM). 72 h post−transfection, expression of <sd-tag id="sdTag383" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag384" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>−<sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TBC1D5" ext_ids="Q92609" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TBC1D5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TBC1D5</sd-tag> was induced with <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="molecule" role="component" text="doxycycline" ext_ids="CHEBI:50845" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="doxycycline" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">doxycycline</sd-tag> (50 ng/ml), and 96 h post−transfection cells were treated with <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Dynasore" ext_ids="5717066" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="Dynasore" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">Dynasore</sd-tag> for 15 min, or pretreated with <sd-tag id="sdTag385" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Dynasore" ext_ids="5717066" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="Dynasore" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">Dynasore</sd-tag> and subsequently starved in combination with <sd-tag id="sdTag386" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Dynasore" ext_ids="5717066" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="Dynasore" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">Dynasore</sd-tag> for additional 45 min. Cells were lysed in <sd-tag id="sdTag222" source="sdapi" category="assay" entity_type="" role="" text="co‐immunoprecipitation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">co‐immunoprecipitation</sd-tag> <span>buffer, and lysates were incubated with <sd-tag id="sdTag381" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> antibody or M2 antibody coupled with agarose overnight at 4°C. Beads were washed 3 times with incubation buffer and subjected to <sd-tag id="sdTag382" source="sdapi" category="assay" entity_type="" role="" text="SDS‐PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS‐PAGE</sd-tag>.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=1104"/></sd-panel></fig></article>

token_classification/10-1002_embr-201338003.xml

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+<article doi="10.1002/embr.201338003" abstract="Several autophagy proteins contain an LC3-interacting region (LIR) responsible for their interaction with Atg8 homolog proteins. Here, we show that ALFY binds selectively to LC3C and the GABARAPs through a LIR in its WD40 domain. Binding of ALFY to GABARAP is indispensable for its recruitment to LC3B-positive structures and, thus, for the clearance of certain p62 structures by autophagy. In addition, the crystal structure of the GABARAP-ALFY-LIR peptide complex identifies three conserved residues in the GABARAPs that are responsible for binding to ALFY. Interestingly, introduction of these residues in LC3B is sufficient to enable its interaction with ALFY, indicating that residues outside the LIR-binding hydrophobic pockets confer specificity to the interactions with Atg8 homolog proteins."><fig id="761"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=761"/><sd-panel panel_id="1172"><b>A</b> Transfected <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag><span>−Atg8 homologs were <sd-pretag id="sdPretag14393693907450" parent-tag-id="179">immunoprecipitated</sd-pretag> with μMACS™ from total</span> <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> <span>cell extracts followed by <sd-tag id="sdTag148" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis with anti−</span><sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> and anti−<sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALFY" ext_ids="Q8IZQ1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ALFY</sd-tag> antibodies. Data are representative of two independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=1172"/></sd-panel><sd-panel panel_id="1174"><b>C</b> The indicated <sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="35S" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sup>35</sup>S</sd-tag>−labelled <i>in vitro</i>−translated <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>−tagged constructs were incubated with <sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag>, <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag>−<sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> or <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag>−<sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GABARAP" ext_ids="O95166" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GABARAP</sd-tag> conjugated to glutathione Sepharose, and their binding was evaluated by <span><sd-tag id="sdTag221" source="sdapi" category="assay" entity_type="" role="" text="autoradiography" ext_ids="BAO_0002527" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="autoradiography" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">autoradiography</sd-tag> (<sd-tag id="sdTag222" source="sdapi" category="assay" entity_type="" role="" text="ARG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">ARG</sd-tag>)</span>. 5% of the <i>in vitro</i>−translated protein (arrow head) used was loaded. Equal amounts of <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag> proteins were used as shown by <span><sd-tag id="sdTag223" source="sdapi" category="assay" entity_type="" role="" text="Coomassie Brilliant Blue" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Coomassie Brilliant Blue</sd-tag> (<sd-tag id="sdTag224" source="sdapi" category="assay" entity_type="" role="" text="CBB" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CBB</sd-tag>)</span> staining. Data are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=1174"/></sd-panel><sd-panel panel_id="1175"><b>D</b> Recombinant <sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALFY" ext_ids="Q8IZQ1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ALFY</sd-tag> (aa 2981-3526) was incubated with <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag>‐Atg8 proteins conjugated to glutathione Sepharose. The pulled‐down complexes were subjected to <sd-tag id="sdTag27" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-PAGE</sd-tag> and anti‐<sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="gene" role="component" text="ALFY" ext_ids="23001" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ALFY</sd-tag> and anti‐<sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag> <sd-tag id="sdTag157" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. 5% of the recombinant <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALFY" ext_ids="Q8IZQ1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ALFY</sd-tag> protein used was loaded as input. Data are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=1175"/></sd-panel></fig><fig id="762"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=762"/><sd-panel panel_id="1177"><b>B</b> <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="35S" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sup>35</sup>S</sd-tag>−labelled <i>in vitro</i>−translated <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>−<span><sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ALFY" ext_ids="23001" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ALFY</sd-tag></span> (aa 2981-3526) wild−type and different LIR mutants were incubated with <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag>−<sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GABARAP" ext_ids="O95166" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GABARAP</sd-tag> or −<sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3C" ext_ids="Q9BXW4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3C" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3C</sd-tag> and binding evaluated by <sd-tag id="sdTag44" source="sdapi" category="assay" entity_type="" role="" text="ARG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">ARG</sd-tag>. 10 and 2% of the <i>in vitro</i>−translated proteins used were loaded to illustrate binding affinity. <sd-tag id="sdTag45" source="sdapi" category="assay" entity_type="" role="" text="CBB" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CBB</sd-tag> staining shows equal amounts of <sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag> proteins used. Data are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=1177"/></sd-panel><sd-panel panel_id="1178"><b>C</b> <sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="protein" role="reporter" text="MBP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MBP</sd-tag>, <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="protein" role="reporter" text="MBP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MBP</sd-tag>−<sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALFY" ext_ids="Q8IZQ1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ALFY</sd-tag> (aa 3255-3526) or the <span><sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ALFY" ext_ids="23001" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ALFY</sd-tag></span>−LIR mutant (F3346A) conjugated to amylose resins was incubated in the absence or presence of purified <sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GABARAP" ext_ids="O95166" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GABARAP</sd-tag>. The pulled−down complexes were subjected to <sd-tag id="sdTag51" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-PAGE</sd-tag> and visualized by <sd-tag id="sdTag52" source="sdapi" category="assay" entity_type="" role="" text="CBB" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CBB</sd-tag> staining. Data are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=1178"/></sd-panel><sd-panel panel_id="1179"><b>D</b> Thermodynamic parameters of <span><sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALFY" ext_ids="Q8IZQ1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ALFY</sd-tag></span>−LIR peptide (aa 3341-3354) to Atg8 homologs. All titrations were performed at 25°C as described in Supplementary Methods. ITC data were fitted to a one−site binding model. ND, not detected.<graphic href="https://api.sourcedata.io/file.php?panel_id=1179"/></sd-panel><sd-panel panel_id="1180"><b>E</b> <sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="35S" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sup>35</sup>S</sd-tag>−labelled <i>in vitro</i>−translated <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> or <sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>−<sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Bchs" ext_ids="Q9VML2" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="bchs" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="https://www.uniprot.org/uniprot/">Bchs</sd-tag> (aa 3326-3341) were incubated with <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag> or <sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag>−<sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="protein" role="assayed" text="dAtg8a" ext_ids="X2JJA8///X2JEE0///Q9W2S2" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Atg8a///Atg8a///Atg8a" ext_tax_ids="7227///7227///7227" ext_tax_names="Drosophila melanogaster///Drosophila melanogaster///Drosophila melanogaster" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">dAtg8a</sd-tag> and binding evaluated by <sd-tag id="sdTag57" source="sdapi" category="assay" entity_type="" role="" text="ARG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">ARG</sd-tag>. 5% of the <i>in vitro</i>−translated protein used was loaded. <span><sd-tag id="sdTag225" source="sdapi" category="assay" entity_type="" role="" text="Ponceau" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ponceau</sd-tag> staining</span> shows equal amounts of <sd-tag id="sdTag177" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag> proteins used. Data are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=1180"/></sd-panel></fig><fig id="763"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=763"/><sd-panel panel_id="1184"><b>D</b> <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>−<sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> and <sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag><span>−<sd-tag id="sdTag178" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3B</sd-tag> (Q26K/H27Y/H57D) were <sd-tag id="sdTag179" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> with</span> <span><sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag></span><span>−<sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="gene" role="component" text="TRAP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TRAP</sd-tag>®</span> from total cell lysate of stably transfected <sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> FlpIn <span>cells, followed by <sd-tag id="sdTag184" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-PAGE</sd-tag> and</span> <sd-tag id="sdTag63" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> with the indicated antibodies. Data are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=1184"/></sd-panel><sd-panel panel_id="1185"><b>E</b> <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="protein" role="reporter" text="MBP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MBP</sd-tag>‐<sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALFY" ext_ids="Q8IZQ1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ALFY</sd-tag><sub>3255-3526</sub> conjugated to amylose resin was incubated with <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag> or the indicated <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAP" ext_ids="11337" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAP</sd-tag> mutants. The pulled‐down complexes were subjected to <sd-tag id="sdTag185" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-PAGE</sd-tag> and visualized by <sd-tag id="sdTag76" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> with anti‐<sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="protein" role="reporter" text="MBP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MBP</sd-tag> and anti‐<sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GABARAP" ext_ids="O95166" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GABARAP</sd-tag> antibodies. Data are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=1185"/></sd-panel><sd-panel panel_id="1186"><b>F</b> <sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="protein" role="reporter" text="MBP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MBP</sd-tag>−tagged <sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALFY" ext_ids="Q8IZQ1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ALFY</sd-tag><sub>3255-3526</sub> and <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="gene" role="intervention" text="p62" ext_ids="8878" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">p62</sd-tag><sub>168-391</sub> or their corresponding LIR mutants (F3346A and W340A, respectively) were conjugated to amylose resin and incubated with purified <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag>, <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAP" ext_ids="11337" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAP</sd-tag>, <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GABARAP" ext_ids="O95166" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GABARAP</sd-tag> mutant (K24Q/Y25H/D54H), <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> or <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3B</sd-tag> mutant (Q26K/H27Y/H57D). The bound proteins were visualized by <sd-tag id="sdTag86" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> with anti−<sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GABARAP" ext_ids="O95166" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GABARAP</sd-tag><span>, anti−<sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and anti−</span><sd-tag id="sdTag189" source="sdapi" category="entity" entity_type="protein" role="reporter" text="MBP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MBP</sd-tag> antibodies. Data are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=1186"/></sd-panel><sd-panel panel_id="1187"><b>G</b> <sd-tag id="sdTag192" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="35S" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sup>35</sup>S</sd-tag>‐labelled <i>in vitro</i>‐translated <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALFY" ext_ids="Q8IZQ1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ALFY</sd-tag> (aa 2981-3526) wild‐type and K3343A/D3344A/Y3351A mutant were incubated with <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag>‐<sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> and <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GABARAP" ext_ids="O95166" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GABARAP</sd-tag> and binding evaluated by <sd-tag id="sdTag94" source="sdapi" category="assay" entity_type="" role="" text="ARG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">ARG</sd-tag>. 10% of the <i>in vitro</i>‐translated proteins used was loaded. <sd-tag id="sdTag95" source="sdapi" category="assay" entity_type="" role="" text="CBB" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CBB</sd-tag> staining shows equal amounts of <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag> proteins used. Data are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=1187"/></sd-panel></fig><fig id="764"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=764"/><sd-panel panel_id="1188"><b>A</b> <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> FlpIn <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>−<sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GABARAP" ext_ids="O95166" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GABARAP</sd-tag> cells were treated with proteasomal inhibitor (<sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag><span>, 2 h) or subjected to <sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino acid</sd-tag> starvation (</span><sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag>, 2 h), before staining with anti−<sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALFY" ext_ids="Q8IZQ1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ALFY</sd-tag> antibodies. Scale bar, 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=1188"/></sd-panel><sd-panel panel_id="1189"><b>B</b> <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>−tagged full−length <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="gene" role="component" text="ALFY" ext_ids="72145" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Wdfy3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ALFY</sd-tag> wild−type or <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3" ext_ids="67443///66734" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag>−interacting region (LIR)−mutant was expressed into <i><sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="gene" role="component" text="Alfy" ext_ids="72145" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Wdfy3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Alfy</sd-tag></i>−deficient <sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> <span>using an <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="organism" role="component" text="adenovirus" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Adenovirus" ext_tax_ids="10535" ext_tax_names="unidentified adenovirus" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">adenovirus</sd-tag> system. At 48 h after infection, the</span> <sd-tag id="sdTag204" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were cultured in normal media or <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> for 1.5 h before staining with anti−<sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9CQV6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Map1lc3b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag> or anti−<sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GABARAP" ext_ids="O95166" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GABARAP</sd-tag> antibodies. Scale bars 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=1189"/></sd-panel><sd-panel panel_id="1190"><b>C</b> <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were treated with control or siRNA targeting <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAP" ext_ids="11337" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAP</sd-tag>, <sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAPL1" ext_ids="23710" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAPL1</sd-tag> and <sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAPL2" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAPL2</sd-tag><span>. 72 h after transfection cells were <sd-tag id="sdTag208" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> with anti−</span><sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3B</sd-tag>, anti−<sd-tag id="sdTag115" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALFY" ext_ids="Q8IZQ1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ALFY</sd-tag> and anti−<sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> antibodies. Scale bars, 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=1190"/></sd-panel><sd-panel panel_id="1191"><b>D</b> <sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were treated with control or siRNA targeting <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALFY" ext_ids="Q8IZQ1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDFY3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ALFY</sd-tag>. 72 h after transfection, cells were treated with <sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="puromycin" ext_ids="CHEBI:17939" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="puromycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">puromycin</sd-tag> with or without <sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> <span>for 2 h and total cell lysates were fractionated into <sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="molecule" role="component" text="TX−100" ext_ids="CHEBI:9750" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Triton X-100" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">TX−100</sd-tag>−soluble and insoluble fractions. The <sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="molecule" role="component" text="TX−100" ext_ids="CHEBI:9750" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Triton X-100" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">TX−100</sd-tag>−soluble/insoluble fractions were then <sd-tag id="sdTag210" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> with the indicated antibodies. Data are representative of three independent experiments.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=1191"/></sd-panel><sd-panel panel_id="1192"><b>E</b> <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALFY" ext_ids="Q6VNB8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Wdfy3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ALFY</sd-tag> WT and KO <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were treated with <sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="puromycin" ext_ids="CHEBI:17939" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="puromycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">puromycin</sd-tag> or <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> with or without <sd-tag id="sdTag137" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> <span>for 2 h and the total cell lysates were then fractionated into <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="molecule" role="component" text="Triton X−100" ext_ids="CHEBI:9750" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Triton X-100" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Triton X−100</sd-tag> (</span><sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="molecule" role="component" text="TX−100" ext_ids="CHEBI:9750" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Triton X-100" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">TX−100</sd-tag>)−soluble and insoluble fractions. The <sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="molecule" role="component" text="TX−100" ext_ids="CHEBI:9750" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Triton X-100" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">TX−100</sd-tag>−soluble/insoluble fractions were then <sd-tag id="sdTag220" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> with the indicated antibodies. Data are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=1192"/></sd-panel></fig></article>

token_classification/10-1002_embr-201338310.xml

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+<article doi="10.1002/embr.201338310" abstract="The mechanisms that coordinate the regulation of autophagy with developmental signaling during multicellular organism development remain largely unknown. Here, we show that impaired function of ribosomal protein RPL-43 causes an accumulation of SQST-1 aggregates in the larval intestine, which are removed upon autophagy induction. Using this model to screen for autophagy regulators, we identify 139 genes that promote autophagy activity upon inactivation. Various signaling pathways, including Sma/Mab TGF-β signaling, lin-35/Rb signaling, the XBP-1-mediated ER stress response, and the ATFS-1-mediated mitochondrial stress response, regulate the expression of autophagy genes independently of the TFEB homolog HLH-30. Our study thus provides a framework for understanding the role of signaling pathways in regulating autophagy under physiological conditions."><fig id="2596"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2596"/><sd-panel panel_id="7435"><b>A-D</b> <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> is very weakly expressed and diffusely localized in the <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="subcellular" role="component" text="cytoplasm" ext_ids="GO:0005737" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="cytoplasm" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">cytoplasm</sd-tag> in wild‐type larval <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="tissue" role="component" text="intestine" ext_ids="UBERON:0000160" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="intestine" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">intestine</sd-tag>, but is expressed at much higher levels and accumulates into numerous aggregates in the <sd-tag id="sdTag271" source="sdapi" category="entity" entity_type="tissue" role="component" text="intestine" ext_ids="UBERON:0000160" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="intestine" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">intestine</sd-tag> in <i><sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="gene" role="intervention" text="bp399" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bp399</sd-tag></i> mutant <sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="organism" role="component" text="larvae" ext_ids="6239" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Caenorhabditis elegans" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">larvae</sd-tag>. (A) and (C) represent <sd-tag id="sdTag272" source="sdapi" category="assay" entity_type="" role="" text="DIC" ext_ids="BAO_0002511" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="differential interference contrast microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">DIC</sd-tag> images of the animals in (B) and (D), respectively.<graphic href="https://api.sourcedata.io/file.php?panel_id=7435"/></sd-panel><sd-panel panel_id="7436"><b>E</b> Compared to wild‐type, <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> levels are much higher in <i><sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="gene" role="intervention" text="bp399" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bp399</sd-tag></i> and <i><sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="gene" role="intervention" text="bp412" ext_ids="176921" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG-3" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bp412</sd-tag></i> mutant <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="organism" role="component" text="larvae" ext_ids="6239" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Caenorhabditis elegans" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">larvae</sd-tag> as shown by <sd-tag id="sdTag20" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> assay. <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> levels in <i><sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="gene" role="intervention" text="bp399" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bp399</sd-tag></i> mutants are greatly reduced after <sd-tag id="sdTag273" source="sdapi" category="time" entity_type="" role="" text="12 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">12 h</sd-tag> of starvation. 200 young adult animals for each genotype were collected for analysis.<graphic href="https://api.sourcedata.io/file.php?panel_id=7436"/></sd-panel><sd-panel panel_id="7439"><b>H, I</b> <sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates in <i><sd-tag id="sdTag274" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>) mutants are separable from <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAAT‐1" ext_ids="Q95XZ6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="laat-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot/">LAAT‐1</sd-tag>::<sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Cherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cherry</sd-tag>‐labeled <sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> under normal conditions, but are delivered to <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> upon starvation. Some aggregates are enclosed by <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (inserts). Scale bar: 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7439"/></sd-panel><sd-panel panel_id="7440"><b>J-Q</b> RNAi inactivation of <i><sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="gene" role="intervention" text="let‐363" ext_ids="172167" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LET-363" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">let‐363</sd-tag></i>, <i><sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rpn‐2" ext_ids="175877" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPN-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpn‐2</sd-tag></i>, <i><sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cogc‐1" ext_ids="3565555" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="COGC-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cogc‐1</sd-tag>,</i> or <i><sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="gene" role="intervention" text="hgrs‐1" ext_ids="177617" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HGRS-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">hgrs‐1</sd-tag></i> suppresses the accumulation of <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates in <i><sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>) mutants. (J), (L), (N), and (P): <sd-tag id="sdTag275" source="sdapi" category="assay" entity_type="" role="" text="DIC" ext_ids="BAO_0002511" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="differential interference contrast microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">DIC</sd-tag> images of the animals in (K), (M), (O), and (Q). Scale bar: 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7440"/></sd-panel><sd-panel panel_id="7441"><b>R</b> <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> levels in <i><sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>) mutants are greatly reduced by inactivation of <i><sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rpt‐3" ext_ids="178988" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPT-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpt‐3</sd-tag></i> and <i><sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rpn‐2" ext_ids="175877" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPN-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpn‐2</sd-tag></i>. 200 young adult animals for each genotype were collected for analysis.<graphic href="https://api.sourcedata.io/file.php?panel_id=7441"/></sd-panel></fig><fig id="2597"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2597"/><sd-panel panel_id="7443"><b>A, B</b> <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates are absent in the <i><sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>)<i>;</i> <i><sd-tag id="sdTag311" source="sdapi" category="entity" entity_type="gene" role="component" text="sma‐3" ext_ids="175955" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SMA-3" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sma‐3</sd-tag></i>(<i>wk20</i>) mutant <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="tissue" role="component" text="intestine" ext_ids="UBERON:0000160" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="intestine" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">intestine</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7443"/></sd-panel><sd-panel panel_id="7444"><b>C</b> Percentage of the indicated animals with different levels of <sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates. S: many <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates in all <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="tissue" role="component" text="intestinal cells" ext_ids="UBERON:0000160" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="intestine" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">intestinal cells</sd-tag>, as in <i><sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>) mutants; M: fewer <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates in some but not all <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="tissue" role="component" text="intestinal cells" ext_ids="UBERON:0000160" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="intestine" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">intestinal cells</sd-tag>; N: no or very few <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates in <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="tissue" role="component" text="intestinal cells" ext_ids="UBERON:0000160" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="intestine" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">intestinal cells</sd-tag>. For each genotype, &gt; 30 animals were examined.<graphic href="https://api.sourcedata.io/file.php?panel_id=7444"/></sd-panel><sd-panel panel_id="7445"><b>D</b> <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> levels in <i><sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>) mutants are dramatically decreased in a <sd-tag id="sdTag79" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> when <i><sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sma‐3" ext_ids="175955" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SMA-3" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sma‐3</sd-tag></i>, <i><sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="gene" role="intervention" text="lin‐35" ext_ids="172249" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LIN-35" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lin‐35</sd-tag>,</i> or <i><sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="gene" role="intervention" text="daf‐2" ext_ids="175410" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="DAF-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">daf‐2</sd-tag></i> is simultaneously depleted. Loss of function of <i><sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="gene" role="intervention" text="daf‐16" ext_ids="172981" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="DAF-16" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">daf‐16</sd-tag></i> partially restores <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag> levels in <i><sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>)<i>; <sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="gene" role="intervention" text="daf‐2" ext_ids="175410" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="DAF-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">daf‐2</sd-tag></i>(<i>RNAi</i>) mutants.<graphic href="https://api.sourcedata.io/file.php?panel_id=7445"/></sd-panel><sd-panel panel_id="7446"><b>E</b> Endogenous <sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LGG‐1" ext_ids="Q09490" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="lgg-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot/">LGG‐1</sd-tag> is elevated in a <sd-tag id="sdTag93" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> in <i><sd-tag id="sdTag313" source="sdapi" category="entity" entity_type="gene" role="intervention" text="dbl‐1" ext_ids="179068" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="dbl-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">dbl‐1</sd-tag></i>(<i>wk70</i>), <i><sd-tag id="sdTag314" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sma‐2" ext_ids="176229" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="sma-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sma‐2</sd-tag></i>(<i>e502</i>), and <i><sd-tag id="sdTag312" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sma‐3" ext_ids="175955" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SMA-3" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sma‐3</sd-tag></i>(<i>wk20</i>) mutants.<graphic href="https://api.sourcedata.io/file.php?panel_id=7446"/></sd-panel><sd-panel panel_id="7447"><b>F</b> mRNA levels of <i><sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="gene" role="assayed" text="bec‐1" ext_ids="177345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BEC-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bec‐1</sd-tag>, <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="gene" role="assayed" text="epg‐8" ext_ids="172847" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="EPG-8" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">epg‐8</sd-tag>, <sd-tag id="sdTag309" source="sdapi" category="entity" entity_type="gene" role="assayed" text="lgg‐1" ext_ids="174050" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LGG-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lgg‐1</sd-tag>,</i> and <i><sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="gene" role="assayed" text="atg‐7" ext_ids="178005" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG-7" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg‐7</sd-tag></i> are upregulated in <i><sd-tag id="sdTag315" source="sdapi" category="entity" entity_type="gene" role="intervention" text="dbl‐1" ext_ids="179068" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="dbl-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">dbl‐1</sd-tag></i>(<i>wk70</i>), <i><sd-tag id="sdTag316" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sma‐2" ext_ids="176229" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="sma-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sma‐2</sd-tag></i>(<i>e502</i>), and <i><sd-tag id="sdTag317" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sma‐3" ext_ids="175955" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SMA-3" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sma‐3</sd-tag></i>(<i>wk20</i>) mutants. **<i>P</i> 0.01. 500 young adult animals were collected for analysis. Error bars indicate s.d. from three experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=7447"/></sd-panel><sd-panel panel_id="7448"><b>G, H</b> No <sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates are observed in the <i><sd-tag id="sdTag318" source="sdapi" category="entity" entity_type="gene" role="component" text="lin‐35" ext_ids="172249" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LIN-35" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lin‐35</sd-tag></i>(<i>n745</i>)<i>; <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>) mutant <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="tissue" role="component" text="intestine" ext_ids="UBERON:0000160" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="intestine" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">intestine</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7448"/></sd-panel><sd-panel panel_id="7449"><b>I, J</b> Numerous <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates are formed in <i><sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>)<i>;</i> <i><sd-tag id="sdTag319" source="sdapi" category="entity" entity_type="gene" role="component" text="lin‐15A" ext_ids="181663" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="lin-15A" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lin‐15A</sd-tag></i>(<i>n767</i>) mutants.<graphic href="https://api.sourcedata.io/file.php?panel_id=7449"/></sd-panel><sd-panel panel_id="7450"><b>K</b> Endogenous <sd-tag id="sdTag137" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LGG‐1" ext_ids="Q09490" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="lgg-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot/">LGG‐1</sd-tag> levels are increased in <i><sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="gene" role="intervention" text="lin‐9" ext_ids="176256" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LIN-9" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lin‐9</sd-tag></i>(<i>n112</i>), <i><sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="gene" role="intervention" text="lin‐15B" ext_ids="181662" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LIN-15B" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lin‐15B</sd-tag></i>(<i>n744</i>), and <i><sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="gene" role="intervention" text="lin‐35" ext_ids="172249" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LIN-35" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lin‐35</sd-tag></i>(<i>n745</i>) mutants.<graphic href="https://api.sourcedata.io/file.php?panel_id=7450"/></sd-panel><sd-panel panel_id="7451"><b>L</b> mRNA levels of <i><sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="gene" role="assayed" text="bec‐1" ext_ids="177345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BEC-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bec‐1</sd-tag>, <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="gene" role="assayed" text="epg‐8" ext_ids="172847" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="EPG-8" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">epg‐8</sd-tag>, <sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="gene" role="assayed" text="lgg‐1" ext_ids="174050" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LGG-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lgg‐1</sd-tag>,</i> and <i><sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="gene" role="assayed" text="atg‐7" ext_ids="178005" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG-7" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg‐7</sd-tag></i> are upregulated in <i><sd-tag id="sdTag320" source="sdapi" category="entity" entity_type="gene" role="intervention" text="lin‐9" ext_ids="176256" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LIN-9" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lin‐9</sd-tag></i>(<i>n112</i>), <i><sd-tag id="sdTag321" source="sdapi" category="entity" entity_type="gene" role="intervention" text="lin‐15B" ext_ids="181662" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LIN-15B" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lin‐15B</sd-tag></i>(<i>n744</i>), and <i><sd-tag id="sdTag322" source="sdapi" category="entity" entity_type="gene" role="intervention" text="lin‐35" ext_ids="172249" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LIN-35" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lin‐35</sd-tag></i>(<i>n745</i>) mutants. **<i>P</i> 0.01. 500 young adult animals were collected for analysis. Error bars indicate s.d. from three experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=7451"/></sd-panel><sd-panel panel_id="7452"><b>M, N</b> <i><sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>)<i>; <sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="gene" role="component" text="daf‐2" ext_ids="175410" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="DAF-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">daf‐2</sd-tag></i>(<i>RNAi</i>) mutant <sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="organism" role="component" text="larvae" ext_ids="6239" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Caenorhabditis elegans" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">larvae</sd-tag> contain no intestinal <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates.<graphic href="https://api.sourcedata.io/file.php?panel_id=7452"/></sd-panel><sd-panel panel_id="7453"><b>O, P</b> <sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag><span>::<sd-tag id="sdTag323" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates are partially restored in</span> <i><sd-tag id="sdTag324" source="sdapi" category="entity" entity_type="gene" role="component" text="daf‐16" ext_ids="172981" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="DAF-16" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">daf‐16</sd-tag></i>(<i>mu86</i>); <i><sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>); <i><sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="gene" role="component" text="daf‐2" ext_ids="175410" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="DAF-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">daf‐2</sd-tag></i>(<i>RNAi</i>) animals.<graphic href="https://api.sourcedata.io/file.php?panel_id=7453"/></sd-panel></fig><fig id="2598"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2598"/><sd-panel panel_id="7454"><p><strong><span class="list-label">A, B</span></strong> <sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Phsp‐4" ext_ids="P20163" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="hsp-4" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot/"><em>hsp‐4</em></sd-tag><em>::<sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag></em> is very weakly expressed in wild‐type animals.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=7454"/></sd-panel><sd-panel panel_id="7455"><b>C</b> Percentage of indicated animals with different levels of <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates. S: strong. M: medium. N: none. &gt;30 animals were examined for each genotype.<graphic href="https://api.sourcedata.io/file.php?panel_id=7455"/></sd-panel><sd-panel panel_id="7456"><b>D, E</b> <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Phsp‐4" ext_ids="P20163" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="hsp-4" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot/">P<i>hsp‐4</i></sd-tag><i>::<sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag></i> expression is much higher in <i><sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="gene" role="component" text="rpt‐3" ext_ids="178988" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPT-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpt‐3</sd-tag></i>(<i>RNAi</i>) animals.<graphic href="https://api.sourcedata.io/file.php?panel_id=7456"/></sd-panel><sd-panel panel_id="7457"><b>F, G</b> Upregulation of <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Phsp‐4" ext_ids="P20163" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="hsp-4" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot/">P<i>hsp‐4</i></sd-tag><i>::<sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag></i> expression in <i><sd-tag id="sdTag203" source="sdapi" category="entity" entity_type="gene" role="component" text="rpt‐3" ext_ids="178988" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPT-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpt‐3</sd-tag></i>(<i>RNAi</i>) animals is suppressed by the <i><sd-tag id="sdTag325" source="sdapi" category="entity" entity_type="gene" role="component" text="xbp‐1" ext_ids="175541" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="XBP-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">xbp‐1</sd-tag></i>(<i>zc12</i>) mutation.<graphic href="https://api.sourcedata.io/file.php?panel_id=7457"/></sd-panel><sd-panel panel_id="7458"><b>H, I</b> <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates are absent in <i><sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>)<i>; <sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="gene" role="component" text="rpt‐3" ext_ids="178988" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPT-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpt‐3</sd-tag></i>(<i>RNAi</i>) animals.<graphic href="https://api.sourcedata.io/file.php?panel_id=7458"/></sd-panel><sd-panel panel_id="7459"><b>J, K</b> Loss of function of <i><sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="gene" role="component" text="xbp‐1" ext_ids="175541" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="XBP-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">xbp‐1</sd-tag></i> restores <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates in <i><sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>)<i>; <sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="gene" role="component" text="rpt‐3" ext_ids="178988" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPT-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpt‐3</sd-tag></i>(<i>RNAi</i>) animals.<graphic href="https://api.sourcedata.io/file.php?panel_id=7459"/></sd-panel><sd-panel panel_id="7461"><b>M</b> The increase in <i><sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="gene" role="assayed" text="bec‐1" ext_ids="177345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BEC-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bec‐1</sd-tag>, <sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="gene" role="assayed" text="epg‐8" ext_ids="172847" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="EPG-8" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">epg‐8</sd-tag>, <sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="gene" role="assayed" text="lgg‐1" ext_ids="174050" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LGG-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lgg‐1</sd-tag>,</i> and <i><sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="gene" role="assayed" text="atg‐7" ext_ids="178005" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG-7" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg‐7</sd-tag></i> mRNA levels in <i><sd-tag id="sdTag230" source="sdapi" category="entity" entity_type="gene" role="intervention" text="npl‐4.1" ext_ids="173952" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="NPL-4.1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">npl‐4.1</sd-tag></i>, <i><sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rpt‐3" ext_ids="178988" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPT-2" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpt‐3</sd-tag>,</i> and <i><sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="gene" role="intervention" text="pep‐2" ext_ids="172167" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LET-363" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">pep‐2</sd-tag></i> RNAi animals is dependent on <i><sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="gene" role="intervention" text="xbp‐1" ext_ids="175541" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="XBP-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">xbp‐1</sd-tag></i>. *<i>P</i> 0.05, **<i>P</i> 0.01. 500 young adult animals were collected for analysis. Error bars indicate s.d. from three experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=7461"/></sd-panel></fig><fig id="2599"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2599"/><sd-panel panel_id="7462"><b>A</b> <sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Phsp‐60" ext_ids="P50140" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="hsp-60" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot/">P<i>hsp‐60</i></sd-tag><i>::<sd-tag id="sdTag235" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag></i> is weakly expressed in wild‐type animals.<graphic href="https://api.sourcedata.io/file.php?panel_id=7462"/></sd-panel><sd-panel panel_id="7463"><b>B</b> <i><sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="gene" role="component" text="egl‐46" ext_ids="179058" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="EGL-46" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">egl‐46</sd-tag></i>(<i>RNAi</i>) causes upregulation of <sd-tag id="sdTag238" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Phsp‐60" ext_ids="P50140" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="hsp-60" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot/">P<i>hsp‐60</i></sd-tag><i>::<sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag></i>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7463"/></sd-panel><sd-panel panel_id="7464"><b>C</b> Percentage of indicated mutant animals with different levels of <sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates. S: strong. M: medium. N: none. &gt;30 animals were examined in each group.<graphic href="https://api.sourcedata.io/file.php?panel_id=7464"/></sd-panel><sd-panel panel_id="7465"><b>D</b> Levels of <sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> in various genetic mutants. 200 young adult animals for each genotype were collected for analysis.<graphic href="https://api.sourcedata.io/file.php?panel_id=7465"/></sd-panel><sd-panel panel_id="7466"><b>E, F</b> Loss of function of <i><sd-tag id="sdTag263" source="sdapi" category="entity" entity_type="gene" role="component" text="atfs‐1" ext_ids="179922" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATFS-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atfs‐1</sd-tag></i> suppresses the upregulation of <sd-tag id="sdTag267" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Phsp‐60" ext_ids="P50140" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="hsp-60" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot/">P<i>hsp‐60</i></sd-tag><i>::<sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag></i> in <i><sd-tag id="sdTag326" source="sdapi" category="entity" entity_type="gene" role="component" text="egl‐46" ext_ids="179058" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="EGL-46" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">egl‐46</sd-tag></i>(<i>n1126</i>) mutants. (E): <sd-tag id="sdTag268" source="sdapi" category="assay" entity_type="" role="" text="DIC" ext_ids="BAO_0002511" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="differential interference contrast microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">DIC</sd-tag> image of (F).<graphic href="https://api.sourcedata.io/file.php?panel_id=7466"/></sd-panel><sd-panel panel_id="7467"><b>G, H</b> The dramatic decrease in the number of <sd-tag id="sdTag292" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQST‐1" ext_ids="F1LIM5///Q22436" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="sqst-1///sqst-1" ext_tax_ids="6239///6239" ext_tax_names="Caenorhabditis elegans///Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SQST‐1</sd-tag>::<sd-tag id="sdTag293" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> aggregates in the <sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="tissue" role="component" text="intestine" ext_ids="UBERON:0000160" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="intestine" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">intestine</sd-tag> in <i><sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="gene" role="component" text="rpl‐43" ext_ids="175070" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RPL-43" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">rpl‐43</sd-tag></i>(<i>bp399</i>)<i>; <sd-tag id="sdTag297" source="sdapi" category="entity" entity_type="gene" role="component" text="egl‐46" ext_ids="179058" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="EGL-46" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">egl‐46</sd-tag></i>(<i>RNAi</i>) mutants (G) is restored by simultaneous loss of function of <i><sd-tag id="sdTag327" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atfs‐1" ext_ids="179922" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATFS-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atfs‐1</sd-tag></i>(<i>gk3094</i>) (H).<graphic href="https://api.sourcedata.io/file.php?panel_id=7467"/></sd-panel><sd-panel panel_id="7468"><b>I, J</b> <sd-tag id="sdTag300" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>::<sd-tag id="sdTag301" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LGG‐1" ext_ids="Q09490" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="lgg-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="https://www.uniprot.org/uniprot/">LGG‐1</sd-tag> forms numerous puncta in the <sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="tissue" role="component" text="intestine" ext_ids="UBERON:0000160" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="intestine" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">intestine</sd-tag> in <i><sd-tag id="sdTag303" source="sdapi" category="entity" entity_type="gene" role="intervention" text="egl‐46" ext_ids="179058" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="EGL-46" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">egl‐46</sd-tag></i>(<i>RNAi</i>) (I), <i><sd-tag id="sdTag304" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gfi‐1" ext_ids="179022" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GFI-1" ext_tax_ids="6239" ext_tax_names="Caenorhabditis elegans" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gfi‐1</sd-tag></i>(<i>RNAi</i>) (J) animals.<graphic href="https://api.sourcedata.io/file.php?panel_id=7468"/></sd-panel></fig></article>

token_classification/10-1002_embr-201438501.xml

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+<?xml version='1.0' encoding='UTF-8'?>
+<article doi="10.1002/embr.201438501" abstract="Autophagy eliminates dysfunctional mitochondria in an intricate process known as mitophagy. ULK1 is critical for the induction of autophagy, but its substrate(s) and mechanism of action in mitophagy remain unclear. Here, we show that ULK1 is upregulated and translocates to fragmented mitochondria upon mitophagy induction by either hypoxia or mitochondrial uncouplers. At mitochondria, ULK1 interacts with FUNDC1, phosphorylating it at serine 17, which enhances FUNDC1 binding to LC3. A ULK1-binding-deficient mutant of FUNDC1 prevents ULK1 translocation to mitochondria and inhibits mitophagy. Finally, kinase-active ULK1 and a phospho-mimicking mutant of FUNDC1 rescue mitophagy in ULK1-null cells. Thus, we conclude that FUNDC1 regulates ULK1 recruitment to damaged mitochondria, where FUNDC1 phosphorylation by ULK1 is crucial for mitophagy."><fig id="1141"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1141"/><sd-panel panel_id="2328"><div><strong>A</strong> Levels of <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> in <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> exposed to <sd-tag id="sdTag456" source="sdapi" category="physical" entity_type="" role="" text="hypoxia" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hypoxia</sd-tag> (1% <sd-tag id="sdTag392" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="O2" ext_ids="CHEBI:15379" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dioxygen" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">O<sub>2</sub></sd-tag>) for the indicated times.</div><div><sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag>, <sd-tag id="sdTag4" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag></div><graphic href="https://api.sourcedata.io/file.php?panel_id=2328"/></sd-panel><sd-panel panel_id="2329"><p><strong>B</strong> Quantification of the ratio of <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> to <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> in (A).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2329"/></sd-panel><sd-panel panel_id="2330"><p><strong>C</strong> Levels of <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> in <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> treated with <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> (20 μM) for the indicated times.</p><p><sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag></p><graphic href="https://api.sourcedata.io/file.php?panel_id=2330"/></sd-panel><sd-panel panel_id="2331"><b>D</b> Quantification of the ratio of <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> to <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> in (C).<graphic href="https://api.sourcedata.io/file.php?panel_id=2331"/></sd-panel><sd-panel panel_id="2332"><b>E</b> <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> <span>were exposed to <sd-tag id="sdTag455" source="sdapi" category="physical" entity_type="" role="" text="hypoxia" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hypoxia</sd-tag> (1%</span> <sd-tag id="sdTag415" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="O2" ext_ids="CHEBI:15379" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dioxygen" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">O<sub>2</sub></sd-tag>) for 12 h or <sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> <span>(20 μM) for <sd-tag id="sdTag449" source="sdapi" category="time" entity_type="" role="" text="6 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">6 h</sd-tag> and then fixed by 4% paraformaldehyde. Cells were stained with anti‐</span><sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TIM23" ext_ids="Q9WTQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Timm23" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">TIM23</sd-tag> (mouse) and anti‐<sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> <span>(rabbit) primary antibodies, then <sd-tag id="sdTag450" source="sdapi" category="assay" entity_type="" role="" text="Alexa Fluor‐488" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Alexa Fluor‐488</sd-tag>‐labeled donkey anti‐rabbit <sd-tag id="sdTag451" source="sdapi" category="entity" entity_type="subcellular" role="component" text="IgG" ext_ids="GO:0071735" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="IgG immunoglobulin complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">IgG</sd-tag> and <sd-tag id="sdTag452" source="sdapi" category="assay" entity_type="" role="" text="Alexa Fluor‐555" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Alexa Fluor‐555</sd-tag>‐labeled donkey anti‐mouse <sd-tag id="sdTag453" source="sdapi" category="entity" entity_type="subcellular" role="component" text="IgG" ext_ids="GO:0071735" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="IgG immunoglobulin complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">IgG</sd-tag> secondary antibodies before analysis by</span> <sd-tag id="sdTag26" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence microscopy" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunofluorescence microscopy</sd-tag>. Scale bar, 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=2332"/></sd-panel><sd-panel panel_id="2333"><p><strong>F</strong> <sd-tag id="sdTag27" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag>s of subcellular fractions from control <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> or <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> that were exposed to <sd-tag id="sdTag454" source="sdapi" category="physical" entity_type="" role="" text="hypoxia" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hypoxia</sd-tag> (1% <sd-tag id="sdTag416" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="O2" ext_ids="CHEBI:15379" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dioxygen" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">O<sub>2</sub></sd-tag>) for <sd-tag id="sdTag457" source="sdapi" category="time" entity_type="" role="" text="12 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">12 h</sd-tag>. PNS, post‐nuclear supernatant; Cyto, <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="cytosol" ext_ids="GO:0005829" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="cytosol" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">cytosol</sd-tag>; <sd-pretag id="sdPretag14393884472240" parent-tag-id="491">Mito</sd-pretag>, <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>.</p><p><sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag></p><graphic href="https://api.sourcedata.io/file.php?panel_id=2333"/></sd-panel><sd-panel panel_id="2334"><p><strong>G</strong> <sd-tag id="sdTag39" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag>s of subcellular fractions from control <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> or <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> that were treated with <sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> (20 μM) for <sd-tag id="sdTag458" source="sdapi" category="time" entity_type="" role="" text="6 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">6 h</sd-tag>. PNS, post‐nuclear supernatant; Cyto, <sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="cytosol" ext_ids="GO:0005829" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="cytosol" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">cytosol</sd-tag>; <sd-pretag id="sdPretag14393884979030" parent-tag-id="491">Mito</sd-pretag>, <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>.</p><p><sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag></p><graphic href="https://api.sourcedata.io/file.php?panel_id=2334"/></sd-panel></fig><fig id="1142"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1142"/><sd-panel panel_id="2335"><b>A</b> <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were co−transfected with <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q8IVP5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag>−<sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> and <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>−<sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag>. Cells were lysed and <sd-tag id="sdTag52" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> with anti−<sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> <span>antibody <sd-tag id="sdTag460" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> after transfection.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=2335"/></sd-panel><sd-panel panel_id="2336"><b>B</b> <sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="protein" role="reporter" text="FLAG" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FLAG</sd-tag>−<sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q8IVP5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag> was co−transfected with <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>−vector or <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>−<sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O75385" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> <span>for <sd-tag id="sdTag461" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> in</span> <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells, and then, cell lysates were <sd-tag id="sdTag66" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> with anti−<sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> antibody.<graphic href="https://api.sourcedata.io/file.php?panel_id=2336"/></sd-panel><sd-panel panel_id="2337"><p><strong>C</strong><sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were exposed to <sd-tag id="sdTag463" source="sdapi" category="physical" entity_type="" role="" text="hypoxia" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hypoxia</sd-tag> (1% <sd-tag id="sdTag393" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="O2" ext_ids="CHEBI:15379" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dioxygen" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">O<sub>2</sub></sd-tag>) for <sd-tag id="sdTag464" source="sdapi" category="time" entity_type="" role="" text="12 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">12 h</sd-tag> or <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> (20 μM) for <sd-tag id="sdTag465" source="sdapi" category="time" entity_type="" role="" text="3 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">3 h</sd-tag>, followed by <sd-tag id="sdTag70" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitation" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitation</sd-tag> using anti‐<sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> antibody.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2337"/></sd-panel><sd-panel panel_id="2338"><p><strong>D</strong> The expression of <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q8IVP5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag> is induced by 10 ng/ml <sd-tag id="sdTag468" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="tetracycline" ext_ids="CHEBI:27902" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="tetracycline" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">tetracycline</sd-tag> (Tet) in <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="139341" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>‐inducible <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells. Cells were transfected with <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="8408" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag> or <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag469" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O75385" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> (K46N) for <sd-tag id="sdTag470" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag>. Then, the cell lysates were prepared for <sd-tag id="sdTag394" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> using indicated antibodies.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2338"/></sd-panel><sd-panel panel_id="2339"><p><strong>E</strong><em><sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="8408" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>+/+</sup></em> cells were transfected with <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q8IVP5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag>‐<sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>, and <sd-tag id="sdTag471" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="8408" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag>-/- cells were transfected with <sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="gene" role="component" text="FUNDC1" ext_ids="139341" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>‐<sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> alone, <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q8IVP5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag>‐<sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> and <sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O75385" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag>, or <sd-tag id="sdTag472" source="sdapi" category="entity" entity_type="gene" role="component" text="FUNDC1" ext_ids="139341" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>‐<sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> and <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag417" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O75385" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> (K46N). Cells were harvested and lysed for <sd-tag id="sdTag98" source="sdapi" category="assay" entity_type="" role="" text="immunoblots" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblots</sd-tag><sd-tag id="sdTag474" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> after transfection.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2339"/></sd-panel><sd-panel panel_id="2340"><p><strong>F</strong> Purified <sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag>‐<sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q8IVP5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag> and <sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag>‐<sd-tag id="sdTag478" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q8IVP5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag> (S17A) were subjected to an <sd-tag id="sdTag475" source="sdapi" category="assay" entity_type="" role="" text="in vitro kinase assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><em>in vitro</em> kinase assay</sd-tag> with <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>‐<sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O75385" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> <sd-tag id="sdTag480" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> by anti‐<sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> antibody from <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>‐<sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O75385" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag>‐transfected cells about <sd-tag id="sdTag476" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> post‐transfection. Phosphorylated <sd-tag id="sdTag479" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q8IVP5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag> was detected by anti‐p‐S17‐<sd-tag id="sdTag477" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="139341" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag> antibody. The red asterisks mark the target bands.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2340"/></sd-panel><sd-panel panel_id="2341"><p><strong>G</strong> <sd-tag id="sdTag310" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag><sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag>, <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q9DB70" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag>, and the phosphorylated <sd-tag id="sdTag482" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q9DB70" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag> in <sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> exposed to <sd-tag id="sdTag483" source="sdapi" category="physical" entity_type="" role="" text="hypoxia" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hypoxia</sd-tag> (1% <sd-tag id="sdTag396" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="O2" ext_ids="CHEBI:15379" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dioxygen" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">O<sub>2</sub></sd-tag>) for the indicated times.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2341"/></sd-panel><sd-panel panel_id="2342"><p><strong>H</strong><sd-tag id="sdTag123" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis of the kinetics of <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag>, <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q9DB70" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag>, and the phosphorylated in <sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> treated with <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag>(20 μM) for the indicated times.</p><p><sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag></p><graphic href="https://api.sourcedata.io/file.php?panel_id=2342"/></sd-panel><sd-panel panel_id="2343"><p>I, J The single mutant which can abolish the <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> and <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q9DB70" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag> interaction was identified. <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were co‐transfected with <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag> and the indicated constructs. <sd-tag id="sdTag487" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> after transfection, cells were lysed for <sd-tag id="sdTag134" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitation" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitation</sd-tag> by anti‐<sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag> antibody.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2343"/></sd-panel><sd-panel panel_id="2344"><p><strong>K</strong><sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transfected with <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q9DB70" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag>‐<sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> and its mutants after the endogenous <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag> was knocked down by siRNA. <sd-tag id="sdTag488" source="sdapi" category="time" entity_type="" role="" text="36 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">36 h</sd-tag> after transfection, cells were harvested in the absence or presence of 50 nM <sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (<sd-tag id="sdTag489" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BAF1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BAF1</sd-tag>) and then lysed for <sd-tag id="sdTag144" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> with the indicated antibodies.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2344"/></sd-panel><sd-panel panel_id="2345"><p><strong>L</strong> <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were co‐transfected with <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>‐<sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> or its mutants and <sd-tag id="sdTag491" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Mito" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Mito</sd-tag><sd-tag id="sdTag492" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Dsred" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Dsred</sd-tag> after the endogenous <sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q9DB70" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag> was knocked down by siRNA. <sd-tag id="sdTag493" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> post‐transfection, cells were treated with <sd-tag id="sdTag490" source="sdapi" category="physical" entity_type="" role="" text="hypoxic" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hypoxic</sd-tag> (1% <sd-tag id="sdTag397" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="O2" ext_ids="CHEBI:15379" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dioxygen" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">O<sub>2</sub></sd-tag>) conditions for <sd-tag id="sdTag494" source="sdapi" category="time" entity_type="" role="" text="12 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">12 h</sd-tag> or <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> (20 μM) for <sd-tag id="sdTag495" source="sdapi" category="time" entity_type="" role="" text="6 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">6 h</sd-tag> before fixed by 4% paraformaldehyde and stained with indicated antibodies. Scale bar, 10 μm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2345"/></sd-panel></fig><fig id="1143"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1143"/><sd-panel panel_id="2346"><p><strong>A</strong><em><sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>+/+</sup></em> and <em><sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag><sup>−/−</sup></em> cells were cultured under <sd-tag id="sdTag497" source="sdapi" category="physical" entity_type="" role="" text="hypoxic" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hypoxic</sd-tag> (1% <sd-tag id="sdTag398" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="O2" ext_ids="CHEBI:15379" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dioxygen" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">O<sub>2</sub></sd-tag>) condition for <sd-tag id="sdTag499" source="sdapi" category="time" entity_type="" role="" text="12 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">12 h</sd-tag> or <sd-tag id="sdTag500" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> in the absence or presence of 50 nM <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (<sd-tag id="sdTag498" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BAF1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BAF1</sd-tag>). Cell lysates were <sd-tag id="sdTag165" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2346"/></sd-panel><sd-panel panel_id="2347"><b>B</b> <i><sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag><sup>+/+</sup></i> and <i><sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></i> cells were treated with <sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> (20 μM) for the indicated times in the absence or presence of 50 nM <sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (<sd-tag id="sdTag502" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BAF1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BAF1</sd-tag>). Cell lysates were <sd-tag id="sdTag177" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2347"/></sd-panel><sd-panel panel_id="2348"><b>C</b> <i><sd-tag id="sdTag178" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag><sup>+/+</sup></i> and <i><sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></i> cells were transfected with <sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>−<sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> <span>for <sd-tag id="sdTag505" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> and then harvested in the absence or presence of 50 nM</span> <sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (<sd-tag id="sdTag504" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BAF1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BAF1</sd-tag>). Cell lysates were <sd-tag id="sdTag183" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2348"/></sd-panel><sd-panel panel_id="2349"><p><strong>D</strong> <em><sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></em> cells were transfected with <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> or <sd-tag id="sdTag189" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag506" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> (K46N), then cultured under <sd-tag id="sdTag507" source="sdapi" category="physical" entity_type="" role="" text="hypoxic" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hypoxic</sd-tag> (1% <sd-tag id="sdTag401" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="O2" ext_ids="CHEBI:15379" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dioxygen" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">O<sub>2</sub></sd-tag>) conditions for <sd-tag id="sdTag509" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> in the absence or presence of 50 nM <sd-tag id="sdTag191" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (<sd-tag id="sdTag508" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BAF1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BAF1</sd-tag>). Cells lysates were <sd-tag id="sdTag192" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2349"/></sd-panel><sd-panel panel_id="2350"><b>E</b><i><sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></i> cells were transfected with <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>−<sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O70405" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> or <sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>−<sd-tag id="sdTag511" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag> and then treated with <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> <span>(20 μM) for <sd-tag id="sdTag510" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag>. Cells were harvested in the absence or presence of 50 nM</span> <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (<sd-tag id="sdTag512" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BAF1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BAF1</sd-tag>). Cell lysates were <sd-tag id="sdTag513" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2350"/></sd-panel><sd-panel panel_id="2351"><p><strong>F</strong> <em><sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag></em>‐knockdown <sd-tag id="sdTag345" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transfected with <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q8IVP5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag>‐<sd-tag id="sdTag203" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> or <sd-tag id="sdTag424" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q8IVP5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag>-<sd-tag id="sdTag413" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> (S17A) for the indicated times. Cell lysates were used for <sd-tag id="sdTag350" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2351"/></sd-panel><sd-panel panel_id="2352"><p><strong>G</strong> <em><sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>+/+</sup></em> cells were transfected with <sd-tag id="sdTag516" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>‐<sd-tag id="sdTag358" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>, and <em><sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></em> cells were transfected with <sd-tag id="sdTag357" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q9DB70" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag>‐<sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> or <sd-tag id="sdTag518" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>-<sd-tag id="sdTag359" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> (S17D). <sd-tag id="sdTag517" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> after transfection, cells were fixed with 4% paraformaldehyde and stained with anti‐<sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> (mouse) and anti‐<sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (rabbit) primary antibodies for <sd-tag id="sdTag354" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence microscopy" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunofluorescence microscopy</sd-tag>. Scale bar, 10 μm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2352"/></sd-panel><sd-panel panel_id="2353"><p><strong>H</strong> <em><sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="gene" role="component" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></em> cells were transfected with <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>‐<sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> or <sd-tag id="sdTag519" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q9DB70" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag>-<sd-tag id="sdTag360" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> (S17D) for <sd-tag id="sdTag522" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> in the absence or presence of 50 nm <sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (<sd-tag id="sdTag521" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BAF1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BAF1</sd-tag>) for an additional <sd-tag id="sdTag520" source="sdapi" category="time" entity_type="" role="" text="6 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">6 h</sd-tag> before harvesting. Cell lysates were <sd-tag id="sdTag220" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2353"/></sd-panel><sd-panel panel_id="2354"><p><strong>I</strong> <em><sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="gene" role="component" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></em> cells were transfected with <sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>‐<sd-tag id="sdTag230" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> or <sd-tag id="sdTag523" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>-<sd-tag id="sdTag369" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> (S17D) for <sd-tag id="sdTag525" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> in the absence or presence of 50 nm <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (<sd-tag id="sdTag524" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BAF1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BAF1</sd-tag>) for an additional <sd-tag id="sdTag526" source="sdapi" category="time" entity_type="" role="" text="6 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">6 h</sd-tag> before harvesting. Cell lysates were detected with the <sd-tag id="sdTag233" source="sdapi" category="assay" entity_type="" role="" text="citrate synthase activity" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">citrate synthase activity</sd-tag> kit.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2354"/></sd-panel><sd-panel panel_id="2355"><p><strong>J</strong> <sd-tag id="sdTag235" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="" ext_tax_names="" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were transfected with <sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q8IVP5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag>‐<sd-tag id="sdTag237" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>, <sd-tag id="sdTag527" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="139341" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>-<sd-tag id="sdTag371" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> (S17A), or <sd-tag id="sdTag528" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="139341" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="FUNDC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>-<sd-tag id="sdTag374" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> (S17D). <sd-tag id="sdTag529" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> after transfection, cell lysates were <sd-tag id="sdTag242" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> with anti‐<sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> antibody.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2355"/></sd-panel></fig><fig id="1144"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1144"/><sd-panel panel_id="2356"><b>A</b> <i><sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>+/+</sup></i> or <i><sd-tag id="sdTag245" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></i> cells were cultured under <sd-tag id="sdTag531" source="sdapi" category="physical" entity_type="" role="" text="hypoxic" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hypoxic</sd-tag> (1% <sd-tag id="sdTag405" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="O2" ext_ids="CHEBI:15379" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dioxygen" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">O<sub>2</sub></sd-tag>) or normoxic conditions in the absence or presence of 50 nM <sd-tag id="sdTag250" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (<sd-tag id="sdTag532" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BAF1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BAF1</sd-tag>). <i><sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></i> cells were transfected with <sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O75385" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag>, and <i><sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></i> <i><sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>‐KD</i> cells were transfected with <sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag257" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O75385" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> and <sd-pretag id="sdPretag14393919291480" parent-tag-id="537">FUNDC1</sd-pretag>‐<sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>, then cultured under <sd-tag id="sdTag533" source="sdapi" category="physical" entity_type="" role="" text="hypoxic" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hypoxic</sd-tag> (1% <sd-tag id="sdTag406" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="O2" ext_ids="CHEBI:15379" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dioxygen" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">O<sub>2</sub></sd-tag>) conditions for 24 h in the absence or presence of 50 nM <sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (<sd-tag id="sdTag534" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BAF1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BAF1</sd-tag>). Cells were harvested and lysed for <sd-tag id="sdTag260" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting assays" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">immunoblotting assays</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2356"/></sd-panel><sd-panel panel_id="2357"><b>B</b> <i><sd-tag id="sdTag261" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>+/+</sup></i> or <i><sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></i> cells were treated with or without <sd-tag id="sdTag267" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> (20 μM) in the absence or presence of 50 nM <sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (<sd-tag id="sdTag535" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BAF1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BAF1</sd-tag>). <i><sd-tag id="sdTag263" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></i> cells were transfected with <sd-tag id="sdTag270" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐ULK1 and <i><sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></i> <i><sd-tag id="sdTag269" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>‐KD</i> cells were transfected with <sd-tag id="sdTag271" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ULK1" ext_ids="O75385" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ULK1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ULK1</sd-tag> and <span><sd-tag id="sdTag537" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FUNDC1" ext_ids="Q9DB70" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FUNDC1</sd-tag></span>‐<sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> and then treated with <sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> <span>(20 μM) for <sd-tag id="sdTag538" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> in the absence or presence of 50 nM</span> <sd-tag id="sdTag274" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (<sd-tag id="sdTag536" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BAF1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">BAF1</sd-tag>). Cells were harvested and lysed for <sd-tag id="sdTag279" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting assays" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">immunoblotting assays</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2357"/></sd-panel><sd-panel panel_id="2358"><b>C</b> <i><sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>+/+</sup></i>, <i><sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></i> <i><sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>‐KD</i>, or <i><sd-tag id="sdTag282" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ULK1" ext_ids="22241" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ulk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ULK1</sd-tag><sup>−/−</sup></i> <i><sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FUNDC1" ext_ids="72018" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fundc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FUNDC1</sd-tag>‐KD</i> cells rescued by introduction of <sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐ULK1 and FUNDC1‐<sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> were cultured under <sd-tag id="sdTag539" source="sdapi" category="physical" entity_type="" role="" text="hypoxic" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hypoxic</sd-tag> (1% <sd-tag id="sdTag409" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="O2" ext_ids="CHEBI:15379" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dioxygen" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">O<sub>2</sub></sd-tag><span>) conditions for <sd-tag id="sdTag541" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> or with</span> <sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> <span>(20 μM) for <sd-tag id="sdTag540" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag>. Samples were analyzed by</span> <sd-tag id="sdTag291" source="sdapi" category="assay" entity_type="" role="" text="electron microscopy" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">electron microscopy</sd-tag>. Scale bar, 2 μm. The yellow asterisks mark <sd-tag id="sdTag292" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>. The red arrows indicate <sd-tag id="sdTag293" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="double‐membraned autophagic structures" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">double‐membraned autophagic structures</sd-tag>. The yellow arrow denotes <sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autolysosomes" ext_ids="GO:0044754" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autolysosomes</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2358"/></sd-panel><sd-panel panel_id="2359"><b>D-E</b> <span>The <sd-tag id="sdTag544" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondrial" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondrial</sd-tag> coverage and <sd-tag id="sdTag543" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondrial" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondrial</sd-tag>−containing <sd-tag id="sdTag542" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="AVs" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AVs</sd-tag> shown in (C) were quantified. Recon, reconstitution.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=2359"/></sd-panel></fig></article>

token_classification/10-1002_emmm-201201443.xml

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+<article doi="10.1002/emmm.201201443" abstract="Maintaining skeletal muscle mass is essential for general health and prevention of disease progression in various neuromuscular conditions. Currently, no treatments are available to prevent progressive loss of muscle mass in any of these conditions. Hibernating mammals are protected from muscle atrophy despite prolonged periods of immobilization and starvation. Here, we describe a mechanism underlying muscle preservation and translate it to non-hibernating mammals. Although Akt has an established role in skeletal muscle homeostasis, we find that serum- and glucocorticoid-inducible kinase 1 (SGK1) regulates muscle mass maintenance via downregulation of proteolysis and autophagy as well as increased protein synthesis during hibernation. We demonstrate that SGK1 is critical for the maintenance of skeletal muscle homeostasis and function in non-hibernating mammals in normal and atrophic conditions such as starvation and immobilization. Our results identify a novel therapeutic target to combat loss of skeletal muscle mass associated with muscle degeneration and atrophy."><fig id="1145"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1145"/><sd-panel panel_id="2361"><div><b>A.</b> Left column, an active summer <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="organism" role="assayed" text="squirrel" ext_ids="43179" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Ictidomys tridecemlineatus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">squirrel</sd-tag>; right column, a torpid <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="organism" role="assayed" text="squirrel" ext_ids="43179" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Ictidomys tridecemlineatus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">squirrel</sd-tag>.</div><graphic href="https://api.sourcedata.io/file.php?panel_id=2361"/></sd-panel><sd-panel panel_id="2362"><div><b>B.</b> The morphology of <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="quadriceps" ext_ids="UBERON:0004498///UBERON:0001377" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of quadriceps femoris///quadriceps femoris" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">quadriceps</sd-tag> is unchanged by hibernation as seen in <sd-tag id="sdTag138" source="sdapi" category="assay" entity_type="" role="" text="haematoxylin and eosin (H&amp;E)" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">haematoxylin and eosin (H&amp;amp;amp;E)</sd-tag> stained sections (scale bar 90 µm).</div><graphic href="https://api.sourcedata.io/file.php?panel_id=2362"/></sd-panel><sd-panel panel_id="2363"><div><b>C.</b> <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Dystrophin" ext_ids="I3N0I4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="DMD" ext_tax_ids="43179" ext_tax_names="Ictidomys tridecemlineatus" ext_urls="https://www.uniprot.org/uniprot/">Dystrophin</sd-tag> staining was performed to outline the <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="subcellular" role="component" text="sarcolemma" ext_ids="GO:0042383" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="sarcolemma" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">sarcolemma</sd-tag> to determine percentage distribution of minimum Feret's diameter.</div><graphic href="https://api.sourcedata.io/file.php?panel_id=2363"/></sd-panel><sd-panel panel_id="2364"><b>D.</b> Average ± SD of minimum Feret's diameter in <sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="quadriceps" ext_ids="UBERON:0004498///UBERON:0001377" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of quadriceps femoris///quadriceps femoris" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">quadriceps</sd-tag> (<i>p</i> = 0.26) and <sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="tibialis anterior" ext_ids="UBERON:0004499///UBERON:0001385" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior///tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">tibialis anterior</sd-tag> (<i>p</i> = 0.33) muscles is not significantly different between summer and hibernation.<graphic href="https://api.sourcedata.io/file.php?panel_id=2364"/></sd-panel></fig><fig id="1146"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1146"/><sd-panel panel_id="2365"><b>A.</b> <sd-tag id="sdTag10" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> of <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="tissue" role="component" text="quadriceps" ext_ids="UBERON:0004498///UBERON:0001377" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of quadriceps femoris///quadriceps femoris" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">quadriceps</sd-tag> <span>muscle from summer active (S) and hibernating (H) <sd-tag id="sdTag190" source="sdapi" category="entity" entity_type="organism" role="experiment" text="squirrels" ext_ids="43179" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Ictidomys tridecemlineatus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">squirrels</sd-tag> using antibodies against the proteins indicated. An increased abundance of P−</span><sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Foxo3a" ext_ids="I3MXH6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FOXA3" ext_tax_ids="43179" ext_tax_names="Ictidomys tridecemlineatus" ext_urls="https://www.uniprot.org/uniprot/">Foxo3a</sd-tag> (serine−253) is accompanied by a decrease in P−<sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Akt" ext_ids="I3MFT2///I3M1D1///I3ML41" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="AKT3///AKT2///AKT1" ext_tax_ids="43179///43179///43179" ext_tax_names="Ictidomys tridecemlineatus///Ictidomys tridecemlineatus///Ictidomys tridecemlineatus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Akt</sd-tag> (serine−478). Corresponding densitometry of P−<sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Akt" ext_ids="I3MFT2///I3M1D1///I3ML41" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="AKT3///AKT2///AKT1" ext_tax_ids="43179///43179///43179" ext_tax_names="Ictidomys tridecemlineatus///Ictidomys tridecemlineatus///Ictidomys tridecemlineatus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Akt</sd-tag> and P−<sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Foxo3a" ext_ids="I3MXH6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FOXA3" ext_tax_ids="43179" ext_tax_names="Ictidomys tridecemlineatus" ext_urls="https://www.uniprot.org/uniprot/">Foxo3a</sd-tag> as a function of total <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Akt" ext_ids="I3M1D1///I3MFT2///I3ML41" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="AKT2///AKT3///AKT1" ext_tax_ids="43179///43179///43179" ext_tax_names="Ictidomys tridecemlineatus///Ictidomys tridecemlineatus///Ictidomys tridecemlineatus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Akt</sd-tag> and <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Foxo3a" ext_ids="I3MXH6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FOXA3" ext_tax_ids="43179" ext_tax_names="Ictidomys tridecemlineatus" ext_urls="https://www.uniprot.org/uniprot/">Foxo3a</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2365"/></sd-panel><sd-panel panel_id="2366"><b>B.</b> Relative mRNA levels for four <sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="gene" role="component" text="Foxo3a" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Foxo3a</sd-tag> downstream targets show no significant changes during hibernation.<graphic href="https://api.sourcedata.io/file.php?panel_id=2366"/></sd-panel><sd-panel panel_id="2367"><b>C.</b> <sd-tag id="sdTag32" source="sdapi" category="assay" entity_type="" role="" text="Western blots" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blots</sd-tag> analysis of <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="protein" role="component" text="mTOR" ext_ids="I3M6B0" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MTOR" ext_tax_ids="43179" ext_tax_names="Ictidomys tridecemlineatus" ext_urls="https://www.uniprot.org/uniprot/">mTOR</sd-tag> downstream targets shows significant upregulation of P−P70 and <span>P−<sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="protein" role="assayed" text="4E−BP1" ext_ids="I3M8K7" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="EIF4EBP1" ext_tax_ids="43179" ext_tax_names="Ictidomys tridecemlineatus" ext_urls="https://www.uniprot.org/uniprot/">4E−BP1</sd-tag></span> during hibernation.<graphic href="https://api.sourcedata.io/file.php?panel_id=2367"/></sd-panel></fig><fig id="1147"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1147"/><sd-panel panel_id="2368"><b>A.</b> <sd-tag id="sdTag36" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analyses and densitometry of <sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="tissue" role="component" text="quadriceps" ext_ids="UBERON:0004498///UBERON:0001377" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of quadriceps femoris///quadriceps femoris" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">quadriceps</sd-tag> <span>muscles from non−hibernating and hibernating <sd-tag id="sdTag191" source="sdapi" category="entity" entity_type="organism" role="experiment" text="squirrels" ext_ids="43179" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Ictidomys tridecemlineatus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">squirrels</sd-tag> demonstrates significant increases in total</span> <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SGK1" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SGK1</sd-tag> and phosphorylated <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SGK1" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SGK1</sd-tag>. <sd-tag id="sdTag39" source="sdapi" category="assay" entity_type="" role="" text="Immunostaining" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunostaining</sd-tag> of <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="tissue" role="component" text="quadriceps" ext_ids="UBERON:0004498///UBERON:0001377" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of quadriceps femoris///quadriceps femoris" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">quadriceps</sd-tag> muscle for total <sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SGK1" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SGK1</sd-tag> shows upregulation during hibernation.<graphic href="https://api.sourcedata.io/file.php?panel_id=2368"/></sd-panel><sd-panel panel_id="2369"><b>B.</b> Levels of phosphorylated <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Foxo3a" ext_ids="I3MXH6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FOXA3" ext_tax_ids="43179" ext_tax_names="Ictidomys tridecemlineatus" ext_urls="https://www.uniprot.org/uniprot/">Foxo3a</sd-tag> in S315 and T32 are significantly increased during hibernation. Densitometric analysis of P‐<sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Foxo3a" ext_ids="I3MXH6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FOXA3" ext_tax_ids="43179" ext_tax_names="Ictidomys tridecemlineatus" ext_urls="https://www.uniprot.org/uniprot/">Foxo3a</sd-tag> as a function of <sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Foxo3a" ext_ids="I3MXH6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="FOXA3" ext_tax_ids="43179" ext_tax_names="Ictidomys tridecemlineatus" ext_urls="https://www.uniprot.org/uniprot/">Foxo3a</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2369"/></sd-panel></fig><fig id="1148"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1148"/><sd-panel panel_id="2370"><b>A.</b><p>The morphology of <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="tibialis anterior" ext_ids="UBERON:0004499///UBERON:0001385" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior///tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">tibialis anterior</sd-tag> muscle as revealed by <sd-tag id="sdTag140" source="sdapi" category="assay" entity_type="" role="" text="haematoxylin–eosin staining" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">haematoxylin-eosin staining</sd-tag> shows increased variation in <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="muscle fiber" ext_ids="CL:0000187" norm_text="" ext_dbs="CL" in_caption="True" ext_names="muscle cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">muscle fiber</sd-tag> size with numerous atrophic <sd-pretag id="sdPretag14611648103840" parent-tag-id="209">muscle <sd-pretag id="sdPretag14611647717720" parent-tag-id="210">fibers</sd-pretag></sd-pretag> (scale bar 90 µm).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2370"/></sd-panel><sd-panel panel_id="2371"><b>B.</b> Percentage distribution and mean minimum Feret's diameter in <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="tissue" role="component" text="tibialis anterior" ext_ids="UBERON:0004499///UBERON:0001385" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior///tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">tibialis anterior</sd-tag> muscle (<i>p</i> = 0.02).<graphic href="https://api.sourcedata.io/file.php?panel_id=2371"/></sd-panel><sd-panel panel_id="2372"><b>C.</b> Increased levels of phosphorylated <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Akt" ext_ids="Q9WUA6///Q60823///P31750" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Akt3///Akt2///Akt1" ext_tax_ids="10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Akt</sd-tag> (S478) in skeletal muscles of <i><sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sgk1" ext_ids="20393" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sgk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sgk1</sd-tag></i><sup><i>−</i>/<i>−</i></sup> <sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2372"/></sd-panel><sd-panel panel_id="2373"><b>D.</b> <i><sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sgk1" ext_ids="20393" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sgk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sgk1</sd-tag></i><sup><i>−</i>/<i>−</i></sup> <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> <span>exhibit decreased running distance after 36 days of exposure to a <sd-tag id="sdTag170" source="sdapi" category="assay" entity_type="" role="" text="running wheel" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">running wheel</sd-tag>, (</span><i>p</i> = 0.01; <i>n</i> = 6 animals per group).<graphic href="https://api.sourcedata.io/file.php?panel_id=2373"/></sd-panel><sd-panel panel_id="2374"><b>E.</b> Isometric force from <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="soleus muscles" ext_ids="UBERON:0001389" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="soleus muscle" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">soleus muscles</sd-tag> of WT and <i><sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sgk1" ext_ids="20393" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sgk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sgk1</sd-tag></i><sup><i>-</i>/<i>-</i></sup> <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> during repetitive electrical stimulations <span>for 500 ms. Amplitudes of <sd-tag id="sdTag201" source="sdapi" category="physical" entity_type="" role="" text="isometric force" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">isometric force</sd-tag> from</span> <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="soleus muscles" ext_ids="UBERON:0001389" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="soleus muscle" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">soleus muscles</sd-tag> at two stimulation frequencies. Specific force is plotted in all cases. Mean values ± SD from <i>n</i> = 9 (<i><sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sgk1" ext_ids="20393" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sgk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sgk1</sd-tag></i><sup><i>−</i>/<i>−</i></sup>) and <i>n</i> = 10 (WT) independent animals (<i>p</i> = 0.01).<graphic href="https://api.sourcedata.io/file.php?panel_id=2374"/></sd-panel></fig><fig id="1149"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1149"/><sd-panel panel_id="2375"><b>A.</b> <sd-tag id="sdTag78" source="sdapi" category="assay" entity_type="" role="" text="H&amp;E" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">H&amp;amp;amp;E</sd-tag> staining of <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="tibialis anterior" ext_ids="UBERON:0004499///UBERON:0001385" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior///tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">tibialis anterior</sd-tag> sections from 2‐month old control and transgenic <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> shows no differences (scale bar 90 µm).<graphic href="https://api.sourcedata.io/file.php?panel_id=2375"/></sd-panel><sd-panel panel_id="2376"><b>B.</b> Morphometric analyses of minimum Feret's diameter of <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA muscle" ext_ids="UBERON:0004499" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA muscle</sd-tag> reveal no changes in <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fiber" ext_ids="CL:0000187" norm_text="" ext_dbs="CL" in_caption="True" ext_names="muscle cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fiber</sd-tag> size distribution or mean <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fiber" ext_ids="CL:0000187" norm_text="" ext_dbs="CL" in_caption="True" ext_names="muscle cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fiber</sd-tag> size.<graphic href="https://api.sourcedata.io/file.php?panel_id=2376"/></sd-panel><sd-panel panel_id="2377"><b>C.</b> <sd-tag id="sdTag84" source="sdapi" category="assay" entity_type="" role="" text="Western blots" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blots</sd-tag> and densitometric analysis of muscle from transgenic and control <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>. Downstream targets of the <sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="protein" role="component" text="mTOR" ext_ids="Q9JLN9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Mtor" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">mTOR</sd-tag> <span>signalling cascade (p<sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="protein" role="assayed" text="70S6K" ext_ids="Q8BSK8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rps6kb1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">70S6K</sd-tag> and</span> <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="protein" role="assayed" text="4EBP1" ext_ids="Q60876" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Eif4ebp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">4EBP1</sd-tag>) demonstrate significant upregulation of their phosphorylated forms in <i><sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sgk1" ext_ids="20393" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sgk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sgk1</sd-tag></i><sup><i>tg</i></sup> <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2377"/></sd-panel><sd-panel panel_id="2378"><b>D.</b> <sd-tag id="sdTag93" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analyses and densitometry of phosphorylated <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FOXO3a" ext_ids="Q9WVH4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FOXO3a</sd-tag> and total <sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FOXO3a" ext_ids="Q9WVH4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FOXO3a</sd-tag> of <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="tissue" role="component" text="tibialis anterior" ext_ids="UBERON:0004499///UBERON:0001385" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior///tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">tibialis anterior</sd-tag> muscles from control and transgenic <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> (<i>n</i> = 4) show an increase of phosphorylation at S315 and T32.<graphic href="https://api.sourcedata.io/file.php?panel_id=2378"/></sd-panel></fig><fig id="1150"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1150"/><sd-panel panel_id="2379"><b>A.</b> <sd-tag id="sdTag104" source="sdapi" category="assay" entity_type="" role="" text="H&amp;E" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">H&amp;amp;amp;E</sd-tag> staining of <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="tibialis anterior" ext_ids="UBERON:0004499///UBERON:0001385" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior///tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">tibialis anterior</sd-tag> sections reveals no changes in muscle architecture (scale bar 90 µm).<graphic href="https://api.sourcedata.io/file.php?panel_id=2379"/></sd-panel><sd-panel panel_id="2380"><b>B.</b> Morphometric analysis demonstrates a decrease in <span><sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="muscle fiber" ext_ids="CL:0000187" norm_text="" ext_dbs="CL" in_caption="True" ext_names="muscle cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">muscle fiber</sd-tag></span> size of the wild−type control <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> compared with <i><sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sgk1" ext_ids="20393" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sgk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sgk1</sd-tag></i><sup><i>tg</i></sup> transgenic littermates (<i>p</i> = 0.0015).<graphic href="https://api.sourcedata.io/file.php?panel_id=2380"/></sd-panel><sd-panel panel_id="2381"><b>C.</b> <sd-tag id="sdTag161" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> and densitometry analysis shows that levels of phosphorylated <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Foxo3a" ext_ids="Q9WVH4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Foxo3a</sd-tag> at S315 and T32 are increased in <i><sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sgk1" ext_ids="20393" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sgk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sgk1</sd-tag></i><sup><i>tg</i></sup>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2381"/></sd-panel></fig><fig id="1151"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1151"/><sd-panel panel_id="2382"><b>A.</b> Transfection of constitutively active <i><sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Sgk1" ext_ids="20393" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sgk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Sgk1</sd-tag></i> (CA) into immobilized <sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="tissue" role="component" text="tibialis anterior" ext_ids="UBERON:0004499///UBERON:0001385" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior///tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">tibialis anterior</sd-tag> muscle (green) reveals increased <sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fiber" ext_ids="CL:0000187" norm_text="" ext_dbs="CL" in_caption="True" ext_names="muscle cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fiber</sd-tag> size diameter when compared to control, <span><sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="protein" role="reporter" text="EGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EGFP</sd-tag></span> <span>only transfected <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="muscle fibers" ext_ids="CL:0000187" norm_text="" ext_dbs="CL" in_caption="True" ext_names="muscle cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">muscle <sd-pretag id="sdPretag14611648361140" parent-tag-id="210">fibers</sd-pretag></sd-tag> of immobilized</span> <sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="tissue" role="component" text="tibialis anterior" ext_ids="UBERON:0004499///UBERON:0001385" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior///tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">tibialis anterior</sd-tag> muscles (100 µm). <sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Laminin γ−1" ext_ids="P02468" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamc1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Laminin γ−1</sd-tag> <span>staining (red) outlines the <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="subcellular" role="component" text="basement membrane" ext_ids="GO:0005604" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="basement membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">basement membrane</sd-tag> and blue staining marks <sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nuclei</sd-tag> (</span><sd-tag id="sdTag124" source="sdapi" category="assay" entity_type="" role="" text="DAPI" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAPI</sd-tag>).<graphic href="https://api.sourcedata.io/file.php?panel_id=2382"/></sd-panel><sd-panel panel_id="2383"><b>B.</b> Representation of the minimum Feret's diameter average ± SD (control and immobilized; <i>n</i> <span>= 9-10 per group; 800-950 <sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="fibers" ext_ids="CL:0000187" norm_text="" ext_dbs="CL" in_caption="True" ext_names="muscle cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">fibers</sd-tag> were measured) (*</span><i>p</i> = 0.029, *<i>p</i> = 0.034, *<i>p</i> = 0.047, <i>p</i> = 0.43, respectively).<graphic href="https://api.sourcedata.io/file.php?panel_id=2383"/></sd-panel><sd-panel panel_id="2384"><b>C.</b> Percentage distribution of the minimum Feret's diameter of <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="tissue" role="component" text="tibialis anterior" ext_ids="UBERON:0004499///UBERON:0001385" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior///tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">tibialis anterior</sd-tag> <span>muscle immobilized and transfected with eGFP (<sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>), wild−type</span> <i><sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Sgk1" ext_ids="20393" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sgk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Sgk1</sd-tag></i> (WT), kinase dead <i><sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Sgk1" ext_ids="20393" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sgk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Sgk1</sd-tag></i> (KD) and constitutively active <i><sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Sgk1" ext_ids="20393" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sgk1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Sgk1</sd-tag></i> (CA) compared to non−immobilized control <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA muscle" ext_ids="UBERON:0004499" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA muscle</sd-tag> (black dotted line).<graphic href="https://api.sourcedata.io/file.php?panel_id=2384"/></sd-panel></fig></article>

token_classification/10-1002_emmm-201302771.xml

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+<?xml version='1.0' encoding='UTF-8'?>
+<article doi="10.1002/emmm.201302771" abstract="Tyrosine kinase inhibitors (TKIs) are effective therapies for leukaemia. Alzheimer is a neurodegenerative disease characterized by accumulation of β-amyloid (plaques) and hyper-phosphorylated Tau (tangles). Here we show that AD animals have high levels of insoluble parkin and decreased parkin-Beclin-1 interaction, while peripheral administration of TKIs, including Nilotinib and Bosutinib, increases soluble parkin leading to amyloid clearance and cognitive improvement. Blocking Beclin-1 expression with shRNA or parkin deletion prevents tyrosine kinase (TK) inhibition-induced amyloid clearance, suggesting that functional parkin-Beclin-1 interaction mediates amyloid degradation. Isolation of autophagic vacuoles (AVs) in AD mouse brain shows accumulation of parkin and amyloid, consistent with previous results in AD brains, while Bosutinib and Nilotinib increase parkin-Beclin-1 interaction and result in protein deposition in the lysosome. These data suggest that decreased parkin solubility impedes parkin-Beclin-1 interaction and amyloid clearance. We identified two FDA-approved anti-cancer drugs as potential treatment for AD."><fig id="181"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=181"/><sd-panel panel_id="16020"><p>Graph represents <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> levels of TKIs over a 24 hr period after IP injection with <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Imatinib" ext_ids="CHEBI:38918" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Imatinib</sd-tag>, <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Nilotinib" ext_ids="CHEBI:52172" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nilotinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Nilotinib</sd-tag>, <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> and <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:4612" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> (N = 7). [Correction added after publication on 4 July 2013: The y axis of the graph shown in Fig. 1A has been corrected from "concentration (mM)" to "concentration (nM)"]</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16020"/></sd-panel><sd-panel panel_id="16021"><p><sd-tag id="sdTag100" source="sdapi" category="assay" entity_type="" role="" text="WB" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">WB</sd-tag> in Tg-<sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="gene" role="component" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag> total <sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> lysates on 4-12% <sd-tag id="sdTag334" source="sdapi" category="assay" entity_type="" role="" text="NuPAGE SDS gel" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NuPAGE SDS gel</sd-tag> (Invitrogen) show total <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Abl" ext_ids="Q4JIM5///P00520" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Abl2///Abl1" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Abl</sd-tag> (top blot) T412 <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Abl" ext_ids="Q4JIM5///P00520" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Abl2///Abl1" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Abl</sd-tag> (2<sup>nd</sup> blot), soluble <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="protein" role="assayed" text="parkin" ext_ids="Q9WVS6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">parkin</sd-tag> level (3<sup>rd</sup> blot), and <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (4<sup>th</sup> blot) relative to <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="MAP-2" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MAP-2</sd-tag> (N = 9).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16021"/></sd-panel><sd-panel panel_id="16022"><p>Quantitative <sd-tag id="sdTag112" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag> showing soluble (STEN extract) and insoluble (4 M urea extract) <sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag><sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="protein" role="assayed" text="parkin" ext_ids="Q9WVS6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">parkin</sd-tag> in Tg-<sd-tag id="sdTag115" source="sdapi" category="entity" entity_type="gene" role="intervention" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag> (N = 9). <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="gene" role="component" text="Parkin" ext_ids="50873" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Parkin</sd-tag><sup>−/−</sup><sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="tissue" role="component" text="brains" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brains</sd-tag> were used as a specificity control.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16022"/></sd-panel><sd-panel panel_id="16023"><p>(D) <sd-tag id="sdTag123" source="sdapi" category="assay" entity_type="" role="" text="Blots" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Blots</sd-tag> represent <sd-tag id="sdTag122" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag><sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Beclin-1" ext_ids="O88597" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Becn1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Beclin-1</sd-tag> in <sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> probed with <sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="protein" role="assayed" text="parkin" ext_ids="Q9WVS6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">parkin</sd-tag> antibody</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16023"/></sd-panel><sd-panel panel_id="16024"><p>(D) <sd-tag id="sdTag132" source="sdapi" category="assay" entity_type="" role="" text="Blots" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Blots</sd-tag> represent <sd-tag id="sdTag133" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag><sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Beclin-1" ext_ids="O88597" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Becn1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Beclin-1</sd-tag> in <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> probed with <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="protein" role="assayed" text="parkin" ext_ids="Q9WVS6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">parkin</sd-tag> antibody, and (E) control <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="subcellular" role="component" text="IgG" ext_ids="GO:0071735" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="IgG immunoglobulin complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">IgG</sd-tag> in parallel with immunoprecipitates.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16024"/></sd-panel><sd-panel panel_id="16025"><p>(F) <sd-tag id="sdTag141" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag><sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Beclin-1" ext_ids="Q14457" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Beclin-1</sd-tag> probed with <sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="protein" role="assayed" text="parkin" ext_ids="O60260" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PARK2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">parkin</sd-tag> and the reverse experiment in post-mortem <sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="organism" role="experiment" text="human" ext_ids="9606" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Homo sapiens" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">human</sd-tag> AD <sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="tissue" role="component" text="cortex" ext_ids="UBERON:0002129" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebellar cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> analyzed on 4-12% <sd-tag id="sdTag335" source="sdapi" category="assay" entity_type="" role="" text="SDS-NuPAGE gel" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-NuPAGE gel</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16025"/></sd-panel><sd-panel panel_id="16027"><p>In situ <sd-tag id="sdTag148" source="sdapi" category="assay" entity_type="" role="" text="proximity ligation assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">proximity ligation assay</sd-tag> (<sd-tag id="sdTag151" source="sdapi" category="assay" entity_type="" role="" text="PLA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">PLA</sd-tag>) shows endogenous <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="protein" role="assayed" text="parkin" ext_ids="Q9WVS6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">parkin</sd-tag>-<sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Beclin-1" ext_ids="O88597" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Becn1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Beclin-1</sd-tag> complexes in (G) WT <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="organism" role="component" text="C57BL/6" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">C57BL/6</sd-tag><sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> (N = 5) and (H) <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="gene" role="component" text="parkin" ext_ids="50873" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">parkin</sd-tag><sup>−/−</sup> as control.</p><p><sd-tag id="sdTag150" source="sdapi" category="assay" entity_type="" role="" text="PLA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">PLA</sd-tag> in Tg-<sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="gene" role="intervention" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag><sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> IP injected once daily for 3 weeks with (I) <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:4612" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> (J) 5 mg/kg <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> and (K) 10 mg/kg <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Nilotinib" ext_ids="CHEBI:52172" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nilotinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Nilotinib</sd-tag> (N = 5).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16027"/></sd-panel><sd-panel panel_id="16028"><p><sd-tag id="sdTag168" source="sdapi" category="assay" entity_type="" role="" text="PLA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">PLA</sd-tag> in <sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="organism" role="component" text="human" ext_ids="9606" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Homo sapiens" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">human</sd-tag> post-mortem <sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="tissue" role="component" text="brains" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brains</sd-tag> in the (L) <sd-tag id="sdTag171" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cortex" ext_ids="UBERON:0002129" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebellar cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> of a normal subject and (M) <sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cortex" ext_ids="UBERON:0002129" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebellar cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> of an AD <sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="organism" role="experiment" text="patient" ext_ids="9606" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Homo sapiens" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">patient</sd-tag>; the <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="hippocampus" ext_ids="UBERON:0002421" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="hippocampal formation" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">hippocampus</sd-tag> of (N) a normal subject and (O) an AD <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="organism" role="experiment" text="patient" ext_ids="9606" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Homo sapiens" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">patient</sd-tag>; the <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="caudate" ext_ids="UBERON:0001873" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="caudate nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">caudate</sd-tag> of (P) a normal subject and (Q) an AD <sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="organism" role="experiment" text="patient" ext_ids="9606" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Homo sapiens" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">patient</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16028"/></sd-panel><sd-panel panel_id="16029">Graph represents <sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="organism" role="component" text="human" ext_ids="9606" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Homo sapiens" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">human</sd-tag> <span><sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag></span><sub>1-42</sub><sd-tag id="sdTag186" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag> <span>in rat <sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="cell_line" role="component" text="B35" ext_ids="CVCL_1951" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="B35" ext_tax_ids="10116" ext_tax_names="Rattus norvegicus" ext_urls="https://identifiers.org/cellosaurus:">B35</sd-tag> neuroblastoma cells transfected with</span> <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="organism" role="component" text="human" ext_ids="9606" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Homo sapiens" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">human</sd-tag> <span>cDNA <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Aβ" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Aβ</sd-tag></span><sub>1-42</sub> (or LacZ) or <span><sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Beclin-1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Beclin-1</sd-tag></span> shRNA for 24 hr, and then treated with 1 μM <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> for an additional 24 hr (N = 12). *Significantly different to control or as indicated, Mean ± SEM, ANOVA with NeumannKeuls multiple comparison.<graphic href="https://api.sourcedata.io/file.php?panel_id=16029"/></sd-panel></fig><fig id="182"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=182"/><sd-panel panel_id="896"><p>Staining of 20 μm <sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> sections shows <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="plaque" ext_ids="GO:0097418" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="neurofibrillary tangle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plaque</sd-tag> formation with <sd-tag id="sdTag192" source="sdapi" category="assay" entity_type="" role="" text="6E10" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">6E10</sd-tag> antibody and <sd-tag id="sdTag193" source="sdapi" category="assay" entity_type="" role="" text="DAB" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAB</sd-tag> in the <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> in different (A,B) Tg-<sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="gene" role="component" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag> + <sd-tag id="sdTag189" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:4612" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> and (C) <sd-tag id="sdTag190" source="sdapi" category="assay" entity_type="" role="" text="thioflavin-S" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">thioflavin-S</sd-tag> staining in Tg-<sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="gene" role="component" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag> treated with <sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:4612" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> (N = 7). (D,E) Tg-<sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="gene" role="component" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag> treated with 5 mg/kg <sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> for 3-weeks and (F) <sd-tag id="sdTag191" source="sdapi" category="assay" entity_type="" role="" text="thioflavin-s" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">thioflavin-s</sd-tag> staining.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=896"/></sd-panel><sd-panel panel_id="16030"><p>Staining of 20 μm thick <sd-tag id="sdTag204" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> sections shows (G) <sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="protein" role="assayed" text="parkin" ext_ids="Q9WVS6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">parkin</sd-tag>, (H) <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> and (I) merged figure in <sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cortex" ext_ids="UBERON:0002129" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebellar cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> of Tg-<sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="gene" role="component" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag><sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> after 3 weeks of <sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:4612" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> treatment, and (J) <sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="protein" role="assayed" text="parkin" ext_ids="Q9WVS6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">parkin</sd-tag>, (K) <sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> and (L) merged figure in <sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cortex" ext_ids="UBERON:0002129" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebellar cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> of Tg-<sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="gene" role="component" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag><sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> after 3 weeks of 5 mg/kg <sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> treatment. (M) <sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Parkin" ext_ids="Q9WVS6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Parkin</sd-tag>, (N) <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> and (O) merged figure in <sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="hippocampus" ext_ids="UBERON:0002421" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="hippocampal formation" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">hippocampus</sd-tag> of Tg-<sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="gene" role="component" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag><sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> after 3 weeks of <sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:4612" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> treatment, and (P) <sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="protein" role="assayed" text="parkin" ext_ids="Q9WVS6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">parkin</sd-tag>, (Q) <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> and (R) merged figure in <sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cortex" ext_ids="UBERON:0002129" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebellar cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> of Tg-<sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="gene" role="component" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag><sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> after 3 weeks of <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> treatment (N = 7).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16030"/></sd-panel><sd-panel panel_id="16032"><span>(S) Graphs represent quantification of <sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="protein" role="assayed" text="amyloid" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">amyloid</sd-tag><sd-tag id="sdTag232" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="plaques" ext_ids="GO:0097418" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="neurofibrillary tangle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plaques</sd-tag> in Tg-</span><sd-tag id="sdTag233" source="sdapi" category="entity" entity_type="gene" role="component" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag> with and without <sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=16032"/></sd-panel><sd-panel panel_id="16033"><sd-tag id="sdTag241" source="sdapi" category="assay" entity_type="" role="" text="WB" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">WB</sd-tag> in Tg-<sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="gene" role="intervention" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag> total <sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> <span>lysates on 4-12% <sd-tag id="sdTag336" source="sdapi" category="assay" entity_type="" role="" text="NuPAGE SDS gel" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NuPAGE SDS gel</sd-tag> (Invitrogen) showing (T) levels of <sd-tag id="sdTag238" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BACE1" ext_ids="P56818" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Bace1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">BACE1</sd-tag> (1</span><sup>st</sup> <span>blot), <sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ADAM-10" ext_ids="O35598" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Adam10" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ADAM-10</sd-tag> (2</span><sup>nd</sup> <span>blot) and <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="protein" role="assayed" text="presinilin-1" ext_ids="P49769" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Psen1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">presinilin-1</sd-tag> (3</span><sup>rd</sup> blot) relative to <sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag><graphic href="https://api.sourcedata.io/file.php?panel_id=16033"/></sd-panel><sd-panel panel_id="16034"><sd-tag id="sdTag250" source="sdapi" category="assay" entity_type="" role="" text="WB" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">WB</sd-tag> in Tg-<sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="gene" role="component" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag> total <sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> <span>lysates on 4-12% <sd-tag id="sdTag337" source="sdapi" category="assay" entity_type="" role="" text="NuPAGE SDS gel" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NuPAGE SDS gel</sd-tag> (Invitrogen) showing (U) total</span> <sd-tag id="sdTag253" source="sdapi" category="entity" entity_type="protein" role="assayed" text="APP" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">APP</sd-tag> (top blot), CTFs (2<sup>nd</sup> blot) and phospho-tyrosine (3<sup>rd</sup> blot) relative to <sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> (N = 9).<graphic href="https://api.sourcedata.io/file.php?panel_id=16034"/></sd-panel></fig><fig id="183"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=183"/><sd-panel panel_id="16048"><p>Graphs represent <sd-tag id="sdTag259" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag> of human <sd-tag id="sdTag260" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> in (A) <sd-tag id="sdTag261" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> levels and (B) <sd-tag id="sdTag258" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="blood" ext_ids="UBERON:0000178" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="blood" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">blood</sd-tag><sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> levels in 8-month old Tg-<sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="gene" role="intervention" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag><sd-tag id="sdTag263" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> injected I.P. every other day for 6 weeks with <sd-tag id="sdTag264" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> or <sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Nilotinib" ext_ids="CHEBI:52172" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nilotinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Nilotinib</sd-tag> (N = 10).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16048"/></sd-panel><sd-panel panel_id="16049"><p><sd-tag id="sdTag267" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag> of human soluble and insoluble <sd-tag id="sdTag269" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> (C) <sd-tag id="sdTag270" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> and (D) <sd-tag id="sdTag271" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-40</sub> levels in 8-month old Tg-<sd-tag id="sdTag272" source="sdapi" category="entity" entity_type="gene" role="intervention" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag><sd-tag id="sdTag273" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> injected IP daily for 3 weeks with 5 mg/kg <sd-tag id="sdTag274" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> (N = 9).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16049"/></sd-panel><sd-panel panel_id="16040"><sd-tag id="sdTag276" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag> of (E) <sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag> <span>p-<sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Tau" ext_ids="P10637" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Mapt" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Tau</sd-tag> levels in 8-month old Tg-</span><sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="gene" role="intervention" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag> <sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> injected IP daily for 3 weeks with 5 mg/kg <sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> (N = 9).<graphic href="https://api.sourcedata.io/file.php?panel_id=16040"/></sd-panel><sd-panel panel_id="16041"><sd-tag id="sdTag283" source="sdapi" category="assay" entity_type="" role="" text="WB" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">WB</sd-tag> in Tg-<sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="gene" role="component" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag> total <sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> <span>lysates on 4-12% <sd-tag id="sdTag338" source="sdapi" category="assay" entity_type="" role="" text="NuPAGE SDS gel" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NuPAGE SDS gel</sd-tag> (Invitrogen) show total</span> <sd-tag id="sdTag286" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Tau" ext_ids="P10637" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Mapt" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Tau</sd-tag> (1<sup>st</sup> blot), serine 396 p-<sd-tag id="sdTag287" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Tau" ext_ids="P10637" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Mapt" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Tau</sd-tag> (2<sup>nd</sup> blot), threonine 231 (AT180, 3<sup>rd</sup> blot) and serine 199 p-<sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Tau" ext_ids="P10637" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Mapt" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Tau</sd-tag> (AT8, 4<sup>th</sup> blot) relative to <sd-tag id="sdTag289" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> (N = 7).<graphic href="https://api.sourcedata.io/file.php?panel_id=16041"/></sd-panel></fig><fig id="184"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=184"/><sd-panel panel_id="16042"><p>Staining of 20μm <sd-tag id="sdTag293" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> sections shows intracellular <sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> within the (A) <sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="hippocampus" ext_ids="UBERON:0002421" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="hippocampal formation" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">hippocampus</sd-tag> of <sd-tag id="sdTag296" source="sdapi" category="entity" entity_type="organism" role="component" text="lentiviral" ext_ids="11646" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Lentivirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">lentiviral</sd-tag><sd-tag id="sdTag297" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> injected WT <sd-tag id="sdTag298" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>, and (B) <sd-tag id="sdTag299" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> clearance of intracellular <sd-tag id="sdTag300" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub>. Staining of 20μm <sd-tag id="sdTag339" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> sections shows intracellular <sd-tag id="sdTag301" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> within the (C) <sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cortex" ext_ids="UBERON:0002129" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebellar cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> of WT <sd-tag id="sdTag303" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> with the <sd-tag id="sdTag304" source="sdapi" category="entity" entity_type="organism" role="component" text="lentiviral" ext_ids="11646" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Lentivirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">lentiviral</sd-tag><sd-tag id="sdTag305" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub>, and (D) <sd-tag id="sdTag306" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> clearance of intracellular <sd-tag id="sdTag307" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> (N = 7).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16042"/></sd-panel><sd-panel panel_id="16043"><sd-tag id="sdTag312" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag> of human soluble and insoluble <sd-tag id="sdTag313" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> at 6 weeks post-injection of <sd-tag id="sdTag314" source="sdapi" category="entity" entity_type="organism" role="component" text="lentiviral" ext_ids="11646" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Lentivirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">lentiviral</sd-tag><sd-tag id="sdTag315" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> and daily treatment with 5 mg/kg <sd-tag id="sdTag316" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> (N = 9) for 3 weeks. * Significantly different to control or as indicated, Mean ± SEM, ANOVA with Neumann Keuls multiple comparison.<graphic href="https://api.sourcedata.io/file.php?panel_id=16043"/></sd-panel><sd-panel panel_id="16044"><sd-tag id="sdTag321" source="sdapi" category="assay" entity_type="" role="" text="WB" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">WB</sd-tag> <span>on 4-12% <sd-tag id="sdTag333" source="sdapi" category="assay" entity_type="" role="" text="NuPAGE SDS gel" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NuPAGE SDS gel</sd-tag> of total</span> <sd-tag id="sdTag322" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> lysates in 1 year old wild type and <span><sd-tag id="sdTag320" source="sdapi" category="entity" entity_type="gene" role="intervention" text="parkin" ext_ids="50873" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">parkin</sd-tag></span><sup>−/−</sup><sd-tag id="sdTag323" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> treated with 5 mg/kg <sd-tag id="sdTag324" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> <span>for 3 weeks on 4-12% <sd-tag id="sdTag340" source="sdapi" category="assay" entity_type="" role="" text="NuPAGE SDS gel" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">NuPAGE SDS gel</sd-tag> (Invitrogen) showing</span> <sd-tag id="sdTag325" source="sdapi" category="entity" entity_type="protein" role="assayed" text="parkin" ext_ids="Q9WVS6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">parkin</sd-tag> (1<sup>st</sup> blot)total <sd-tag id="sdTag326" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Abl" ext_ids="P00520///Q4JIM5" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Abl1///Abl2" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Abl</sd-tag> (2<sup>nd</sup> blot), T412 <sd-tag id="sdTag327" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Abl" ext_ids="P00520///Q4JIM5" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Abl1///Abl2" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Abl</sd-tag> (3<sup>rd</sup> blot), <sd-tag id="sdTag328" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Beclin-1" ext_ids="O88597" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Becn1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Beclin-1</sd-tag> (4th blot) and <sd-tag id="sdTag329" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (5<sup>th</sup> blot) relative to <sd-tag id="sdTag330" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> (N = 7).<graphic href="https://api.sourcedata.io/file.php?panel_id=16044"/></sd-panel><sd-panel panel_id="16045"><p>Staining of 20μm <sd-tag id="sdTag344" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> sections shows <sd-tag id="sdTag345" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="plaque" ext_ids="GO:0097418" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="neurofibrillary tangle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plaque</sd-tag> formation with <sd-tag id="sdTag346" source="sdapi" category="assay" entity_type="" role="" text="6E10" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">6E10</sd-tag> antibody and <sd-tag id="sdTag347" source="sdapi" category="assay" entity_type="" role="" text="DAB" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAB</sd-tag> 6 weeks post-injection with (G) <sd-tag id="sdTag348" source="sdapi" category="entity" entity_type="organism" role="component" text="lentiviral" ext_ids="11646" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Lentivirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">lentiviral</sd-tag><sd-tag id="sdTag349" source="sdapi" category="entity" entity_type="protein" role="component" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> + 3 weeks <sd-tag id="sdTag350" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:4612" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> treatment and (H) IP injection with 5 mg/kg <sd-tag id="sdTag351" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> 3 weeks post-<sd-tag id="sdTag352" source="sdapi" category="entity" entity_type="organism" role="component" text="lentiviral" ext_ids="11646" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Lentivirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">lentiviral</sd-tag> expression (3 weeks treatment) clears <sd-tag id="sdTag353" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="plaques" ext_ids="GO:0097418" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="neurofibrillary tangle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plaques</sd-tag> in WT <sd-tag id="sdTag354" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> (N = 7).(I) Lentiviral <sd-tag id="sdTag355" source="sdapi" category="entity" entity_type="protein" role="component" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> + <sd-tag id="sdTag356" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:4612" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> and (J) IP injection with 5 mg/kg <sd-tag id="sdTag357" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> 3 weeks post-<sd-tag id="sdTag358" source="sdapi" category="entity" entity_type="organism" role="component" text="lentiviral" ext_ids="11646" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Lentivirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">lentiviral</sd-tag> expression (3 weeks treatment) in <sd-tag id="sdTag361" source="sdapi" category="entity" entity_type="gene" role="intervention" text="parkin" ext_ids="50873" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">parkin</sd-tag><sup>−/−</sup><sd-tag id="sdTag360" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> (N = 7).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16045"/></sd-panel></fig><fig id="185"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=185"/><sd-panel panel_id="16046"><p>Graphs represent <sd-tag id="sdTag367" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag> (N = 5) in <sd-tag id="sdTag365" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vacuoles</sd-tag> (<sd-tag id="sdTag387" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="AVs" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AVs</sd-tag>) in the <sd-tag id="sdTag368" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> of 4 and 8 months old Tg-<sd-tag id="sdTag369" source="sdapi" category="entity" entity_type="gene" role="component" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag><sd-tag id="sdTag370" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> treated with 10 mg/kg <sd-tag id="sdTag371" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Nilotinib" ext_ids="CHEBI:52172" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nilotinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Nilotinib</sd-tag> or 5 mg/kg <sd-tag id="sdTag372" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> (N = 5) for 3 weeks showing (A)human<sd-tag id="sdTag374" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> (Insert is <sd-tag id="sdTag375" source="sdapi" category="assay" entity_type="" role="" text="WB" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">WB</sd-tag> analysis of <sd-tag id="sdTag388" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="AVs" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AVs</sd-tag> showing <sd-tag id="sdTag381" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3-B" ext_ids="Q9CQV6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Map1lc3b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LC3-B</sd-tag> in AV10 and AV20 (1<sup>st</sup> blot) and <sd-tag id="sdTag382" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP2a" ext_ids="P17047" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP2a</sd-tag> in Lys (2<sup>nd</sup> blot) fraction) and (B)<sd-tag id="sdTag378" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-40</sub>,(C) p-<sd-tag id="sdTag379" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Tau" ext_ids="P10637" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Mapt" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Tau</sd-tag> and (D) <sd-tag id="sdTag380" source="sdapi" category="entity" entity_type="protein" role="assayed" text="parkin" ext_ids="Q9WVS6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">parkin</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16046"/></sd-panel><sd-panel panel_id="16047"><p><sd-tag id="sdTag391" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag> in <sd-tag id="sdTag392" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vacuoles</sd-tag> of 1 year old WT and <sd-tag id="sdTag399" source="sdapi" category="entity" entity_type="gene" role="intervention" text="parkin" ext_ids="50873" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">parkin</sd-tag><sup>−/−</sup><sd-tag id="sdTag394" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> (N = 5) injected with <sd-tag id="sdTag389" source="sdapi" category="entity" entity_type="organism" role="component" text="lentiviral" ext_ids="11646" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Lentivirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">lentiviral</sd-tag><sd-tag id="sdTag390" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> for 3 weeks and treated with 10 mg/kg <sd-tag id="sdTag395" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Nilotinib" ext_ids="CHEBI:52172" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nilotinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Nilotinib</sd-tag> and 5 mg/kg <sd-tag id="sdTag396" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> for 3 additional weeks showing (E) human<sd-tag id="sdTag397" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Aβ" ext_ids="P05067" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Aβ</sd-tag><sub>1-42</sub> and (F) p-<sd-tag id="sdTag398" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Tau" ext_ids="P10637" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Mapt" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Tau</sd-tag> levels.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16047"/></sd-panel></fig><fig id="186"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=186"/><sd-panel panel_id="16076"><p>(A) Represents results of <sd-tag id="sdTag404" source="sdapi" category="assay" entity_type="" role="" text="Morris water maze" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Morris water maze</sd-tag> test in <sd-tag id="sdTag405" source="sdapi" category="entity" entity_type="organism" role="component" text="lentiviral" ext_ids="11646" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Lentivirus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">lentiviral</sd-tag><sd-tag id="sdTag406" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Aβ" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Aβ</sd-tag><sub>1-42</sub>-injected ± <sd-tag id="sdTag407" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> WT (N = 12) and <sd-tag id="sdTag408" source="sdapi" category="entity" entity_type="gene" role="intervention" text="parkin" ext_ids="50873" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">parkin</sd-tag><sup>−/−</sup> (N = 10) <sd-tag id="sdTag409" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>, and (B) <sd-tag id="sdTag410" source="sdapi" category="assay" entity_type="" role="" text="heat maps" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">heat maps</sd-tag> for each group.</p><p>Graphs represent total number of entry into platform area and distance travelled.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16076"/></sd-panel><sd-panel panel_id="16077"><p>Represents results of <sd-tag id="sdTag412" source="sdapi" category="assay" entity_type="" role="" text="Morris water maze" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Morris water maze</sd-tag> test in Tg-<sd-tag id="sdTag413" source="sdapi" category="entity" entity_type="gene" role="intervention" text="APP" ext_ids="351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="APP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APP</sd-tag> ± <sd-tag id="sdTag414" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bosutinib" ext_ids="CHEBI:39112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bosutinib" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bosutinib</sd-tag> (N = 12) <sd-tag id="sdTag415" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>.</p><p>Graphs represent total number of entry into platform area and distance travelled.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=16077"/></sd-panel></fig></article>

token_classification/10-1002_emmm-201303356.xml

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+<?xml version='1.0' encoding='UTF-8'?>
+<article doi="10.1002/emmm.201303356" abstract="In addition to key roles in embryonic neurogenesis and myelinogenesis, γ-aminobutyric acid (GABA) serves as the primary inhibitory mammalian neurotransmitter. In yeast, we have identified a new role for GABA that augments activity of the pivotal kinase, Tor1. GABA inhibits the selective autophagy pathways, mitophagy and pexophagy, through Sch9, the homolog of the mammalian kinase, S6K1, leading to oxidative stress, all of which can be mitigated by the Tor1 inhibitor, rapamycin. To confirm these processes in mammals, we examined the succinic semialdehyde dehydrogenase (SSADH)-deficient mouse model that accumulates supraphysiological GABA in the central nervous system and other tissues. Mutant mice displayed increased mitochondrial numbers in the brain and liver, expected with a defect in mitophagy, and morphologically abnormal mitochondria. Administration of rapamycin to these mice reduced mTOR activity, reduced the elevated mitochondrial numbers, and normalized aberrant antioxidant levels. These results confirm a novel role for GABA in cell signaling and highlight potential pathomechanisms and treatments in various human pathologies, including SSADH deficiency, as well as other diseases characterized by elevated levels of GABA."><fig id="1152"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1152"/><sd-panel panel_id="2386"><div><b>A</b> <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Peroxisomes" ext_ids="GO:0005777" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="peroxisome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Peroxisomes</sd-tag> were induced by growing the WT strain expressing <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Pot1" ext_ids="P36002" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PTK1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Pot1</sd-tag>‐<sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> in <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="undefined" role="component" text="oleate medium" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">oleate medium</sd-tag> to mid‐log‐phase, then transferred to <sd-tag id="sdTag380" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD‐N" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD‐N</sd-tag> starvation medium with or without <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GABA" ext_ids="CHEBI:16865" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="gamma-aminobutyric acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GABA</sd-tag> to trigger pexophagy for 6 h. <sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> cleavage was analyzed at the indicated time points by <sd-tag id="sdTag7" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.</div><graphic href="https://api.sourcedata.io/file.php?panel_id=2386"/></sd-panel><sd-panel panel_id="2387"><b>B</b> <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Mitochondria</sd-tag> were induced by growing the WT strain expressing <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="protein" role="assayed" text="OM45" ext_ids="P16547" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="OM45" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">OM45</sd-tag>‐<sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> in <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="undefined" role="component" text="YPL medium" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YPL medium</sd-tag> to mid‐log‐phase and subsequently transferring cells to either <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD‐N" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD‐N</sd-tag> with or without <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GABA" ext_ids="CHEBI:16865" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="gamma-aminobutyric acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GABA</sd-tag> to trigger mitophagy for 12 h. <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> cleavage was analyzed at the indicated time points by <sd-tag id="sdTag13" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2387"/></sd-panel><sd-panel panel_id="2388"><b>C</b> Mitophagy was monitored by <sd-tag id="sdTag20" source="sdapi" category="assay" entity_type="" role="" text="fluorescence microscopy" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">fluorescence microscopy</sd-tag> using a WT strain expressing <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="protein" role="assayed" text="OM45" ext_ids="P16547" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="OM45" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">OM45</sd-tag>‐<sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> grown in <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="undefined" role="component" text="YPL medium" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YPL medium</sd-tag> for 12 h to mid‐log‐phase in the presence of <sd-tag id="sdTag26" source="sdapi" category="assay" entity_type="" role="" text="FM4‐64" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FM4‐64</sd-tag>, and transferred to either <sd-tag id="sdTag381" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD‐N" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD‐N</sd-tag> medium with or without <sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GABA" ext_ids="CHEBI:16865" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="gamma-aminobutyric acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GABA</sd-tag> for 24 h. Bar, 5 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=2388"/></sd-panel><sd-panel panel_id="2389"><b>D</b> The Cvt pathway was monitored using the WT strain in <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD medium" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD medium</sd-tag> with or without <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GABA" ext_ids="CHEBI:16865" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="gamma-aminobutyric acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GABA</sd-tag>, grown to mid‐log‐phase, after which samples were analyzed for <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Ape1" ext_ids="P14904" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APE1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Ape1</sd-tag> maturation.<graphic href="https://api.sourcedata.io/file.php?panel_id=2389"/></sd-panel><sd-panel panel_id="2390"><b>E</b> Ribophagy was monitored by growing the WT strain expressing <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Rpl25" ext_ids="P04456" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="RPL25" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Rpl25</sd-tag>‐<sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> in <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD medium" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD medium</sd-tag> to mid‐log‐phase and transferring cells to <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD‐N" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD‐N</sd-tag> either with or without <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GABA" ext_ids="CHEBI:16865" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="gamma-aminobutyric acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GABA</sd-tag> for 24 h.<graphic href="https://api.sourcedata.io/file.php?panel_id=2390"/></sd-panel><sd-panel panel_id="2391"><b>F</b> Autophagy was monitored by growing the WT strain expressing <sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Atg8</sd-tag> in <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD medium" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD medium</sd-tag> to mid‐log‐phase and transferring cells to <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD‐N" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD‐N</sd-tag> either with or without <sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GABA" ext_ids="CHEBI:16865" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="gamma-aminobutyric acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GABA</sd-tag> for 6 h.<graphic href="https://api.sourcedata.io/file.php?panel_id=2391"/></sd-panel></fig><fig id="1153"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1153"/><sd-panel panel_id="2392"><p><strong>A</strong><sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Peroxisomes" ext_ids="GO:0005777" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="peroxisome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Peroxisomes</sd-tag> were induced in <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="undefined" role="component" text="oleate medium" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">oleate medium</sd-tag> and pexophagy was monitored as described for Fig 1A.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=2392"/></sd-panel><sd-panel panel_id="2393"><b>B</b> Pexophagy was monitored by <sd-tag id="sdTag63" source="sdapi" category="assay" entity_type="" role="" text="fluorescence microscopy" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">fluorescence microscopy</sd-tag> using a WT strain expressing <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Pot1" ext_ids="P36002" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PTK1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Pot1</sd-tag>‐<sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> grown in <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="undefined" role="component" text="oleate medium" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">oleate medium</sd-tag> to mid‐log‐phase in the presence of <sd-tag id="sdTag67" source="sdapi" category="assay" entity_type="" role="" text="FM4‐64" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FM4‐64</sd-tag>, and transferred to either <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD‐N" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD‐N</sd-tag> medium with or without <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GABA" ext_ids="CHEBI:16865" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="gamma-aminobutyric acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GABA</sd-tag> or to <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD‐N" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD‐N</sd-tag> with <sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GABA" ext_ids="CHEBI:16865" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="gamma-aminobutyric acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GABA</sd-tag> and <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> for 6 h. Bar, 5 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=2393"/></sd-panel><sd-panel panel_id="2394"><b>C</b> <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Mitochondria</sd-tag> were induced in <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="undefined" role="component" text="YPL medium" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YPL medium</sd-tag> and mitophagy was assessed as described for Fig .<graphic href="https://api.sourcedata.io/file.php?panel_id=2394"/></sd-panel></fig><fig id="1154"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1154"/><sd-panel panel_id="2395"><b>A</b> WT cells expressing <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="protein" role="assayed" text="OM45" ext_ids="P16547" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="OM45" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">OM45</sd-tag>‐<sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>, along with the <i><sd-tag id="sdTag365" source="sdapi" category="entity" entity_type="gene" role="intervention" text="uga2" ext_ids="852291" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="UGA2" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">uga2</sd-tag>∆</i> strain over‐expressing the <i><sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GAD1" ext_ids="855291" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAD1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAD1</sd-tag></i> gene and expressing <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="assayed" text="OM45" ext_ids="P16547" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="OM45" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">OM45</sd-tag>‐<sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> were grown in <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="undefined" role="component" text="YPL medium" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YPL medium</sd-tag> to mid‐log‐phase. To monitor mitophagy, strains were transferred to SD‐N starvation medium (with or without <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag>).<graphic href="https://api.sourcedata.io/file.php?panel_id=2395"/></sd-panel><sd-panel panel_id="2396"><b>B</b> WT strain along with the <i><sd-tag id="sdTag366" source="sdapi" category="entity" entity_type="gene" role="intervention" text="uga2" ext_ids="852291" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="UGA2" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">uga2</sd-tag>∆</i> strain over‐expressing the <i><sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GAD1" ext_ids="855291" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAD1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAD1</sd-tag></i> gene was grown in <sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="undefined" role="component" text="oleate medium" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">oleate medium</sd-tag> and pexophagy was monitored as described in Fig , with or without <sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag>. Samples were taken at the indicated time points, and <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Pot1" ext_ids="P36002" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PTK1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Pot1</sd-tag> degradation was analyzed by <sd-tag id="sdTag123" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> (45 kD).<graphic href="https://api.sourcedata.io/file.php?panel_id=2396"/></sd-panel><sd-panel panel_id="2397"><b>C</b> To monitor autophagy, WT cells expressing <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Atg8</sd-tag> along with the <i><sd-tag id="sdTag368" source="sdapi" category="entity" entity_type="gene" role="intervention" text="uga2" ext_ids="852291" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="UGA2" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">uga2</sd-tag>∆</i> strain over‐expressing the <i><sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GAD1" ext_ids="855291" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAD1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAD1</sd-tag></i> gene and expressing <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Atg8</sd-tag> were grown in <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD medium" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD medium</sd-tag> and transferred to <sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD‐N" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD‐N</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2397"/></sd-panel></fig><fig id="1155"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1155"/><sd-panel panel_id="2398"><b>A,B</b> WT cells were cultured under pexophagy (A) or mitophagy (B) conditions with or without <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GABA" ext_ids="CHEBI:16865" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="gamma-aminobutyric acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GABA</sd-tag> and <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag>. <sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="protein" role="assayed" text="S6" ext_ids="P0CX37///P0CX38" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="RPS6A///RPS6B" ext_tax_ids="559292///559292" ext_tax_names="Saccharomyces cerevisiae S288C///Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">S6</sd-tag> phosphorylation at the indicated time points was analyzed by <sd-tag id="sdTag137" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> with a loading control.<graphic href="https://api.sourcedata.io/file.php?panel_id=2398"/></sd-panel><sd-panel panel_id="2399"><b>C</b> Samples were analyzed for <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Pot1" ext_ids="P36002" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PTK1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Pot1</sd-tag> degradation by <sd-tag id="sdTag141" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> (45 kD).<graphic href="https://api.sourcedata.io/file.php?panel_id=2399"/></sd-panel><sd-panel panel_id="2400"><b>D</b> <sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> production during mitophagy was analyzed by <sd-tag id="sdTag145" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2400"/></sd-panel></fig><fig id="1156"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1156"/><sd-panel panel_id="2402"><b>A</b> <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="protein" role="assayed" text="S6" ext_ids="P0CX37///P0CX38" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="RPS6A///RPS6B" ext_tax_ids="559292///559292" ext_tax_names="Saccharomyces cerevisiae S288C///Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">S6</sd-tag> phosphorylation after 6 h in <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="undefined" role="component" text="SD‐N" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SD‐N</sd-tag> was analyzed by <sd-tag id="sdTag151" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> with a loading control.<graphic href="https://api.sourcedata.io/file.php?panel_id=2402"/></sd-panel><sd-panel panel_id="2403"><b>B</b> <sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> production monitoring autophagy at the indicated time points was analyzed by <sd-tag id="sdTag158" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2403"/></sd-panel></fig><fig id="1157"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1157"/><sd-panel panel_id="2404"><b>A,B</b> WT, WT with <sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GABA" ext_ids="CHEBI:16865" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="gamma-aminobutyric acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GABA</sd-tag>, WT with <sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GABA" ext_ids="CHEBI:16865" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="gamma-aminobutyric acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GABA</sd-tag> and 10 mM <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GSH" ext_ids="CHEBI:16856" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="glutathione" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GSH</sd-tag> and WT with <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="GABA" ext_ids="CHEBI:16865" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="gamma-aminobutyric acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">GABA</sd-tag> and 200 nM <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> were tested for <sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="intracellular ROS" ext_ids="CHEBI:26523" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="reactive oxygen species" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">intracellular ROS</sd-tag> levels under (A) pexophagy and (B) mitophagy conditions. After 24 h incubation, cells were stained with <sd-tag id="sdTag338" source="sdapi" category="assay" entity_type="" role="" text="DHR−123" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DHR−123</sd-tag> and <sd-tag id="sdTag168" source="sdapi" category="assay" entity_type="" role="" text="propidium iodide" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">propidium iodide</sd-tag> for 1 h. Living cells were analyzed for <sd-tag id="sdTag169" source="sdapi" category="assay" entity_type="" role="" text="DHR−123" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DHR−123</sd-tag> fluorescence by <sd-tag id="sdTag170" source="sdapi" category="assay" entity_type="" role="" text="flow cytometry" ext_ids="BAO_0000005" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="flow cytometry" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">flow cytometry</sd-tag>. Data represent mean + s.d. (<i>n</i> = 3). *<i>P</i> <span>&lt; 0.005, **</span><i>P</i> <span>&lt; 0.01</span><graphic href="https://api.sourcedata.io/file.php?panel_id=2404"/></sd-panel><sd-panel panel_id="2405"><b>C,D</b> <sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Yeast" ext_ids="4932" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Saccharomyces cerevisiae" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Yeast</sd-tag> cells stained with 5 μM <sd-tag id="sdTag174" source="sdapi" category="assay" entity_type="" role="" text="propidium iodide" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">propidium iodide</sd-tag> were used to differentiate between living and dead cells under (C) pexophagy or (D) mitophagy conditions. Significant differences between the treatments and strains were determined using an unpaired two‐tailed t‐test. **<i>P</i> &lt; 0.01.<graphic href="https://api.sourcedata.io/file.php?panel_id=2405"/></sd-panel><sd-panel panel_id="2406"><b>E</b> Pexophagy assay was monitored by the degradation of <sd-tag id="sdTag178" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Pot1" ext_ids="P36002" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PTK1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Pot1</sd-tag>‐<sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> and analyzed for <sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> cleavage by <sd-tag id="sdTag181" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2406"/></sd-panel><sd-panel panel_id="2407"><b>F</b> Mitophagy assay was monitored by the degradation of <sd-tag id="sdTag189" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Om45" ext_ids="P16547" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="OM45" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Om45</sd-tag>‐<sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> and analyzed for <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> cleavage by <sd-tag id="sdTag188" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2407"/></sd-panel></fig><fig id="1158"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1158"/><sd-panel panel_id="2408"><b>A,B</b> Example images of <sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Parkin" ext_ids="5071" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PARK2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Parkin</sd-tag>‐expressing <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa cells" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa cells</sd-tag> analyzed using a tandem fluorochrome protein (mito‐<sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="protein" role="reporter" text="RFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RFP</sd-tag>‐<sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>) mitophagy assay under (A) control conditions or (B) displaying mitophagy depicted by the red mitochondrial structures localized to <sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag>. Bar, 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=2408"/></sd-panel><sd-panel panel_id="2409"><b>C</b> Percentage of cells displaying mitophagy + s.d., **<i>P</i> &lt; 0.01 using an unpaired two‐tailed t‐test, <i>n</i> &gt; 80.<graphic href="https://api.sourcedata.io/file.php?panel_id=2409"/></sd-panel></fig><fig id="1159"><title></title><label>Figure 8</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1159"/><sd-panel panel_id="2410"><div><b>A</b> <sd-tag id="sdTag210" source="sdapi" category="assay" entity_type="" role="" text="Electron microscopy" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Electron microscopy</sd-tag> images of <sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> from WT (<i>n</i> = 44) and <sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="protein" role="component" text="SSADH" ext_ids="Q8BWF0" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Aldh5a1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">SSADH</sd-tag>‐deficient <sd-tag id="sdTag300" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> (<i><sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Aldh5a1" ext_ids="214579" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Aldh5a1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Aldh5a1</sd-tag></i><sup><i>−/−</i></sup>) (<i>n</i> = 80) were calculated for area size.</div><graphic href="https://api.sourcedata.io/file.php?panel_id=2410"/></sd-panel><sd-panel panel_id="2411"><b>B</b> <sd-tag id="sdTag214" source="sdapi" category="assay" entity_type="" role="" text="Electron microscopy" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Electron microscopy</sd-tag> images showing typical sizes of WT and <i><sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Aldh5a1" ext_ids="214579" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Aldh5a1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Aldh5a1</sd-tag></i><sup><i>−/−</i></sup> <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="tissue" role="component" text="liver" ext_ids="UBERON:0002107" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="liver" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">liver</sd-tag> <sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>. Bar, 0.5 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=2411"/></sd-panel><sd-panel panel_id="2412"><b>C</b> Quantification of <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>l numbers from <sd-tag id="sdTag223" source="sdapi" category="assay" entity_type="" role="" text="electron microscopy" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">electron microscopy</sd-tag> images of <sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="tissue" role="component" text="liver" ext_ids="UBERON:0002107" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="liver" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">liver</sd-tag> from WT (<i>n</i> = 31) and <i><sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Aldh5a1" ext_ids="214579" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Aldh5a1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Aldh5a1</sd-tag></i><sup><i>−/−</i></sup> <sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> treated with vehicle (<i>n</i> = 39) or <sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (<i>n</i> = 34) (5 mg/kg body weight per day) via intraperitoneal injections for 3 successive days starting at day 7 of life.<graphic href="https://api.sourcedata.io/file.php?panel_id=2412"/></sd-panel><sd-panel panel_id="2413"><b>D</b> Quantification of <sd-tag id="sdTag230" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>l numbers from <sd-tag id="sdTag225" source="sdapi" category="assay" entity_type="" role="" text="electron microscopy" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">electron microscopy</sd-tag> images of <sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> from WT (<i>n</i> = 23) and <i><sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Aldh5a1" ext_ids="214579" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Aldh5a1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Aldh5a1</sd-tag></i><sup><i>−/−</i></sup> <sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> treated with vehicle (<i>n</i> = 30) or <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (<i>n</i> = 41) (5 mg/kg body weight per day) via intraperitoneal injections for 3 successive days starting at day 7 of life.<graphic href="https://api.sourcedata.io/file.php?panel_id=2413"/></sd-panel><sd-panel panel_id="2414"><b>E</b> <i><sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Aldh5a1" ext_ids="214579" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Aldh5a1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Aldh5a1</sd-tag></i><sup><i>−/−</i></sup> <sd-tag id="sdTag232" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> were treated with vehicle or <sd-tag id="sdTag233" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (10 mg/kg body weight per day) via intraperitoneal injections for 10 successive days starting at day 10 of life. WT <sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> served as non‐disease controls (set to 1). After sacrifice, <sd-tag id="sdTag235" source="sdapi" category="entity" entity_type="tissue" role="component" text="liver" ext_ids="UBERON:0002107" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="liver" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">liver</sd-tag> homogenates were used to measure <sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="SOD enzyme" ext_ids="GO:1902693" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="superoxide dismutase complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">SOD enzyme</sd-tag> activity using a <sd-tag id="sdTag316" source="sdapi" category="assay" entity_type="" role="" text="colorimetric SOD activity assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">colorimetric SOD activity assay</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2414"/></sd-panel><sd-panel panel_id="2415"><b>F</b> <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Mitochondria</sd-tag>l <sd-tag id="sdTag237" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SOD2" ext_ids="P09671" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sod2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">SOD2</sd-tag> protein levels were quantified from <sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="tissue" role="component" text="liver" ext_ids="UBERON:0002107" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="liver" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">liver</sd-tag> microsections using <sd-tag id="sdTag238" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence microscopy" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunofluorescence microscopy</sd-tag> and automated image analysis (WT set to 1).<graphic href="https://api.sourcedata.io/file.php?panel_id=2415"/></sd-panel><sd-panel panel_id="2416"><b>G</b> <sd-tag id="sdTag250" source="sdapi" category="assay" entity_type="" role="" text="Immunofluorescence images" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Immunofluorescence images</sd-tag> showing typical <sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="subcellular" role="component" text="nuclear" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nuclear</sd-tag> staining (<sd-tag id="sdTag252" source="sdapi" category="assay" entity_type="" role="" text="DAPI" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAPI</sd-tag>, blue) and <sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SOD2" ext_ids="P09671" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sod2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">SOD2</sd-tag> staining (red) from WT, <i><sd-tag id="sdTag245" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Aldh5a1" ext_ids="214579" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Aldh5a1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Aldh5a1</sd-tag></i><sup><i>−/−</i></sup> <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> treated with vehicle and <i><sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Aldh5a1" ext_ids="214579" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Aldh5a1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Aldh5a1</sd-tag></i><sup><i>−/−</i></sup> <sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> treated with <sd-tag id="sdTag249" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag>. Bar, 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=2416"/></sd-panel></fig><fig id="1160"><title></title><label>Figure 9</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1160"/><sd-panel panel_id="2417"><b>A</b> Quantification of <sd-tag id="sdTag253" source="sdapi" category="entity" entity_type="protein" role="assayed" text="S6" ext_ids="P62754" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rps6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">S6</sd-tag> phosphorylation of <sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="tissue" role="component" text="liver" ext_ids="UBERON:0002107" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="liver" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">liver</sd-tag> lysates from WT (<i>n</i> = 5) and <i><sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Aldh5a1" ext_ids="214579" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Aldh5a1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Aldh5a1</sd-tag></i><sup><i>−/−</i></sup> <sd-tag id="sdTag257" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> treated with vehicle (<i>n</i> = 4) or <sd-tag id="sdTag258" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (<i>n</i> = 5) after normalization (WT set to 1).<graphic href="https://api.sourcedata.io/file.php?panel_id=2417"/></sd-panel><sd-panel panel_id="2418"><b>B</b> <sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="protein" role="assayed" text="S6" ext_ids="P62754" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rps6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">S6</sd-tag> phosphorylation of <sd-tag id="sdTag261" source="sdapi" category="entity" entity_type="tissue" role="component" text="liver" ext_ids="UBERON:0002107" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="liver" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">liver</sd-tag> lysates analyzed by <sd-tag id="sdTag262" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2418"/></sd-panel><sd-panel panel_id="2419"><b>C</b> Quantification of <sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="protein" role="assayed" text="S6" ext_ids="P62754" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rps6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">S6</sd-tag> phosphorylation of <sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> lysates from WT (<i>n</i> = 2) and <i><sd-tag id="sdTag269" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Aldh5a1" ext_ids="214579" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Aldh5a1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Aldh5a1</sd-tag></i><sup><i>−/−</i></sup> <sd-tag id="sdTag270" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> treated with vehicle (<i>n</i> = 3) or <sd-tag id="sdTag271" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (<i>n</i> = 3) after normalization (WT set to 1).<graphic href="https://api.sourcedata.io/file.php?panel_id=2419"/></sd-panel><sd-panel panel_id="2420"><b>D</b> <sd-tag id="sdTag272" source="sdapi" category="entity" entity_type="protein" role="assayed" text="S6" ext_ids="P62754" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rps6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">S6</sd-tag> phosphorylation of <sd-tag id="sdTag274" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag> lysates analyzed by <sd-tag id="sdTag275" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=2420"/></sd-panel></fig></article>

token_classification/10-1016_j-celrep-2013-06-034.xml

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+<article doi="10.1016/j.celrep.2013.06.034" abstract="A key feature in Huntington disease (HD) is the accumulation of mutant Huntingtin (HTT) protein, which may be regulated by posttranslational modifications. Here, we define the primary sites of SUMO modification in the amino-terminal domain of HTT, show modification downstream of this domain, and demonstrate that HTT is modified by the stress-inducible SUMO-2. A systematic study of E3 SUMO ligases demonstrates that PIAS1 is an E3 SUMO ligase for both HTT SUMO-1 and SUMO-2 modification and that reduction of dPIAS in a mutant HTT Drosophila model is protective. SUMO-2 modification regulates accumulation of insoluble HTT in HeLa cells in a manner that mimics proteasome inhibition and can be modulated by overexpression and acute knockdown of PIAS1. Finally, the accumulation of SUMO-2-modified proteins in the insoluble fraction of HD postmortem striata implicates SUMO-2 modification in the age-related pathogenic accumulation of mutant HTT and other cellular proteins that occurs during HD progression."><fig id="4998"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4998"/><sd-panel panel_id="15219"><span>(B) <sd-tag id="sdTag1" source="sdapi" category="time" entity_type="" role="" text="Time course" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Time course</sd-tag> of <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> modification of <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="protein" role="reporter" text="His" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His</sd-tag>-tagged <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>ex1p (25Q)-purified proteins (WT, K6R, K9R, K6,9R, K6,9,15R, and S13,16D) was performed in vitro. SUMOylation was visualized using anti-<sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="protein" role="reporter" text="His" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His</sd-tag> antibody. WT <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>ex1p is SUMOylated within 16 min, K6R or K9R mutations delay SUMOylation, and combined mutations (K6,9R or K6,9,15R) greatly reduce SUMOylation. Mutations that mimic phosphorylation (S13,16D) alter kinetics of <sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> modification with SUMO modification observed beginning by 4 min.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15219"/></sd-panel></fig><fig id="4999"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4999"/><sd-panel panel_id="15220"><span>(A) <sd-tag id="sdTag10" source="sdapi" category="assay" entity_type="" role="" text="qRT-PCR" ext_ids="BAO_0002084" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="real-time PCR " ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">qRT-PCR</sd-tag> analysis of SUMO-modifying proteins and enzymes in <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cortex" ext_ids="UBERON:0000956" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebral cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> and <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="striata" ext_ids="UBERON:0002435" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="striatum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">striata</sd-tag> of WT <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> at 12 weeks. Relative expression for all the SUMO enzymes is normalized to <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag> <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="β-actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">β-actin</sd-tag>.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15220"/></sd-panel><sd-panel panel_id="15221"><p>(B and C) <sd-tag id="sdTag34" source="sdapi" category="assay" entity_type="" role="" text="qRT-PCR" ext_ids="BAO_0002084" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="real-time PCR " ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">qRT-PCR</sd-tag> of SUMO mRNAs from 12-week-old WT and <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="organism" role="experiment" text="R6/2" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">R6/2</sd-tag> <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="organism" role="experiment" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag> <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cortex" ext_ids="UBERON:0000956" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebral cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> (B) and <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="striatum" ext_ids="UBERON:0002435" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="striatum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">striatum</sd-tag> (C). SUMO enzyme mRNAs are differentially expressed in <sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="organism" role="experiment" text="R6/2" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">R6/2</sd-tag> versus control with statistically significant increases in <sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="gene" role="assayed" text="SENP1" ext_ids="223870" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Senp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP1</sd-tag> (p = 0.01), <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="gene" role="assayed" text="SENP3" ext_ids="80886" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Senp3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP3</sd-tag> (p = 0.02), and <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="gene" role="assayed" text="SUMO-1" ext_ids="22218" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sumo1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-1</sd-tag> (p = 0.003) in <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cortex" ext_ids="UBERON:0000956" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebral cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> and <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="gene" role="assayed" text="SENP1" ext_ids="223870" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Senp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP1</sd-tag> (p = 0.02), <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="gene" role="assayed" text="SENP6" ext_ids="215351" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Senp6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP6</sd-tag> (p = 0.04), <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="gene" role="assayed" text="PIAS3" ext_ids="229615" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Pias3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIAS3</sd-tag> (p = 0.007), <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="gene" role="assayed" text="SUMO-1" ext_ids="22218" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sumo1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-1</sd-tag> (p = 0.02), and <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="gene" role="assayed" text="SUMO-2" ext_ids="170930" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Sumo2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-2</sd-tag> (p = 0.02) in <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="striatum" ext_ids="UBERON:0002435" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="striatum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">striatum</sd-tag>. Samples were analyzed in quadruplicate and normalized to <sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="organism" role="experiment" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag> <sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="β-actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">β-actin</sd-tag>. Data are shown as <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="organism" role="experiment" text="R6/2" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">R6/2</sd-tag> expression relative to WT levels set at 1 for each enzyme with ± SD (n = 4). *p &lt; 0.05. n.s., not significant.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15221"/></sd-panel><sd-panel panel_id="15222"><p>(D and E) <sd-tag id="sdTag49" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis of <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-2" ext_ids="P61957" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sumo2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">SUMO-2</sd-tag> in 14-week <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="organism" role="experiment" text="R6/2" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">R6/2</sd-tag> <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cortex" ext_ids="UBERON:0000956" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebral cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> (D) and <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="striatum" ext_ids="UBERON:0002435" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="striatum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">striatum</sd-tag> (E) versus aged-matched controls. <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-2" ext_ids="P61957" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sumo2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">SUMO-2</sd-tag> is upregulated in <sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="organism" role="experiment" text="R6/2" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">R6/2</sd-tag> <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="striatum" ext_ids="UBERON:0002435" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="striatum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">striatum</sd-tag> versus control (p = 0.026; n = 4). Protein is normalized to <sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="α-tubulin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">α-tubulin</sd-tag> and quantitated using ImageJ.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15222"/></sd-panel></fig><fig id="5000"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5000"/><sd-panel panel_id="15223"><span>(A) <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells transfected with</span> <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="protein" role="reporter" text="His" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His</sd-tag><span>-tagged <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>ex1p (46Q) or 46QP-K6,9,15R (3R) along with <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-</span><span><sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SUMO-1" ext_ids="7341" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-1</sd-tag></span> <span>or <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-</span><sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SUMO-2" ext_ids="6613" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-2</sd-tag><span>, lysed under denaturing conditions, and <sd-tag id="sdTag115" source="sdapi" category="entity" entity_type="molecule" role="component" text="nickel" ext_ids="CHEBI:28112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nickel atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nickel</sd-tag> purified (<sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="undefined" role="component" text="Ni-NTA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ni-NTA</sd-tag>). Unmodified</span> <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>-46Q is indicated by the arrow and SUMO-modified <sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> <span>by the boxed region. The lysine mutant (3R) serves as a negative control. <sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="undefined" role="component" text="Ni-NTA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ni-NTA</sd-tag> represents <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="molecule" role="component" text="nickel" ext_ids="CHEBI:28112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nickel atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nickel</sd-tag>-purified</span> <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="protein" role="reporter" text="His" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His</sd-tag>-tagged <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>, and WC TCA represents 10% of the whole-cell lysate expression of <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> <span>and <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="protein" role="reporter" text="myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">myc</sd-tag>-<sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="protein" role="component" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> (transfection control).</span> <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag> is modified by <sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> (left) and <span><sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-2</sd-tag></span> (right).<graphic href="https://api.sourcedata.io/file.php?panel_id=15223"/></sd-panel><sd-panel panel_id="15224">(B) SUMO isopeptidases (<span><sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SENP1" ext_ids="29843" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SENP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP1</sd-tag></span><span>, <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SENP2" ext_ids="59343" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SENP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP2</sd-tag>,</span> <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SENP3" ext_ids="26168" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SENP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP3</sd-tag><span>, <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SENP5" ext_ids="205564" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SENP5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP5</sd-tag>, and</span> <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SENP6" ext_ids="26054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SENP6" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP6</sd-tag>) modulate SUMO-modified <sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> when overexpressed together with <sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> (46QP-H4 or 3R) and <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> (<sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag>). <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SENP1" ext_ids="29843" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SENP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP1</sd-tag><span>, <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SENP2" ext_ids="59343" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SENP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP2</sd-tag>, and</span> <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SENP6" ext_ids="26054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SENP6" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP6</sd-tag> decrease <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> <span>SUMOylation. Graph depicts quantitation of <sd-tag id="sdTag83" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> using the Odyssey Infrared Imaging System (LI-COR) to calculate the ratio of</span> <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> purified versus the <sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag> modified by SUMO multiplied by 100.<graphic href="https://api.sourcedata.io/file.php?panel_id=15224"/></sd-panel><sd-panel panel_id="15225"><p>(C) Titration of <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag>. Denaturing <sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="molecule" role="component" text="nickel" ext_ids="CHEBI:28112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nickel atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nickel</sd-tag> purification of <sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>ex1p (46QP-H4) following transfection with decreasing amounts of <sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SUMO-1" ext_ids="7341" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-1</sd-tag> reduces the amount of SUMO-modified <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> to undetectable levels. The <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="undefined" role="component" text="Ni-NTA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ni-NTA</sd-tag> blot displayed in the gray scale shows purified <sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>ex1 and SUMO-modified <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>ex1 using <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> antibody. Note that 0.5 μg of <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> (¼ the amount of <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> cDNA ) was used for identifying the <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> E3 ligase for <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>ex1p. Graph depicts quantitation of <sd-tag id="sdTag111" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> using the Odyssey Infrared Imaging System to calculate the ratio of <sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag> purified versus the <sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> modified by SUMO multiplied by 100. Note that all experiments were performed in triplicate, and a representative figure is shown.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15225"/></sd-panel></fig><fig id="5001"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5001"/><sd-panel panel_id="15226"><p>(A) Under limiting SUMO conditions (1/4 <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag>, lanes 3-9), <sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIAS1" ext_ids="8554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIAS1</sd-tag> increases <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag>-SUMO modification above 1/4 SUMO alone. Purified <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> (arrow) and SUMO-<sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> (boxed region) were detected using anti-<sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>. Graph depicts quantitation of the <sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="undefined" role="component" text="Ni-NTA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ni-NTA</sd-tag> <sd-tag id="sdTag130" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> using the Odyssey Infrared Imaging Software (LI-COR) to calculate the ratio of <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> purified versus the <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> modified by SUMO multiplied by 100.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15226"/></sd-panel><sd-panel panel_id="15227"><p>(B) <sd-tag id="sdTag140" source="sdapi" category="assay" entity_type="" role="" text="Western analysis" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Western analysis</sd-tag> of overexpression of <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag>ex1 (46QP-H4 or 3R), <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-2</sd-tag> (<sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-2</sd-tag>), and all the PIAS proteins (<sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIAS1" ext_ids="8554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIAS1</sd-tag>, <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIASxα" ext_ids="9063" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIASxα</sd-tag>, <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIASxβ" ext_ids="9063" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIASxβ</sd-tag>, <sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIAS3" ext_ids="10401" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIAS3</sd-tag>, and <sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIASy" ext_ids="51588" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS4" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIASy</sd-tag>). Under nonlimiting <sd-tag id="sdTag147" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-2</sd-tag> conditions, <sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIAS1" ext_ids="8554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIAS1</sd-tag> enhances SUMO modification of <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>. WC TCA shows overall <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="protein" role="reporter" text="myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">myc</sd-tag>-<sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> (transfection control) and <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> levels. Graph quantitating the ratio of <sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> purified versus the <sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> modified using the Odyssey (LICOR).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15227"/></sd-panel><sd-panel panel_id="15228"><p>(C) Left panel is the <sd-tag id="sdTag160" source="sdapi" category="assay" entity_type="" role="" text="autoradiography" ext_ids="BAO_0002527" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="autoradiography" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">autoradiography</sd-tag> results of a <sd-tag id="sdTag161" source="sdapi" category="assay" entity_type="" role="" text="GST pull-down assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST pull-down assay</sd-tag> showing that radiolabeled human <sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PIAS1" ext_ids="O75925" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PIAS1</sd-tag> interacts with <sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>ex1p. Right panel is a phosphorimager analysis of <sd-tag id="sdTag166" source="sdapi" category="assay" entity_type="" role="" text="GST pull-downs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST pull-downs</sd-tag>, performed in triplicate, showing the percentage of <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="35S" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">35S</sd-tag>-labeled PIAS protein that bound the <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag> proteins: <sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag> alone, unexpanded <sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> with and without the proline-rich region (20QP and 20Q), expanded <sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag> with and without the proline-rich region (51QP and 51Q), and the proline-rich region alone (Pro). Error bars were calculated as an estimate of SE = STDEV(n)/SQRT(n-1).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15228"/></sd-panel></fig><fig id="5002"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5002"/><sd-panel panel_id="15230"><p>(B) Longer <sd-tag id="sdTag177" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> polypeptides are modified by <sd-tag id="sdTag178" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag>. <sd-tag id="sdTag179" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> overexpressing <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag>ex1p (46QP-H4 or 3R), unexpanded <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>-586 fragment (25Q-586 or 25Q-3R-586 aa), and expanded <sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>-586 fragment (137Q-586 or 137Q-3R-586 aa) with <sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SUMO-1" ext_ids="7341" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-1</sd-tag> (<sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag>). Cell lysates were subjected to <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> <sd-tag id="sdTag175" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitation" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitation</sd-tag> (<sd-tag id="sdTag176" source="sdapi" category="assay" entity_type="" role="" text="IP" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">IP</sd-tag>) using <sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> antibody. <sd-tag id="sdTag185" source="sdapi" category="assay" entity_type="" role="" text="Western analysis" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Western analysis</sd-tag> performed with the Odyssey (LI-COR) allows detection of <sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> (data not shown) and SUMO simultaneously and shows that all forms of <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> are <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> modified using the anti-<sd-tag id="sdTag189" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> antibody. HTTex1p is covalently <sd-tag id="sdTag190" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> modified (lane 3), and the modification disappears when Lys are mutated to Arg (3R) (lane 4). Both unexpanded (lane 4 and 5) and expanded <sd-tag id="sdTag191" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>-586 fragments (lane 6 and 7) are covalently <sd-tag id="sdTag192" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> modified in both the presence and absence of the three Lys in the N-terminal region of <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> (3R). Free <sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> is indicated with the arrow, and SUMO-modified <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> is indicated by the boxes. Inset on the right, from a replicate experiment, shows comigration of expanded <sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> (anti-<sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>) and <sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> (anti-<sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>) displayed in the gray scale and in color when the two antibodies are merged (<sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> in red, <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-1</sd-tag> in green, and yellow when colocalizing).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15230"/></sd-panel><sd-panel panel_id="15231"><p>(C) Bait plasmids (<sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>-586-25Q or <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>-586-73Q aa) were transformed into the <sd-tag id="sdTag204" source="sdapi" category="entity" entity_type="organism" role="component" text="L40ccua MATa" ext_ids="4932" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Saccharomyces cerevisiae" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">L40ccua MATa</sd-tag> <sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="organism" role="component" text="yeast" ext_ids="4932" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Saccharomyces cerevisiae" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">yeast</sd-tag> strain. <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="organism" role="component" text="Yeast" ext_ids="4932" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Saccharomyces cerevisiae" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Yeast</sd-tag> clones encoding bait proteins were individually mated against a matrix of MATα <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="organism" role="component" text="yeast" ext_ids="4932" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Saccharomyces cerevisiae" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">yeast</sd-tag> clones encoding 16,888 prey proteins (with <sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="gene" role="component" text="Gal4" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Gal4</sd-tag> activation domain fusions) using pipetting and spotting robots. Diploid yeasts were spotted onto <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="undefined" role="component" text="SDIV" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDIV</sd-tag> (-<sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="molecule" role="component" text="Leu" ext_ids="CHEBI:25017" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="leucine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Leu</sd-tag>-<sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="molecule" role="component" text="Trp" ext_ids="CHEBI:27897" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="tryptophan" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Trp</sd-tag>-<sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="molecule" role="component" text="Ura" ext_ids="CHEBI:17568" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="uracil" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Ura</sd-tag>-<sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="protein" role="reporter" text="His" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His</sd-tag>) agar plates for selection of PPIs as well as nylon membranes placed on <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="undefined" role="component" text="SDIV" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDIV</sd-tag> <sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="molecule" role="component" text="agar" ext_ids="CHEBI:2509" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="agar" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">agar</sd-tag> plates for <sd-tag id="sdTag214" source="sdapi" category="assay" entity_type="" role="" text="β-galactosidase" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">β-galactosidase</sd-tag> assays. After 5-6 days of incubation at 30ºC, digitized images of the agar plates and nylon membranes were assessed for growth and <sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="subcellular" role="reporter" text="β-galactosidase" ext_ids="GO:0009341" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="beta-galactosidase complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">β-galactosidase</sd-tag> activity using the software Visual Grid (GPC Biotech).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15231"/></sd-panel><sd-panel panel_id="15232"><p>(D) Overexpression of <sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIAS1" ext_ids="8554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIAS1</sd-tag> alone, with unexpanded <sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag> constructs (25Q-586 aa) plus <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SUMO-1" ext_ids="7341" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-1</sd-tag> (<sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag342" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SUMO-1" ext_ids="7341" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-1</sd-tag>), shows that <sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PIAS1" ext_ids="O75925" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PIAS1</sd-tag> binds both full-length <sd-tag id="sdTag230" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> and <sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>-586 fragment (25Q-586 aa). WT <sd-tag id="sdTag232" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> was used in these experiments to preclude confounding aggregation effects. Western analysis detection was performed using Odyssey and is displayed in the gray scale but is shown in color on the merge (<sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> is red, and <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PIAS1" ext_ids="O75925" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PIAS1</sd-tag> is green). WB, <sd-tag id="sdTag235" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15232"/></sd-panel><sd-panel panel_id="15233"><p>(E) <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells overexpressing either expanded 586 aa-<sd-tag id="sdTag241" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> or the phosphomimetic (S13,16D = DD) with <sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-2</sd-tag> plus and minus <sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIAS1" ext_ids="8554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIAS1</sd-tag>. <sd-tag id="sdTag249" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag> was purified by <sd-tag id="sdTag245" source="sdapi" category="assay" entity_type="" role="" text="IP" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">IP</sd-tag> using <sd-tag id="sdTag343" source="sdapi" category="entity" entity_type="molecule" role="component" text="hydrazide" ext_ids="CHEBI:35362" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="hydrazide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">hydrazide</sd-tag> beads (Bioclone) crosslinked to <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> (Enzo) antibody and subjected to <sd-tag id="sdTag238" source="sdapi" category="assay" entity_type="" role="" text="western analysis" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">western analysis</sd-tag> using anti-<sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> (<sd-tag id="sdTag258" source="sdapi" category="assay" entity_type="" role="" text="MAB5490" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MAB5490</sd-tag>). Arrows indicate <sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="gene" role="component" text="SUMO-2" ext_ids="6613" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-2</sd-tag>-modified <sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15233"/></sd-panel><sd-panel panel_id="15234"><p>(F) <sd-tag id="sdTag251" source="sdapi" category="assay" entity_type="" role="" text="IP" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">IP</sd-tag> of <sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag> with <sd-tag id="sdTag250" source="sdapi" category="entity" entity_type="molecule" role="component" text="hydrazide" ext_ids="CHEBI:35362" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="hydrazide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">hydrazide</sd-tag>-linked beads shows that both unexpanded and expanded <sd-tag id="sdTag253" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> 586 aa phosphomimetics (S13, 16D-586 aa) are modified by <sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-2</sd-tag>. Arrows indicate SUMO-conjugated <sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>. Note that all experiments including the Y2H assay were done in triplicate; representative experiments are shown. Arrows indicate <sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="gene" role="component" text="SUMO-2" ext_ids="6613" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-2</sd-tag>-modified <sd-tag id="sdTag257" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15234"/></sd-panel></fig><fig id="5003"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5003"/><sd-panel panel_id="15235"><p>(A) Western analysis of whole-cell lysates from <sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells transfected with <sd-tag id="sdTag269" source="sdapi" category="entity" entity_type="protein" role="reporter" text="His" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His</sd-tag>-<sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SUMO-1" ext_ids="7341" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-1</sd-tag> or <sd-tag id="sdTag270" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SUMO-2" ext_ids="6613" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-2</sd-tag> and/or 97Q-<sd-tag id="sdTag264" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag> exon 1 and treated with 5 μM <sd-tag id="sdTag263" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> for 18 hr. Lysates were separated using differential centrifugation into a detergent-soluble fraction (SOLUBLE) with 1% <sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="molecule" role="component" text="Triton X-100" ext_ids="CHEBI:9750" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Triton X-100" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Triton X-100</sd-tag> and a detergent-insoluble fraction (INSOLUBLE) with 4% <sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="molecule" role="component" text="SDS" ext_ids="CHEBI:8984" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sodium dodecyl sulfate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">SDS</sd-tag>. <sd-tag id="sdTag271" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> probed with anti-<sd-tag id="sdTag272" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> shows full-length endogenous <sd-tag id="sdTag273" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> in the SOLUBLE fraction (upper arrow) and 97Q-<sd-tag id="sdTag267" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>ex1 (lower arrow) (left panel). In the INSOLUBLE fraction, <sd-tag id="sdTag274" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> HMW species are indicated by the bracket and asterisks (right panel).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15235"/></sd-panel><sd-panel panel_id="15236"><p>(B) <sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> and <sd-tag id="sdTag276" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SUMO-2" ext_ids="6613" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-2</sd-tag> cause mutant <sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag> to accumulate as HMW species (bracke and asterisk). <sd-tag id="sdTag278" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> showing <sd-tag id="sdTag279" source="sdapi" category="assay" entity_type="" role="" text="IP" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">IP</sd-tag> with <sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> antibody crosslinked beads from the detergent-insoluble fraction probed with the anti-<sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> antibody.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15236"/></sd-panel><sd-panel panel_id="15237"><p>(C) Mutant <sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag> (97Q-Httex1) fibrils are detected with anti-<sd-tag id="sdTag286" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> in the insoluble fraction with treatment of <sd-tag id="sdTag287" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> or addition of exogenous <sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SUMO-2" ext_ids="6613" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-2</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15237"/></sd-panel><sd-panel panel_id="15238"><p>(D) <sd-tag id="sdTag293" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> with increasing concentrations of <sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SUMO-2" ext_ids="6613" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SUMO-2</sd-tag> detected with anti-<sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="protein" role="reporter" text="His" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His</sd-tag> antibody (left panel). Middle panel is the same <sd-tag id="sdTag296" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> probed with anti-<sd-tag id="sdTag297" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> showing soluble forms of <sd-tag id="sdTag298" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag>. Right panel presents <sd-tag id="sdTag299" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> from detergent-insoluble fraction with monomeric <sd-tag id="sdTag300" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> (97Q) at 55 kDa, and the asterisk (*) indicates the HMW species. Note that all experiments were performed in triplicate; representative figures are shown.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15238"/></sd-panel></fig><fig id="5004"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5004"/><sd-panel panel_id="15239"><p>(A) <sd-tag id="sdTag304" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis of <sd-tag id="sdTag305" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells over-expressing exogenous <sd-tag id="sdTag306" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIAS1" ext_ids="8554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIAS1</sd-tag> in the presence of mutant <sd-tag id="sdTag307" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> (97Q) when separated into detergent-soluble and detergent-insoluble fractions. No difference is detected in monomeric <sd-tag id="sdTag308" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> (top panel, Soluble), but HMW <sd-tag id="sdTag309" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> levels increase with <sd-tag id="sdTag310" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIAS1" ext_ids="8554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIAS1</sd-tag> overexpression. Anti-<sd-tag id="sdTag303" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PIAS1" ext_ids="O75925" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PIAS1</sd-tag> antibody (Invitrogen) was used to detect <sd-tag id="sdTag311" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIAS1" ext_ids="8554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIAS1</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15239"/></sd-panel><sd-panel panel_id="15240"><p>(B) Acute knockdown of <sd-tag id="sdTag313" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIAS1" ext_ids="8554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIAS1</sd-tag> decreases HMW <sd-tag id="sdTag314" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HTT" ext_ids="P42858" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">HTT</sd-tag> species in the detergent-insoluble fraction. <sd-tag id="sdTag312" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PIAS1" ext_ids="O75925" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PIAS1</sd-tag> knockdown is detected in detergent-soluble and -insoluble fractions using anti-<sd-tag id="sdTag315" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PIAS1" ext_ids="8554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PIAS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PIAS1</sd-tag> antibody.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15240"/></sd-panel><sd-panel panel_id="15241"><p>(C) <sd-tag id="sdTag318" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Drosophila melanogaster" ext_ids="7227" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Drosophila melanogaster" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Drosophila melanogaster</sd-tag> expressing mutant <sd-tag id="sdTag319" source="sdapi" category="entity" entity_type="gene" role="component" text="HTT" ext_ids="3064" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HTT" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HTT</sd-tag>ex1p (93Q) in a reduced <sd-tag id="sdTag322" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Su(var)2-10" ext_ids="35927" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Su(var)2-10" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Su(var)2-10</sd-tag>/<sd-tag id="sdTag324" source="sdapi" category="entity" entity_type="gene" role="intervention" text="dPIAS" ext_ids="35927" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Su(var)2-10" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">dPIAS</sd-tag> genetic background exhibits statistically significantly reduced <sd-tag id="sdTag321" source="sdapi" category="entity" entity_type="cell_type" role="assayed" text="photoreceptor neuron" ext_ids="CL:0000540///CL:0000210" norm_text="" ext_dbs="CL///CL" in_caption="True" ext_names="neuron///photoreceptor cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org//// https://identifiers.org/">photoreceptor neuron</sd-tag> degeneration (left panel, p = 0.033) when comparing <sd-tag id="sdTag323" source="sdapi" category="entity" entity_type="gene" role="intervention" text="dPIAS" ext_ids="35927" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Su(var)2-10" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">dPIAS</sd-tag>/+ to +/+ <sd-tag id="sdTag326" source="sdapi" category="entity" entity_type="organism" role="assayed" text="flies" ext_ids="7227" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Drosophila melanogaster" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">flies</sd-tag> and increased overall <sd-tag id="sdTag344" source="sdapi" category="assay" entity_type="" role="" text="survival" ext_ids="OBI_0000699" norm_text="" ext_dbs="OBI" in_caption="True" ext_names="survival assessment" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/">survival</sd-tag> (right panel, p = 0.047) when comparing <sd-tag id="sdTag328" source="sdapi" category="entity" entity_type="gene" role="intervention" text="dPIAS" ext_ids="35927" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Su(var)2-10" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">dPIAS</sd-tag>1/+ to +/+ <sd-tag id="sdTag332" source="sdapi" category="entity" entity_type="organism" role="assayed" text="flies" ext_ids="7227" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Drosophila melanogaster" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">flies</sd-tag>. Significance was measured by Student's t test.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15241"/></sd-panel><sd-panel panel_id="15242"><p>(D) HMW <sd-tag id="sdTag334" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO-2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO-2</sd-tag> accumulates in postmortem HD <sd-tag id="sdTag335" source="sdapi" category="entity" entity_type="tissue" role="component" text="striata" ext_ids="UBERON:0002435" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="striatum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">striata</sd-tag>. <sd-tag id="sdTag336" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis of the insoluble fraction from three control and three HD postmortem <sd-tag id="sdTag337" source="sdapi" category="entity" entity_type="tissue" role="component" text="striata" ext_ids="UBERON:0002435" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="striatum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">striata</sd-tag> as described (Experimental Procedures).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15242"/></sd-panel></fig></article>

token_classification/10-1016_j-celrep-2014-10-053.xml

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+<article doi="10.1016/j.celrep.2014.10.053" abstract="Endosome-to-Golgi retrieval is an essential membrane trafficking pathway required for many important physiological processes and linked to neurodegenerative disease and infection by bacterial and viral pathogens. The prototypical cargo protein for this pathway is the cation-independent mannose 6-phosphate receptor (CIMPR), which delivers lysosomal hydrolases to endosomes. Efficient retrieval of CIMPR to the Golgi requires the retromer complex, but other aspects of the endosome-to-Golgi retrieval pathway are poorly understood. Employing an image-based antibody-uptake assay, we conducted a genome-wide RNAi loss-of-function screen for novel regulators of this trafficking pathway and report ∼90 genes that are required for endosome-to-Golgi retrieval of a CD8-CIMPR reporter protein. Among these regulators of endosome-to-Golgi retrieval are a number of multipass membrane-spanning proteins, a class of proteins often overlooked with respect to a role in membrane trafficking. We further demonstrate a role for three multipass membrane proteins, SFT2D2, ZDHHC5, and GRINA, in endosome-to-Golgi retrieval."><fig id="5024"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5024"/><sd-panel panel_id="15274">(E) Representative images of the pilot validation screen for the negative control (no siRNA) and for five sets of siRNA-treated cells with reduced TGN retrieval ratio. Different phenotypes that give rise to reduced TGN retrieval ratios are discussed in the text. Scale bar, 100 μm (top two rows) and 38 μm (bottom row).<graphic href="https://api.sourcedata.io/file.php?panel_id=15274"/></sd-panel></fig><fig id="5025"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5025"/></fig><fig id="5026"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5026"/><sd-panel panel_id="15278"><span>(A) Primary screen anti-<sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CD8" ext_ids="P01732///P10966" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="CD8A///CD8B" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">CD8</sd-tag> antibody-uptake images for control cells (top) and <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SFT2D2" ext_ids="375035" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SFT2D2</sd-tag> KD cells (bottom).</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15278"/></sd-panel><sd-panel panel_id="15279">(B) Cells stably expressing <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SFT2D2" ext_ids="O95562" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SFT2D2</sd-tag><span>-<sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> show localization of</span> <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SFT2D2" ext_ids="O95562" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SFT2D2</sd-tag> <span>to <sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="gene" role="intervention" text="perinuclear" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">perinuclear</sd-tag> membranes and <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="endosomes" ext_ids="GO:0005768" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">endosomes</sd-tag>, including <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag>-positive <sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="endosomes" ext_ids="GO:0005768" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">endosomes</sd-tag> (arrowheads in inset). Treatment with <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nocodazole" ext_ids="CHEBI:34892" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nocodazole" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nocodazole</sd-tag> disperses the <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="endosomes" ext_ids="GO:0005768" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">endosomes</sd-tag> and even more clearly shows colocalization of</span> <sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SFT2D2" ext_ids="O95562" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SFT2D2</sd-tag><span>-<sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> and <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag> (arrowheads in inset).</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15279"/></sd-panel><sd-panel panel_id="15280">(C) Cells stably expressing <span><sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SFT2D2" ext_ids="O95562" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SFT2D2</sd-tag></span>-<sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> <span>were costained with antibodies against various post-<sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Golgi" ext_ids="GO:0005794" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="Golgi apparatus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Golgi</sd-tag> SNARE proteins. Colocalization was quantified by Pearson's correlation coefficient (right-hand graph) and indicates very extensive colocalization with <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="protein" role="assayed" text="STX6" ext_ids="O43752" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="STX6" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">STX6</sd-tag>, <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="protein" role="assayed" text="STX7" ext_ids="O15400" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="STX7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">STX7</sd-tag>, and <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VAMP8" ext_ids="Q9BV40" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VAMP8" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VAMP8</sd-tag>. The image panels illustrate colocalization of</span> <span><sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SFT2D2" ext_ids="O95562" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SFT2D2</sd-tag></span>-<sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> <span>and <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="protein" role="assayed" text="STX5" ext_ids="Q13190" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="STX5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">STX5</sd-tag> at the <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Golgi" ext_ids="GO:0005794" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="Golgi apparatus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Golgi</sd-tag> (top, arrowhead) but much more extensive colocalization of</span> <span><sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SFT2D2" ext_ids="O95562" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SFT2D2</sd-tag></span>-<sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> <span>and <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="protein" role="assayed" text="STX6" ext_ids="O43752" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="STX6" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">STX6</sd-tag> (bottom, arrowheads). In (B) and (C), the white dashed box delineates the area magnified in the insets.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15280"/></sd-panel><sd-panel panel_id="15281">(D) SNARE protein staining was compared for control and <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SFT2D2" ext_ids="375035" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SFT2D2</sd-tag> <span>KD <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells and quantified. The graph shows the change in cellular intensity measured for each post-</span><span><sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Golgi" ext_ids="GO:0005794" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="Golgi apparatus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Golgi</sd-tag></span> <span>SNARE investigated. Images illustrate the increased cellular intensity of <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VAMP3" ext_ids="Q15836" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VAMP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VAMP3</sd-tag> in</span> <sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SFT2D2" ext_ids="375035" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SFT2D2</sd-tag> KD cells.<graphic href="https://api.sourcedata.io/file.php?panel_id=15281"/></sd-panel><sd-panel panel_id="15282"><p>(E) Control and <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SFT2D2" ext_ids="375035" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SFT2D2</sd-tag> KD <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cell lysates were separated by <sd-tag id="sdTag66" source="sdapi" category="assay" entity_type="" role="" text="LDS-PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LDS-PAGE</sd-tag> and blotted for the indicated SNARE proteins or <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15282"/></sd-panel></fig><fig id="5027"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5027"/><sd-panel panel_id="15283">(A) Primary screen anti-<sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CD8" ext_ids="P01732///P10966" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="CD8A///CD8B" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">CD8</sd-tag> <span>antibody-uptake images for control cells (top) and <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ZDHHC5" ext_ids="25921" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ZDHHC5</sd-tag> KD cells (bottom).</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15283"/></sd-panel><sd-panel panel_id="15284">(B) Cells stably expressing <span><sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ZDHHC5" ext_ids="Q9C0B5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ZDHHC5</sd-tag></span>-<sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> show localization of <span><sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ZDHHC5" ext_ids="Q9C0B5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ZDHHC5</sd-tag></span> <span>to the <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="plasma membrane" ext_ids="GO:0005886" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="plasma membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">plasma membrane</sd-tag> and to intracellular <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="tubules" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">tubules</sd-tag> and <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag>. Some colocalization between</span> <span><sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ZDHHC5" ext_ids="Q9C0B5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ZDHHC5</sd-tag></span> and retromer <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag> is observed (arrowheads in inset). Following <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nocodazole" ext_ids="CHEBI:34892" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nocodazole" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nocodazole</sd-tag> treatment <sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="endosomes" ext_ids="GO:0005768" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">endosomes</sd-tag> are dispersed and some are labeled with <span><sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ZDHHC5" ext_ids="Q9C0B5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ZDHHC5</sd-tag></span> and <sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag> (arrowheads in inset).<graphic href="https://api.sourcedata.io/file.php?panel_id=15284"/></sd-panel><sd-panel panel_id="15285">(C) Control and <sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ZDHHC5" ext_ids="25921" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ZDHHC5</sd-tag> siRNA-treated <span><sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SFT2D2" ext_ids="O95562" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SFT2D2</sd-tag></span>-<sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> cells were mixed and stained for <span><sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ZDHHC5" ext_ids="Q9C0B5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ZDHHC5</sd-tag></span>, <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>, and <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag>. KD cells are marked by an asterisk.<graphic href="https://api.sourcedata.io/file.php?panel_id=15285"/></sd-panel><sd-panel panel_id="15286">(D) Control and <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ZDHHC5" ext_ids="25921" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ZDHHC5</sd-tag> siRNA-treated <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were mixed and stained for <span><sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ZDHHC5" ext_ids="Q9C0B5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ZDHHC5</sd-tag></span><span>, <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="assayed" text="α5-integrin" ext_ids="P08648" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ITGA5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">α5-integrin</sd-tag>, and</span> <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag>. KD cells are indicated with an asterisk.<graphic href="https://api.sourcedata.io/file.php?panel_id=15286"/></sd-panel><sd-panel panel_id="15287">(E) Control (top) and <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ZDHHC5" ext_ids="25921" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ZDHHC5</sd-tag> KD (bottom) <sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> <span>cells were fixed and stained for <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TGN46" ext_ids="O43493" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TGOLN2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TGN46</sd-tag> and <sd-tag id="sdTag115" source="sdapi" category="entity" entity_type="protein" role="assayed" text="β1-integrin" ext_ids="P05556" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ITGB1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">β1-integrin</sd-tag>.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15287"/></sd-panel></fig><fig id="5028"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5028"/><sd-panel panel_id="15288">(A) Primary screen anti-<sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CD8" ext_ids="P01732///P10966" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="CD8A///CD8B" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">CD8</sd-tag> <span>antibody uptake images for control cells (top) and <sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GRINA" ext_ids="2907" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GRINA</sd-tag> KD cells (bottom).</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15288"/></sd-panel><sd-panel panel_id="15289">(B) Control (top) and <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GRINA" ext_ids="2907" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GRINA</sd-tag> KD (bottom) <sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were stained for <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Golgi" ext_ids="GO:0005794" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="Golgi apparatus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Golgi</sd-tag> <span>marker <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GM130" ext_ids="Q08379" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GOLGA2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GM130</sd-tag> and</span> <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Golgi glycoprotein-1" ext_ids="Q92896" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GLG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Golgi glycoprotein-1</sd-tag> <span>(<sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GLG1" ext_ids="Q92896" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GLG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GLG1</sd-tag>).</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15289"/></sd-panel><sd-panel panel_id="15290"><span>(C) Cells stably expressing <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Rab6" ext_ids="Q9NRW1///Q9H0N0///P20340" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="RAB6B///RAB6C///RAB6A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Rab6</sd-tag> were treated with</span> <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GRINA" ext_ids="2907" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GRINA</sd-tag> siRNA (bottom) and compared to control cells (top) upon staining for <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TGN46" ext_ids="O43493" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TGOLN2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TGN46</sd-tag> and <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=15290"/></sd-panel><sd-panel panel_id="15291"><span>(D) Quantitation by <sd-tag id="sdTag139" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag> of lysates from control and</span> <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GRINA" ext_ids="2907" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GRINA</sd-tag>-silenced <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells and <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Rab6" ext_ids="84084///51560///5870" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="RAB6C///RAB6B///RAB6A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">Rab6</sd-tag> cells.<graphic href="https://api.sourcedata.io/file.php?panel_id=15291"/></sd-panel><sd-panel panel_id="15292"><p>(E-G) <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were transiently transfected with <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GRINA" ext_ids="Q7Z429" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GRINA</sd-tag>-<sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> for 24 hr before fixing and staining. (E and F) <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GRINA" ext_ids="Q7Z429" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GRINA</sd-tag>-<sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> colocalizes with both <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TGN46" ext_ids="O43493" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TGOLN2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TGN46</sd-tag> and <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag>. In this example, <sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GRINA" ext_ids="Q7Z429" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GRINA</sd-tag>-<sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> expression (in the cell marked by an asterisk in E) reduced the cell's <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TGN46" ext_ids="O43493" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TGOLN2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TGN46</sd-tag> expression compared to surrounding untransfected cells and caused enlargement of <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag>-positive <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="endosomes" ext_ids="GO:0005768" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">endosomes</sd-tag>. The area in (E) magnified in (F) is indicated by a dashed line. (G) <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GRINA" ext_ids="Q7Z429" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GRINA</sd-tag>-<sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> expression also perturbs <sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CIMPR" ext_ids="P11717" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IGF2R" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CIMPR</sd-tag> localization. In this example, <sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GRINA" ext_ids="Q7Z429" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GRINA</sd-tag>-<sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> transfection (in the cell marked by an asterisk) caused <sd-tag id="sdTag171" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CIMPR" ext_ids="P11717" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IGF2R" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CIMPR</sd-tag> to localize to round vesicular structures positive for <sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GRINA" ext_ids="Q7Z429" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GRINA</sd-tag>-<sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>, some of which appeared larger than regular <sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="endosomes" ext_ids="GO:0005768" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">endosomes</sd-tag>, whereas <sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TGN46" ext_ids="O43493" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TGOLN2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TGN46</sd-tag> staining was almost absent in the transfected cell.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15292"/></sd-panel></fig><fig id="5029"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5029"/><sd-panel panel_id="15293">(A) Control <sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> <span>cells or cells transfected with the indicated siRNAs were treated for 3 hr with <sd-tag id="sdTag177" source="sdapi" category="entity" entity_type="molecule" role="component" text="cycloheximide" ext_ids="CHEBI:27641" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="cycloheximide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">cycloheximide</sd-tag>, lysed, and incubated with agarose-bound <sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="protein" role="component" text="wheat germ agglutinin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">wheat germ agglutinin</sd-tag> to capture <sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="molecule" role="component" text="glycosylated membrane proteins" ext_ids="CHEBI:17089" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="glycoprotein" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glycosylated membrane proteins</sd-tag>. Total cell lysates (left) and <sd-tag id="sdTag178" source="sdapi" category="entity" entity_type="protein" role="reporter" text="lectin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">lectin</sd-tag> pull-down samples (right) were assayed by</span> <sd-tag id="sdTag182" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag>. The experiment was repeated three times, and representative data are shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=15293"/></sd-panel><sd-panel panel_id="15294"><p>(B-E) Quantitative analysis of <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SFT2D2" ext_ids="375035" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SFT2D2</sd-tag>, <sd-tag id="sdTag203" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ZDHHC5" ext_ids="25921" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ZDHHC5</sd-tag>, and <sd-tag id="sdTag204" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GRINA" ext_ids="2907" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GRINA</sd-tag> KD cells <sd-tag id="sdTag199" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunofluorescence</sd-tag> using <sd-tag id="sdTag200" source="sdapi" category="assay" entity_type="" role="" text="automated microscopy" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">automated microscopy</sd-tag> (see Experimental Procedures). (B) Representative images showing <sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag>, <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TGN46" ext_ids="O43493" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TGOLN2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TGN46</sd-tag>, and <sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CIMPR" ext_ids="P11717" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IGF2R" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CIMPR</sd-tag> staining. Scale bar, 50 μm. (C) Quantitative analysis of <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CIMPR" ext_ids="P11717" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IGF2R" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CIMPR</sd-tag> intensity at the <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Golgi" ext_ids="GO:0005794" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="Golgi apparatus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Golgi</sd-tag> indicates a significant increase in <sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SFT2D2" ext_ids="375035" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SFT2D2</sd-tag>, <sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ZDHHC5" ext_ids="25921" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ZDHHC5</sd-tag>, or <sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GRINA" ext_ids="2907" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GRINA</sd-tag> KD cells. (D) <sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SFT2D2" ext_ids="375035" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SFT2D2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SFT2D2</sd-tag>, <sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ZDHHC5" ext_ids="25921" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ZDHHC5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ZDHHC5</sd-tag>, and <sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GRINA" ext_ids="2907" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GRINA" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GRINA</sd-tag> KD increase the Pearson's correlation coefficient for colocalization between <sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CIMPR" ext_ids="P11717" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IGF2R" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CIMPR</sd-tag> and retromer proteins <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="protein" role="assayed" text="VPS35" ext_ids="Q96QK1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VPS35" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">VPS35</sd-tag> or <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SNX1" ext_ids="Q13596" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SNX1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SNX1</sd-tag> while decreasing the correlation between <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CIMPR" ext_ids="P11717" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IGF2R" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CIMPR</sd-tag> and <sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Golgi" ext_ids="GO:0005794" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="Golgi apparatus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Golgi</sd-tag> matrix protein <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GM130" ext_ids="Q08379" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GOLGA2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GM130</sd-tag>. In some cases, identical correlation coefficients were measured in the replicate experiments. (E) Quantitation of the <sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TGN46" ext_ids="O43493" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TGOLN2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TGN46</sd-tag> and <sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GLG1" ext_ids="Q92896" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GLG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GLG1</sd-tag> intensity in the three types of KD cells.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15294"/></sd-panel></fig><fig id="5030"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5030"/></fig></article>

token_classification/10-1016_j-celrep-2015-05-045.xml

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+<article doi="10.1016/j.celrep.2015.05.045" abstract="The polymorphism ATG16L1 T300A, associated with increased risk of Crohn's disease, impairs pathogen defense mechanisms including selective autophagy, but specific pathway interactions altered by the risk allele remain unknown. Here, we use perturbational profiling of human peripheral blood cells to reveal that CLEC12A is regulated in an ATG16L1-T300A-dependent manner. Antibacterial autophagy is impaired in CLEC12A-deficient cells, and this effect is exacerbated in the presence of the ATG16L1(∗)300A risk allele. Clec12a(-/-) mice are more susceptible to Salmonella infection, supporting a role for CLEC12A in antibacterial defense pathways in vivo. CLEC12A is recruited to sites of bacterial entry, bacteria-autophagosome complexes, and sites of sterile membrane damage. Integrated genomics identified a functional interaction between CLEC12A and an E3-ubiquitin ligase complex that functions in antibacterial autophagy. These data identify CLEC12A as early adaptor molecule for antibacterial autophagy and highlight perturbational profiling as a method to elucidate defense pathways in complex genetic disease."><fig id="5012"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5012"/><sd-panel panel_id="15334"><p>(C) <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> cells were transfected with indicated siRNAs and infected with <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="protein" role="reporter" text="DsRed" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DsRed</sd-tag>-labeled <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag>. The percentage of <sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>+ <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> at 1 hr post-infection is shown. Data are shown as means ± SD; n = 75 cells per condition from three biological replicates. Data are representative of three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15334"/></sd-panel><sd-panel panel_id="15335"><p>(D) Representative <sd-tag id="sdTag14" source="sdapi" category="assay" entity_type="" role="" text="epifluorescent microscopy" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">epifluorescent microscopy</sd-tag> images of <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells used to generate data shown in (C). The scale bars represent 10 μm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15335"/></sd-panel><sd-panel panel_id="15311"><span>(E) <sd-tag id="sdTag26" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> of</span> <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> <span>cells transfected with the indicated siRNAs and treated with <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Torin" ext_ids="CHEBI:84327" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="torin 1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Torin</sd-tag> <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="E64D" ext_ids="CHEBI:30270" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="E64" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">E64D</sd-tag>/<sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PepA" ext_ids="CHEBI:7989" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Pepstatin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PepA</sd-tag>. Data are representative of three independent experiments.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15311"/></sd-panel><sd-panel panel_id="15313">(G) <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> <span>cells were transfected with control siRNA, <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="gene" role="intervention" text="CLEC12A" ext_ids="160364" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">CLEC12A</sd-tag> siRNA1, or <sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="gene" role="intervention" text="CLEC12A" ext_ids="160364" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">CLEC12A</sd-tag> siRNA2 as well as <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="gene" role="intervention" text="CLEC12A" ext_ids="160364" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">CLEC12A</sd-tag> rescue constructs (R1 or R2) and infected for 1 hr with</span> <sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="protein" role="reporter" text="DsRed" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DsRed</sd-tag>-labeled <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag>. Data are shown as mean ± SD; n = 75 per condition. Data are representative of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=15313"/></sd-panel><sd-panel panel_id="15314">(H) <sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> <span>cells from (G) were lysed, and <sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-</span><sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="gene" role="intervention" text="CLEC12A" ext_ids="160364" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">CLEC12A</sd-tag> <span>expression levels were assessed by <sd-tag id="sdTag49" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag>. Data are representative of three independent experiments.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15314"/></sd-panel></fig><fig id="5013"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5013"/><sd-panel panel_id="15315"><p>(A) Representative <sd-tag id="sdTag52" source="sdapi" category="assay" entity_type="" role="" text="epifluorescent images" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">epifluorescent images</sd-tag> showing impaired antibacterial autophagy in <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG16L1</sd-tag> KO <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells complemented with the indicated <sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG16L1</sd-tag> protein in the presence of control siRNA or <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="gene" role="intervention" text="CLEC12A" ext_ids="160364" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">CLEC12A</sd-tag> siRNA. The scale bars represent 10 μm. (B) Percentage of <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-<sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> colocalization in WT <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells, <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG16L1</sd-tag> KO <sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells, and <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG16L1</sd-tag> KO <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG16L1</sd-tag><sup>∗</sup>300T or <sup>∗</sup>300A alleles in the presence of control siRNA or <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="gene" role="intervention" text="CLEC12A" ext_ids="160364" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">CLEC12A</sd-tag> siRNA. Data are shown as means ± SD; n = 75. Data shown are representative of three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15315"/></sd-panel></fig><fig id="5014"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5014"/><sd-panel panel_id="15316"><p>(A) <sd-tag id="sdTag68" source="sdapi" category="assay" entity_type="" role="" text="Confocal micrographs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Confocal micrographs</sd-tag> of <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-<sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Listeria" ext_ids="1637" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Listeria" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Listeria</sd-tag> colocalization in WT and <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Clec12a" ext_ids="232413" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Clec12a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Clec12a</sd-tag><sup>−/−</sup> <sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag> at 1 hr post-infection. The scale bars represent 10 μm. (B) Quantification of <sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-<sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Listeria" ext_ids="1637" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Listeria" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Listeria</sd-tag> colocalization in WT and <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Clec12a" ext_ids="232413" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Clec12a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Clec12a</sd-tag><sup>−/−</sup> <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMDMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMDMs</sd-tag>. Data shown represent mean ± SD of n = 3 independent experiments; unpaired t test. <sup>∗∗</sup>p &lt; 0.01.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15316"/></sd-panel><sd-panel panel_id="15317"><p>(C and D) <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> <sd-tag id="sdTag81" source="sdapi" category="assay" entity_type="" role="" text="cfu" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">cfu</sd-tag>s quantified per gram of <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="stool" ext_ids="UBERON:0001988" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="feces" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">stool</sd-tag> (C) and per organ (D) at 4 days post-infection are displayed. Data are shown as mean ± SD; <sup>∗∗</sup>p ≤ 0.01. Data are representative of at least two independent experiments (n = 9 for WT; n = 7 or 8 for <sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Clec12a" ext_ids="232413" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Clec12a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Clec12a</sd-tag><sup>−/−</sup>).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15317"/></sd-panel><sd-panel panel_id="15318"><p>(E) <sd-tag id="sdTag88" source="sdapi" category="assay" entity_type="" role="" text="Clinical score" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Clinical score</sd-tag> for infected <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> at 4 days post-infection. Data are shown as mean ± SD. Data are representative of at least two independent experiments. <sup>∗∗∗∗</sup>p &lt; 0.0001; unpaired t test. (n = 14 for WT; n = 13 for <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Clec12a" ext_ids="232413" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Clec12a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Clec12a</sd-tag><sup>−/−</sup>).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15318"/></sd-panel><sd-panel panel_id="15319"><p>(F) <sd-tag id="sdTag92" source="sdapi" category="assay" entity_type="" role="" text="Survival" ext_ids="OBI_0000699" norm_text="" ext_dbs="OBI" in_caption="True" ext_names="survival assessment" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/">Survival</sd-tag> curve for infected WT and <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Clec12a" ext_ids="232413" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Clec12a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Clec12a</sd-tag><sup>−/−</sup> <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> (n = 9 <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> per genotype).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15319"/></sd-panel></fig><fig id="5015"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5015"/><sd-panel panel_id="15320"><p>(A) <sd-tag id="sdTag99" source="sdapi" category="assay" entity_type="" role="" text="Gentamicin protection assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Gentamicin protection assay</sd-tag> in <sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells showing fold replication of <sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> in cells treated with the indicated siRNAs. Data are shown as mean ± SD; n = 6. Data are representative of four independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15320"/></sd-panel><sd-panel panel_id="15336"><p>(B) Quantitation of <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CLEC12A" ext_ids="Q5QGZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CLEC12A</sd-tag>-<sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="organism" role="assayed" text="bacteria" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">bacteria</sd-tag> and <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-<sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="organism" role="assayed" text="bacteria" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">bacteria</sd-tag> colocalization at indicated time points. Data are shown as mean ± SD; n = 3 independent experiments. (C) Representative <sd-tag id="sdTag113" source="sdapi" category="assay" entity_type="" role="" text="confocal micrographs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">confocal micrographs</sd-tag> of <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells showing association of intracellular <sd-tag id="sdTag115" source="sdapi" category="entity" entity_type="organism" role="assayed" text="bacteria" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">bacteria</sd-tag> with <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CLEC12A" ext_ids="Q5QGZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CLEC12A</sd-tag> at 20, 40, 60, and 80 min post-infection. The scale bars represent 10 μm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15336"/></sd-panel></fig><fig id="5016"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5016"/><sd-panel panel_id="15323"><p>(A-C) Representative <sd-tag id="sdTag127" source="sdapi" category="assay" entity_type="" role="" text="epifluorescent images" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">epifluorescent images</sd-tag> of <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells showing colocalization of (A) <sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CLEC12A" ext_ids="Q5QGZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CLEC12A</sd-tag> (green) and <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="protein" role="assayed" text="galectin 8" ext_ids="O00214" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LGALS8" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">galectin 8</sd-tag> or <sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="protein" role="assayed" text="galectin 3" ext_ids="P17931" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LGALS3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">galectin 3</sd-tag> (red) around intracellular <sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> (blue), (B) <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CLEC12A" ext_ids="Q5QGZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CLEC12A</sd-tag> (green) and <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NDP52" ext_ids="Q13137" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CALCOCO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NDP52</sd-tag> (red) around <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> (blue), and (C) endogenous <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CLEC12A" ext_ids="Q5QGZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CLEC12A</sd-tag> (red) and <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (green) around <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> (blue).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15323"/></sd-panel><sd-panel panel_id="15324"><p>(D) <sd-tag id="sdTag137" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CLEC12A" ext_ids="Q5QGZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CLEC12A</sd-tag> or <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CLEC12A" ext_ids="Q5QGZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CLEC12A</sd-tag> (green) and <sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GABARAPL2" ext_ids="P60520" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GABARAPL2</sd-tag> or <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG16L1" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG16L1</sd-tag> (red) around intracellular <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> (blue). Images are representative of three or more independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15324"/></sd-panel><sd-panel panel_id="15325"><p>(E) Representative <sd-tag id="sdTag148" source="sdapi" category="assay" entity_type="" role="" text="epifluorescent images" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">epifluorescent images</sd-tag> of <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells transfected with a control siRNA or a siRNA against <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="gene" role="intervention" text="CLEC12A" ext_ids="160364" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">CLEC12A</sd-tag> and infected with <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="protein" role="reporter" text="DsRed" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DsRed</sd-tag>-labeled <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> for 1 hr. (F) Quantitation of <sd-tag id="sdTag147" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P62979///P62987///P0CG48///P0CG47" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="RPS27A///UBA52///UBC///UBB" ext_tax_ids="9606///9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>-<sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="organism" role="assayed" text="bacteria" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">bacteria</sd-tag> colocalization at 1 hr post-infection in cells shown in (E). Data are shown as means ± SEM from three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15325"/></sd-panel><sd-panel panel_id="15326"><p>(G) Representative <sd-tag id="sdTag154" source="sdapi" category="assay" entity_type="" role="" text="epifluorescent images" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">epifluorescent images</sd-tag> of <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells transfected and infected as in (E). (H) Quantitation of <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NDP52" ext_ids="Q13137" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CALCOCO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NDP52</sd-tag>-<sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="organism" role="assayed" text="bacteria" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">bacteria</sd-tag> colocalization at 1 hr post-infection in cells shown in (G). Data are shown as means ± SEM from three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15326"/></sd-panel><sd-panel panel_id="15327"><p>(I) Representative <sd-tag id="sdTag163" source="sdapi" category="assay" entity_type="" role="" text="confocal micrographs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">confocal micrographs</sd-tag> of <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells expressing <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="protein" role="assayed" text="CLEC12A" ext_ids="Q5QGZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CLEC12A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">CLEC12A</sd-tag>. Cells were untreated or exposed to hypertonic media containing <sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PEG 1000" ext_ids="CHEBI:46793" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="poly(ethylene glycol)" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PEG 1000</sd-tag>, followed by <sd-tag id="sdTag160" source="sdapi" category="physical" entity_type="" role="" text="hypotonic shock" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hypotonic shock</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15327"/></sd-panel></fig><fig id="5017"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5017"/><sd-panel panel_id="15332"><p>(E) <sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> <sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> cells were transfected with indicated siRNAs for 48 hr and then infected with <sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="protein" role="reporter" text="DsRed" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DsRed</sd-tag>-labeled <sd-tag id="sdTag171" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> for 1 hr. The fraction of <sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-positive intracellular <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="organism" role="assayed" text="Salmonella" ext_ids="90371" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Salmonella enterica subsp. enterica serovar Typhimurium" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Salmonella</sd-tag> is shown. Data are mean ± SD and are representative of three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15332"/></sd-panel><sd-panel panel_id="15333"><p>(F) <sd-tag id="sdTag184" source="sdapi" category="assay" entity_type="" role="" text="Gentamicin protection assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Gentamicin protection assay</sd-tag> in <sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells showing increased intracellular bacterial replication after 48 hr of knockdown of <sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG16L1" ext_ids="55054" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG16L1</sd-tag>, <sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="gene" role="intervention" text="KLHL9" ext_ids="55958" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="KLHL9" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">KLHL9</sd-tag>, <sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NEDD8" ext_ids="4738" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="NEDD8" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NEDD8</sd-tag>, or <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="gene" role="intervention" text="KLHL13" ext_ids="90293" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="KLHL13" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">KLHL13</sd-tag>. Data shown as mean ± SD; n = 4. Data are representative of three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15333"/></sd-panel></fig></article>

token_classification/10-1016_j-celrep-2015-06-022.xml

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+<article doi="10.1016/j.celrep.2015.06.022" abstract="Communication between organelles is crucial for eukaryotic cells to function as one coherent unit. An important means of communication is through membrane contact sites, where two organelles come into close proximity allowing the transport of lipids and small solutes between them. Contact sites are dynamic in size and can change in response to environmental or cellular stimuli; however, how this is regulated has been unclear. Here, we show that Saccharomyces cerevisiae Lam6 resides in several central contact sites: ERMES (ER/mitochondria encounter structure), vCLAMP (vacuole and mitochondria patch), and NVJ (nuclear vacuolar junction). We show that Lam6 is sufficient for expansion of contact sites under physiological conditions and necessary for coordination of contact site size. Given that Lam6 is part of a large protein family and is conserved in vertebrates, our work opens avenues for investigating the underlying principles of organelle communication."><fig id="5019"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5019"/><sd-panel panel_id="15299"><p>(G). <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-tagged <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="subcellular" role="component" text="ERMES" ext_ids="GO:0032865" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="ERMES complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ERMES</sd-tag> complex proteins retain their characteristic punctate structure in Δ<sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="gene" role="component" text="lam6" ext_ids="850761" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lam6</sd-tag>, suggesting that <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="gene" role="component" text="Lam6" ext_ids="850761" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Lam6</sd-tag> is not an essential complex member. Scale bar represents 5 μm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15299"/></sd-panel></fig><fig id="5020"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5020"/><sd-panel panel_id="15300"><span>(A) <sd-tag id="sdTag11" source="sdapi" category="assay" entity_type="" role="" text="Fluorescence microscopy" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Fluorescence microscopy</sd-tag> demonstrates that</span> <span><sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Lam6" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Lam6</sd-tag></span>-<sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> co-localizes with <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="subcellular" role="component" text="ERMES" ext_ids="GO:0032865" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="ERMES complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ERMES</sd-tag> <span>(<sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Mdm34" ext_ids="P53083" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MDM34" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Mdm34</sd-tag>-<sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Cherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cherry</sd-tag>) (yellow arrows) and also localizes to non-</span><sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="subcellular" role="component" text="ERMES" ext_ids="GO:0032865" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="ERMES complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ERMES</sd-tag> <span>locations in the cell (red arrows). These additional locations co-localized with the <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="subcellular" role="component" text="NVJ" ext_ids="GO:0071561" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus-vacuole junction" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">NVJ</sd-tag> (<sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Nvj1" ext_ids="P38881" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NVJ1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Nvj1</sd-tag>-</span><sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag><span>) as well as with the <sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="subcellular" role="component" text="vCLAMP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">vCLAMP</sd-tag> (</span><sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag><span>-<sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Vps39" ext_ids="Q07468" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Vps39</sd-tag>). Scale bar represents 5 μm.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15300"/></sd-panel><sd-panel panel_id="15301">(B) Overexpression and tagging of <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Lam6" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Lam6</sd-tag> confirmed that it co-localizes with <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="subcellular" role="component" text="ERMES" ext_ids="GO:0032865" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="ERMES complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ERMES</sd-tag> (<sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Mdm34" ext_ids="P53083" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MDM34" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Mdm34</sd-tag>-<sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>) (yellow arrows) as well as to additional contact sites (red arrows), <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="subcellular" role="component" text="NVJ" ext_ids="GO:0071561" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus-vacuole junction" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">NVJ</sd-tag> (marked by <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Nvj1" ext_ids="P38881" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NVJ1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Nvj1</sd-tag>) and <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="subcellular" role="component" text="vCLAMP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">vCLAMP</sd-tag> (marked by <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Vps39" ext_ids="Q07468" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Vps39</sd-tag>). Scale bar represents 5 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=15301"/></sd-panel></fig><fig id="5021"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5021"/><sd-panel panel_id="15302">(A) <sd-tag id="sdTag37" source="sdapi" category="assay" entity_type="" role="" text="Fluorescence microscopy" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Fluorescence microscopy</sd-tag> demonstrates that the overexpression of <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Cherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cherry</sd-tag>-<span><sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Lam6" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Lam6</sd-tag></span> (OE-<sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Cherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cherry</sd-tag><span>-<sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAM6" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LAM6</sd-tag>) results in an expansion of the following three contact sites:</span> <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="subcellular" role="component" text="ERMES" ext_ids="GO:0032865" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="ERMES complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ERMES</sd-tag> (<sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Mdm34" ext_ids="P53083" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MDM34" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Mdm34</sd-tag>-<sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>), <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="subcellular" role="component" text="NVJ" ext_ids="GO:0071561" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus-vacuole junction" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">NVJ</sd-tag> (<sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Nvj1" ext_ids="P38881" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NVJ1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Nvj1</sd-tag>-<sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>), and <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="subcellular" role="component" text="vCLAMP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">vCLAMP</sd-tag> (<sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Vps39" ext_ids="Q07468" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Vps39</sd-tag>). This suggests that an increase in <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Lam6" ext_ids="850761" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Lam6</sd-tag> levels in the contact site is sufficient for its expansion. The numbers represent the average contact site size (120 cells per sample). Scale bar represents 5 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=15302"/></sd-panel><sd-panel panel_id="15303"><span>(B) <sd-tag id="sdTag52" source="sdapi" category="assay" entity_type="" role="" text="Immuno-EM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Immuno-EM</sd-tag> verified that</span> <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Lam6" ext_ids="850761" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Lam6</sd-tag> overexpression indeed causes an expansion of contact site size. While <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vCLAMP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">vCLAMP</sd-tag> <span>was hardly visible in WT cells, it could be detected easily in the OE strain (albeit often had <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="ER" ext_ids="GO:0005783" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ER</sd-tag> tubules invading it). The</span> <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="NVJ" ext_ids="GO:0071561" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus-vacuole junction" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">NVJ</sd-tag> <span>underwent expansion as well as evoked PMN in OE strains, and the <sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="ER" ext_ids="GO:0005783" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ER</sd-tag>-<sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> contact became large and elongated instead of small and distinct. N, <sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="nucleus" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nucleus</sd-tag>; M, <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>; V, <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vacuole" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuole</sd-tag>. Scale bar represents 200 nm (see also Figure S3I).</span><graphic href="https://api.sourcedata.io/file.php?panel_id=15303"/></sd-panel></fig><fig id="5022"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=5022"/><sd-panel panel_id="15304"><p>(A) Fluorescent microscopy shows that the <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="ERMES" ext_ids="GO:0032865" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="ERMES complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ERMES</sd-tag> contact (as measured by the number of <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Mdm34" ext_ids="P53083" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MDM34" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Mdm34</sd-tag>-<sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> puncta per cell) expanded in the Δ<sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="gene" role="intervention" text="vps39" ext_ids="851482" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">vps39</sd-tag> background relative to WT. However, the expansion did not occur on the background of Δ<sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="gene" role="intervention" text="vps39" ext_ids="851482" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">vps39</sd-tag> Δ<sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="gene" role="intervention" text="lam6" ext_ids="850761" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lam6</sd-tag>, demonstrating that <sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Lam6" ext_ids="850761" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Lam6</sd-tag> is necessary for <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="ERMES" ext_ids="GO:0032865" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="ERMES complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ERMES</sd-tag> expansion under these conditions. Scale bar represents 5 μm.</p><p>(B) Quantitation of (A). Bars represent the percentage of cells containing the specific number of puncta/cell out of total cells counted for the strain (for WT, n = 234 cells; for Δ<sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="gene" role="intervention" text="vps39" ext_ids="851482" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">vps39</sd-tag>, n = 246; for Δ<sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="gene" role="intervention" text="vps39" ext_ids="851482" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">vps39</sd-tag> Δ<sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="gene" role="intervention" text="lam6" ext_ids="850761" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lam6</sd-tag>, n = 271).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=15304"/></sd-panel><sd-panel panel_id="15305">(C) Fluorescent microscopy demonstrates that downregulating <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="subcellular" role="component" text="ERMES" ext_ids="GO:0032865" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="ERMES complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ERMES</sd-tag> <span>contacts (by growing <sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="gene" role="component" text="GALp" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GALp</sd-tag>-<sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="gene" role="component" text="MDM34" ext_ids="852654" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MDM34" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">MDM34</sd-tag> strains in <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="glucose" ext_ids="CHEBI:17234" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="glucose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glucose</sd-tag>) indeed caused expansion of</span> <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="subcellular" role="component" text="vCLAMP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">vCLAMP</sd-tag> (<sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Vps39" ext_ids="Q07468" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="VAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Vps39</sd-tag>). However, this expansion was diminished in a Δ<sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="gene" role="intervention" text="lam6" ext_ids="850761" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="LAM6" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lam6</sd-tag> background. Scale bar represents 5 μm (see also Figure S4).<graphic href="https://api.sourcedata.io/file.php?panel_id=15305"/></sd-panel></fig></article>

token_classification/10-1016_j-cmet-2013-04-014.xml

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+<article doi="10.1016/j.cmet.2013.04.014" abstract="Mutations in the glucocerebrosidase (gba) gene cause Gaucher disease (GD), the most common lysosomal storage disorder, and increase susceptibility to Parkinson's disease (PD). While the clinical and pathological features of idiopathic PD and PD related to gba (PD-GBA) mutations are very similar, cellular mechanisms underlying neurodegeneration in each are unclear. Using a mouse model of neuronopathic GD, we show that autophagic machinery and proteasomal machinery are defective in neurons and astrocytes lacking gba. Markers of neurodegeneration--p62/SQSTM1, ubiquitinated proteins, and insoluble α-synuclein--accumulate. Mitochondria were dysfunctional and fragmented, with impaired respiration, reduced respiratory chain complex activities, and a decreased potential maintained by reversal of the ATP synthase. Thus a primary lysosomal defect causes accumulation of dysfunctional mitochondria as a result of impaired autophagy and dysfunctional proteasomal pathways. These data provide conclusive evidence for mitochondrial dysfunction in GD and provide insight into the pathogenesis of PD and PD-GBA."><fig id="4677"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4677"/><sd-panel panel_id="14499"><span>(A) Autophagic markers from mixed <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="tissue" role="component" text="midbrain" ext_ids="UBERON:0001891" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="midbrain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">midbrain</sd-tag> <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag></span><sup>+/+</sup><span>, <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag></span><sup>+/−</sup><span>, and <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag></span><sup>−/−</sup> <span>cultures were analyzed via <sd-tag id="sdTag3" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag> using antibodies as indicated.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=14499"/></sd-panel><sd-panel panel_id="14500"><p>(B) Autophagic flux was analyzed in <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup> and <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> <sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="tissue" role="component" text="midbrain" ext_ids="UBERON:0001891" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="midbrain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">midbrain</sd-tag> <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neurons</sd-tag>. <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="cell_type" role="component" text="Neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">Neurons</sd-tag> were treated with 100 nM <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> and 1 μM <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> and flux assayed by comparing <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>I and <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>II levels via <sd-tag id="sdTag23" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag>. <sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="β-actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">β-actin</sd-tag> was used as a loading control.</p><p>(C) Densitometry analyzes of autophagy of (B) expressed as a ratio of <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>II/<sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>I. Error bars, ± SEM. <sup>*</sup>p &lt; 0.05.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14500"/></sd-panel><sd-panel panel_id="14501"><span>(D) Accumulation of <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q64337" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sqstm1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag>/<sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQSTM1" ext_ids="Q64337" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sqstm1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">SQSTM1</sd-tag> was analyzed via <sd-tag id="sdTag27" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.</span> <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="β-actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">β-actin</sd-tag> was used as a loading control.<graphic href="https://api.sourcedata.io/file.php?panel_id=14501"/></sd-panel><sd-panel panel_id="14502"><p>(E) <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="tissue" role="component" text="Midbrain" ext_ids="UBERON:0001891" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="midbrain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Midbrain</sd-tag> <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neurons</sd-tag> were treated with either 10 μM <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> or vehicle control <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag>. Proteins were extracted and analyzed via <sd-tag id="sdTag37" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag> and stained with anti-<sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P62983///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27a///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> antibodies.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14502"/></sd-panel><sd-panel panel_id="14503"><p>(F) <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Ubiquitin" ext_ids="P62984///P62983///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Uba52///Rps27a///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Ubiquitin</sd-tag> linkage of isolated <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="tissue" role="component" text="midbrain" ext_ids="UBERON:0001891" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="midbrain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">midbrain</sd-tag> analyzed using <sd-tag id="sdTag42" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag> with antibodies as indicated. <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="β-actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">β-actin</sd-tag> was used as a loading control.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14503"/></sd-panel><sd-panel panel_id="14504"><span>(G) Proteasomal activity (<sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="protein" role="assayed" text="chymotrypsin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">chymotrypsin</sd-tag> activity) was measured using the <sd-tag id="sdTag47" source="sdapi" category="assay" entity_type="" role="" text="Proteasome Glo assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Proteasome Glo assay</sd-tag> where activity is proportional to the released <sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="gene" role="reporter" text="luciferase" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">luciferase</sd-tag>. RFU, relative <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="gene" role="reporter" text="luciferase" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">luciferase</sd-tag> units. Data represent the mean ± SEM (n = 3, each experiment contained triplicates for each genotype).</span> <sup>*</sup><span>p &lt; 0.05.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=14504"/></sd-panel></fig><fig id="4678"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4678"/><sd-panel panel_id="14505"><p>(A) Levels of soluble and insoluble <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="protein" role="assayed" text="α-synuclein" ext_ids="O55042" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Snca" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">α-synuclein</sd-tag> from <sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="tissue" role="component" text="midbrain" ext_ids="UBERON:0001891" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="midbrain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">midbrain</sd-tag> of P1 <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup> and <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>. <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="molecule" role="component" text="TX-100" ext_ids="CHEBI:9750" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Triton X-100" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">TX-100</sd-tag> soluble and insoluble (<sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="molecule" role="component" text="SDS" ext_ids="CHEBI:8984" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sodium dodecyl sulfate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">SDS</sd-tag>/<sd-tag id="sdTag269" source="sdapi" category="entity" entity_type="molecule" role="component" text="Urea" ext_ids="CHEBI:16199" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="urea" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Urea</sd-tag>) factions were isolated and analyzed via <sd-tag id="sdTag61" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag> with <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="protein" role="assayed" text="α-synuclein" ext_ids="O55042" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Snca" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">α-synuclein</sd-tag> antibodies. <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="β-actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">β-actin</sd-tag> was used as a loading control.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14505"/></sd-panel><sd-panel panel_id="14506"><p>(B) Sagittal <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain stem" ext_ids="UBERON:0002298" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brainstem" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain stem</sd-tag> sections from <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup>, <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/−</sup>, and <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> were stained with <sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="protein" role="assayed" text="α-synuclein" ext_ids="O55042" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Snca" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">α-synuclein</sd-tag> antibodies. Scale bar, 1,000 μm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14506"/></sd-panel></fig><fig id="4679"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4679"/><sd-panel panel_id="14507"><p>(A) <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="Neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">Neurons</sd-tag> and <sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="astrocytes" ext_ids="CL:0000127" norm_text="" ext_dbs="CL" in_caption="True" ext_names="astrocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">astrocytes</sd-tag> from <sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup>, <sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/−</sup>, and <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> were stained with <sd-tag id="sdTag74" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag>. The mean florescence intensity in <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> was analyzed via <sd-tag id="sdTag76" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag> (n = 3, &gt;32 cells analyzed/experiment).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14507"/></sd-panel><sd-panel panel_id="14508"><p>(B) <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="cell_type" role="component" text="Neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">Neurons</sd-tag> from <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup> and <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> bathed in <sd-tag id="sdTag94" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag> containing recording solution and fluorescence intensity analyzed via <sd-tag id="sdTag95" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. After 1 min, 1 μM <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="oligomycin" ext_ids="CHEBI:25675" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oligomycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">oligomycin</sd-tag> was added followed by 1 μM <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> (n = 5, three cells analyzed/experiment).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14508"/></sd-panel><sd-panel panel_id="14509"><p>(C) <sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="cell_type" role="component" text="Neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">Neurons</sd-tag> from <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup> and <sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> incubated with 5 mM <sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="molecule" role="component" text="methyl pyruvate" ext_ids="CHEBI:51850" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="methyl pyruvate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">methyl pyruvate</sd-tag> 5 min prior to imaging. Cells bathed in 25 nM <sd-tag id="sdTag100" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag> and 5 mM <sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="molecule" role="component" text="methyl pyruvate" ext_ids="CHEBI:51850" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="methyl pyruvate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">methyl pyruvate</sd-tag> containing recording solution and fluorescence intensity analyzed via <sd-tag id="sdTag102" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. After 90 s, 1 μM <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="oligomycin" ext_ids="CHEBI:25675" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oligomycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">oligomycin</sd-tag> was added, followed by 1 μM <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> (n = 3, three cells analyzed/experiment).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14509"/></sd-panel><sd-panel panel_id="14510"><p>(D) As in (C), except cells were bathed in 10 mM <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="molecule" role="component" text="methyl succinate" ext_ids="CHEBI:75146" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="monomethyl succinate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">methyl succinate</sd-tag>, (n = 3, four cells/experiment). All data in this figure represent the mean ± SEM, <sup>*</sup>p &lt; 0.05. <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="cell_type" role="component" text="Neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">Neurons</sd-tag> from <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup> and <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> incubated with 5 mM methyl pyruvate 5 min prior to imaging. Cells bathed in 25 nM <sd-tag id="sdTag113" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag> and 5 mM methyl pyruvate containing recording solution and fluorescence intensity analyzed via <sd-tag id="sdTag115" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. After 90 s, 1 μM <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="oligomycin" ext_ids="CHEBI:25675" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oligomycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">oligomycin</sd-tag> was added, followed by 1 μM <sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> (n = 3, three cells analyzed/experiment).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14510"/></sd-panel></fig><fig id="4680"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4680"/><sd-panel panel_id="14511"><p>(A) <sd-tag id="sdTag129" source="sdapi" category="assay" entity_type="" role="" text="Oxygen consumption rates" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Oxygen consumption rates</sd-tag> of <sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup>, <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/−</sup>, and <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> mixed <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="tissue" role="component" text="midbrain" ext_ids="UBERON:0001891" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="midbrain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">midbrain</sd-tag> cultures. Basal <sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="oxygen" ext_ids="CHEBI:25805" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oxygen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">oxygen</sd-tag> consumption was measured over 3 min. The maximal (uncoupled) rate was measured via the addition of <sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> and the non<sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondrial" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondrial</sd-tag> <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="oxygen" ext_ids="CHEBI:25805" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oxygen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">oxygen</sd-tag> consumption analyzed via the addition of <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="antimycin A" ext_ids="CHEBI:22584" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="antimycin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">antimycin A</sd-tag> (n = 3, three runs/experiment).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14511"/></sd-panel><sd-panel panel_id="14512"><p>(B) <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Complex I" ext_ids="GO:0005747" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrial respiratory chain complex I" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Complex I</sd-tag>-<sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="NADH: Ubiquinone reductase" ext_ids="GO:0045257" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="succinate dehydrogenase complex (ubiquinone)" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">NADH: Ubiquinone reductase</sd-tag> activity from <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup>, <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/−</sup>, and <sd-tag id="sdTag137" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> <sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="tissue" role="component" text="brains" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brains</sd-tag> expressed as a ratio to <sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="subcellular" role="normalizing" text="citrate synthase" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">citrate synthase</sd-tag> (n = 3).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14512"/></sd-panel><sd-panel panel_id="14513"><p>(C) Complex II-III: <sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Succinate dehydeogenase" ext_ids="GO:0045273" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="respiratory chain complex II" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Succinate dehydeogenase</sd-tag>, <sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="cytochome c reductase" ext_ids="GO:0045275" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="respiratory chain complex III" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">cytochome c reductase</sd-tag> activity from <sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup>, <sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/−</sup>, and <sd-tag id="sdTag147" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> <sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="tissue" role="component" text="brains" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brains</sd-tag> expressed as a ratio to <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="subcellular" role="normalizing" text="citrate synthase" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">citrate synthase</sd-tag> (n = 3).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14513"/></sd-panel><sd-panel panel_id="14514"><p>(D) <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Complex IV" ext_ids="GO:0005751" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrial respiratory chain complex IV" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Complex IV</sd-tag> activity from <sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup>, <sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/−</sup>, and <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="tissue" role="component" text="brains" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brains</sd-tag> expressed as a ratio to <sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="subcellular" role="normalizing" text="citrate synthase" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">citrate synthase</sd-tag> (n = 3).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14514"/></sd-panel><sd-panel panel_id="14515"><p>(E) <sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="cell_type" role="component" text="Neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">Neurons</sd-tag> were treated with 3 nM <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="decylTPP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">decylTPP</sd-tag> and <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MitoQ10" ext_ids="11388331" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="Mitoquinone mesylate" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">MitoQ<sub>10</sub></sd-tag> for 48 hr and stained with <sd-tag id="sdTag169" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag> and fluorescence intensity analyzed via <sd-tag id="sdTag170" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag> (n = 3, &gt;16 cells/experiment).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14515"/></sd-panel><sd-panel panel_id="14516"><p>(F) <sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup>and <sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> cells treated with 3 nM <sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="decylTPP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">decylTPP</sd-tag> and <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MitoQ10" ext_ids="11388331" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="Mitoquinone mesylate" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">MitoQ<sub>10</sub></sd-tag> for 48 hr were subjected to <sd-tag id="sdTag177" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> using the indicted antibodies. All data in this figure represent the mean ± SEM, <sup>*</sup>p &lt; 0.05.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14516"/></sd-panel></fig><fig id="4681"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4681"/><sd-panel panel_id="14517"><p>(A) <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="Neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">Neurons</sd-tag> and <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="astrocytes" ext_ids="CL:0000127" norm_text="" ext_dbs="CL" in_caption="True" ext_names="astrocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">astrocytes</sd-tag> were <sd-tag id="sdTag182" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> for <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cytochrome c" ext_ids="P62897" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cycs" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cytochrome c</sd-tag> and stained with <sd-tag id="sdTag184" source="sdapi" category="assay" entity_type="" role="" text="Hoechst" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Hoechst</sd-tag>. Far left panels were additionally <sd-tag id="sdTag189" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> for <sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GFAP" ext_ids="P03995" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Gfap" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">GFAP</sd-tag> and <sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="protein" role="assayed" text="MAP2" ext_ids="P20357" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Map2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">MAP2</sd-tag> to mark <sd-tag id="sdTag190" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neurons</sd-tag> and <sd-tag id="sdTag191" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="astrocytes" ext_ids="CL:0000127" norm_text="" ext_dbs="CL" in_caption="True" ext_names="astrocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">astrocytes</sd-tag>. "A" in <sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="nucleus" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nucleus</sd-tag> denotes <sd-tag id="sdTag192" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="astrocytes" ext_ids="CL:0000127" norm_text="" ext_dbs="CL" in_caption="True" ext_names="astrocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">astrocytes</sd-tag>. Scale bar, 20 μm.</p><p>(B) Mitochondrial morphology was blind counted from cells in (A) with <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neurons</sd-tag> scored as <sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="protein" role="assayed" text="MAP2" ext_ids="P20357" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Map2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">MAP2</sd-tag> positive and <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="astrocytes" ext_ids="CL:0000127" norm_text="" ext_dbs="CL" in_caption="True" ext_names="astrocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">astrocytes</sd-tag> as <sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GFAP" ext_ids="P03995" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Gfap" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">GFAP</sd-tag> positive. A "normal" morphology is classified as a mixture of fused and fragmented <sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> that comprise a wild-type network. (n = 3; 100 cells counted/experiment).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14517"/></sd-panel><sd-panel panel_id="14518"><p>(C) Levels of morphology proteins from <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup>, <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/−</sup>, and <sd-tag id="sdTag203" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> isolated <sd-tag id="sdTag204" source="sdapi" category="entity" entity_type="subcellular" role="component" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> were analyzed via <sd-tag id="sdTag205" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> with the indicated antibodies.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14518"/></sd-panel><sd-panel panel_id="14519"><p>(D) <sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="tissue" role="component" text="Midbrain" ext_ids="UBERON:0001891" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="midbrain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Midbrain</sd-tag> <sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup>, <sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/−</sup>, and <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="cell_type" role="component" text="astrocytes" ext_ids="CL:0000127" norm_text="" ext_dbs="CL" in_caption="True" ext_names="astrocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">astrocytes</sd-tag> expressing <sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag><sup>K38A</sup> were <sd-tag id="sdTag219" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> for <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cytochrome c" ext_ids="P62897" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cycs" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cytochrome c</sd-tag> and <sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondrial" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondrial</sd-tag> morphologies analyzed; concurrently cells were stained with <sd-tag id="sdTag222" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag> and fluorescence intensity analyzed via <sd-tag id="sdTag223" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Scale bar, 20 μm (n = 3, &gt;15 cells/experiment). All data in this figure represent the mean ± SEM.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14519"/></sd-panel></fig><fig id="4682"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4682"/><sd-panel panel_id="14525"><p>(A) <sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="tissue" role="component" text="Midbrain" ext_ids="UBERON:0001891" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="midbrain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Midbrain</sd-tag> <sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="cell_type" role="component" text="astrocytes" ext_ids="CL:0000127" norm_text="" ext_dbs="CL" in_caption="True" ext_names="astrocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">astrocytes</sd-tag> were transfected with <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag233" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>, treated with 100 nM <sd-tag id="sdTag230" source="sdapi" category="entity" entity_type="molecule" role="component" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag>, and stained with <sd-tag id="sdTag231" source="sdapi" category="assay" entity_type="" role="" text="MitoTracker Red" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MitoTracker Red</sd-tag> and imaged using <sd-tag id="sdTag232" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14525"/></sd-panel><sd-panel panel_id="14527"><p>(B) <sd-tag id="sdTag237" source="sdapi" category="entity" entity_type="tissue" role="component" text="Midbrain" ext_ids="UBERON:0001891" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="midbrain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Midbrain</sd-tag> <sd-tag id="sdTag238" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup> and <sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neurons</sd-tag> and <sd-tag id="sdTag241" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="astrocytes" ext_ids="CL:0000127" norm_text="" ext_dbs="CL" in_caption="True" ext_names="astrocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">astrocytes</sd-tag> were transfected with <sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>-<sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Parkin" ext_ids="Q9WVS6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Park2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Parkin</sd-tag>. Half the transfected cells were treated for 1 hr with 10 μM <sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> and all bathed in <sd-tag id="sdTag243" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag> containing recording solution and imaged using <sd-tag id="sdTag244" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Scale bar, 20 μm.</p><p>(C) <sd-tag id="sdTag245" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag> fluorescence intensity of cells from (B) was analyzed via <sd-tag id="sdTag246" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Data represent the mean ± SEM, (n = 3, &gt;4 cells analyzed per experiment).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14527"/></sd-panel><sd-panel panel_id="14523"><p>(D) <sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Mitochondria</sd-tag> within <sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="tissue" role="component" text="midbrain" ext_ids="UBERON:0001891" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="midbrain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">midbrain</sd-tag> <sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neurons</sd-tag> were uncoupled by the addition of 10 μM <sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> for 1 and 6 hr. <sd-tag id="sdTag264" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PINK1" ext_ids="Q99MQ3" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Pink1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">PINK1</sd-tag> expression analyzed via <sd-tag id="sdTag257" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> on isolated <sd-tag id="sdTag258" source="sdapi" category="entity" entity_type="subcellular" role="component" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> from <sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>+/+</sup> and <sd-tag id="sdTag260" source="sdapi" category="entity" entity_type="gene" role="intervention" text="gba" ext_ids="14466" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gba" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">gba</sd-tag><sup>−/−</sup> <sd-tag id="sdTag261" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neurons" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neurons</sd-tag>. Mitochondrial CI subunit <sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="NDUFS4" ext_ids="Q9CXZ1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ndufs4" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">NDUFS4</sd-tag> was used as a loading control.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=14523"/></sd-panel></fig><fig id="4683"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=4683"/></fig></article>

token_classification/10-1038_26506.xml

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+<article doi="10.1038/26506" abstract="Autophagy is a process for the bulk degradation of proteins, in which cytoplasmic components of the cell are enclosed by double-membrane structures known as autophagosomes for delivery to lysosomes or vacuoles for degradation. This process is crucial for survival during starvation and cell differentiation. No molecules have been identified that are involved in autophagy in higher eukaryotes. We have isolated 14 autophagy-defective (apg) mutants of the yeast Saccharomyces cerevisiae and examined the autophagic process at the molecular level. We show here that a unique covalent-modification system is essential for autophagy to occur. The carboxy-terminal glycine residue of Apg12, a 186-amino-acid protein, is conjugated to a lysine at residue 149 of Apg5, a 294-amino-acid protein. Of the apg mutants, we found that apg7 and apg10 were unable to form an Apg5/Apg12 conjugate. By cloning APG7, we discovered that Apg7 is a ubiquitin-E1-like enzyme. This conjugation can be reconstituted in vitro and depends on ATP. To our knowledge, this is the first report of a protein unrelated to ubiquitin that uses a ubiquitination-like conjugation system. Furthermore, Apg5 and Apg12 have mammalian homologues, suggesting that this new modification system is conserved from yeast to mammalian cells."><fig id="2614"><title></title><label>figf1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2614"/><sd-panel panel_id="9785">Wild-type, <em><sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg12-1" ext_ids="852518" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/"><sd-pretag id="sdPretag14340161636180" parent-tag-id="9" class="component gene">apg12</sd-pretag>-1</sd-tag></em> mutant and Δ<sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg12" ext_ids="852518" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/"><em>apg12</em></sd-tag> <span>cells were cultured in <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="molecule" role="component" text="nitrogen" ext_ids="CHEBI:25555" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nitrogen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nitrogen</sd-tag>-starvation medium containing 1 mM <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="molecule" role="component" text="PMSF" ext_ids="CHEBI:8102" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phenylmethanesulfonyl fluoride" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMSF</sd-tag>. After incubation for <sd-tag id="sdTag5" source="sdapi" category="time" entity_type="" role="" text="6 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">6 h</sd-tag>, cells were observed under a <sd-tag id="sdTag6" source="sdapi" category="assay" entity_type="" role="" text="phase-contrast microscope" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">phase-contrast microscope</sd-tag>. Arrows indicate <sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic bodies" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic bodies</sd-tag>.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9785"/></sd-panel><sd-panel panel_id="9787"><strong>c</strong>, Wild-type (squares) and Δ<em><sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg12" ext_ids="852518" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg12</sd-tag></em> (circles) were cultured in <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="molecule" role="component" text="nitrogen" ext_ids="CHEBI:25555" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nitrogen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nitrogen</sd-tag><span>-starvation medium and their viability was determined by <sd-tag id="sdTag10" source="sdapi" category="assay" entity_type="" role="" text="phloxine B staining" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">phloxine B staining</sd-tag>.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9787"/></sd-panel><sd-panel panel_id="9788"><p><strong>d</strong>, Quantification of autophagic activity of wild-type and Δ<em><sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg12" ext_ids="852518" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg12</sd-tag></em> cells by <sd-tag id="sdTag15" source="sdapi" category="assay" entity_type="" role="" text="alkaline phosphatase (ALP) assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">alkaline phosphatase (ALP) assay</sd-tag> before (black bars) and after (white bars) <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nitrogen" ext_ids="CHEBI:25555" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nitrogen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nitrogen</sd-tag> starvation for <sd-tag id="sdTag16" source="sdapi" category="time" entity_type="" role="" text="4 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">4 h</sd-tag>. Error bars indicate s.d. of three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9788"/></sd-panel></fig><fig id="2615"><title></title><label>figf2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2615"/><sd-panel panel_id="9790"><p><strong>a</strong>, <strong>b</strong>, Lysates from Δ<em><sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="gene" role="component" text="apg12" ext_ids="852518" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg12</sd-tag></em> cells carrying only vector or 3 × <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-<sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="gene" role="intervention" text="APG12" ext_ids="852518" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APG12</sd-tag> (<strong>a</strong>), and Δ<em><sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg5" ext_ids="855954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg5</sd-tag></em>, <em><sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg7-1" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg7-1</sd-tag></em>, <em><sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg10-1" ext_ids="850684" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG10" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg10-1</sd-tag></em> and Δ<em><sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg1" ext_ids="852695" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg1</sd-tag></em> cells carrying 3 × <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-<sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg12" ext_ids="P38316" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg12</sd-tag> plasmid (<strong>b</strong>) were <sd-tag id="sdTag28" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> using anti-<sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> antibody. The positions of 3 × <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-<sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg12" ext_ids="P38316" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg12</sd-tag> and the larger product (asterisks) are indicated.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9790"/></sd-panel><sd-panel panel_id="9791"><strong>c</strong><span>, <sd-tag id="sdTag36" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag> analysis of wild-type and Δ</span><em><sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg12" ext_ids="852518" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg12</sd-tag></em> cells harbouring <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag><span>-<sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="gene" role="intervention" text="APG5" ext_ids="855954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APG5</sd-tag> plasmid.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9791"/></sd-panel><sd-panel panel_id="9792"><strong>d</strong>, Δ<em><sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="protein" role="assayed" text="apg5" ext_ids="Q12380" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">apg5</sd-tag></em> Δ<em><sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="protein" role="assayed" text="apg12" ext_ids="A6ZLF7///P38316" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ATG12///ATG12" ext_tax_ids="559292///307796" ext_tax_names="Saccharomyces cerevisiae S288C///Saccharomyces cerevisiae YJM789" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">apg12</sd-tag></em> <span>cells were co-transformed with <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>-</span><sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="gene" role="component" text="APG12" ext_ids="852518" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APG12</sd-tag> and <sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-<sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="gene" role="component" text="APG5" ext_ids="855954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APG5</sd-tag><span>. Their lysates were immunoprecipitated with anti-<sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> or anti-</span><sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> <span>antibodies and detected by <sd-tag id="sdTag42" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> using anti-<sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> antibody. The position of the crossreacting <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="subcellular" role="component" text="IgG" ext_ids="GO:0071735" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="IgG immunoglobulin complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">IgG</sd-tag> heavy chain is indicated</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9792"/></sd-panel></fig><fig id="2616"><title></title><label>figf3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2616"/><sd-panel panel_id="9794"><strong>b</strong>, Δ<em><sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg12" ext_ids="852518" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg12</sd-tag></em> cells were transformed with the mutant plasmids and their lysates were <sd-tag id="sdTag54" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> with anti-<sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> antibody.<graphic href="https://api.sourcedata.io/file.php?panel_id=9794"/></sd-panel><sd-panel panel_id="9795"><p><span>c</span><span>, Autophagic activity was measured as described for Fig. 1d.</span></p><graphic href="https://api.sourcedata.io/file.php?panel_id=9795"/></sd-panel><sd-panel panel_id="9796"><strong>d</strong><span>, Transport of pro-<sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="protein" role="assayed" text="API" ext_ids="P14904" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APE1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">API</sd-tag> to the <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="subcellular" role="component" text="vacuole" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuole</sd-tag> was examined by</span> <sd-tag id="sdTag67" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> <span>with anti-<sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="protein" role="assayed" text="API" ext_ids="P14904" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APE1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">API</sd-tag> antiserum. The positions of pro-<sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="protein" role="assayed" text="API" ext_ids="P14904" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APE1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">API</sd-tag> and mature <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="protein" role="assayed" text="API" ext_ids="P14904" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APE1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">API</sd-tag> are indicated.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9796"/></sd-panel></fig><fig id="2617"><title></title><label>figf4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2617"/><sd-panel panel_id="9798">Δ<em><sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="gene" role="intervention" text="APG5" ext_ids="855954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg5</sd-tag></em> cells were transformed with vector alone, wild-type <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="protein" role="assayed" text="APG5" ext_ids="Q12380" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">APG5</sd-tag> or APG5K149R, and then <sd-tag id="sdTag75" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> with anti-<sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> (<strong>b</strong>)<graphic href="https://api.sourcedata.io/file.php?panel_id=9798"/></sd-panel><sd-panel panel_id="9799"><span>Autophagic activity was determined by <sd-tag id="sdTag79" source="sdapi" category="assay" entity_type="" role="" text="alkaline phosphatase assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">alkaline phosphatase assay</sd-tag> (</span><strong>c</strong>).<graphic href="https://api.sourcedata.io/file.php?panel_id=9799"/></sd-panel><sd-panel panel_id="9800">Δ<em><sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg5" ext_ids="855954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg5</sd-tag></em> cells were transformed with vector alone, wild-type APG5 or APG5K149R, and then <sd-tag id="sdTag88" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> anti-<sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="protein" role="assayed" text="API" ext_ids="P14904" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="APE1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">API</sd-tag> (<strong>d</strong>).<graphic href="https://api.sourcedata.io/file.php?panel_id=9800"/></sd-panel></fig><fig id="2618"><title></title><label>figf5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2618"/><sd-panel panel_id="9802"><strong>c</strong>, <sd-tag id="sdTag91" source="sdapi" category="assay" entity_type="" role="" text="In vitro conjugation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><em>In vitro</em> conjugation</sd-tag> <span>of <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg5" ext_ids="Q12380" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg5</sd-tag> and</span> <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg12" ext_ids="P38316" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg12</sd-tag>. A cell lysate of Δ<em><sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="gene" role="component" text="apg12" ext_ids="852518" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg12</sd-tag></em> carrying <sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-<sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="gene" role="component" text="APG5" ext_ids="855954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APG5</sd-tag> (lane 1) was incubated with an equal amount of lysate from Δ<em><sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="gene" role="component" text="apg5" ext_ids="855954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg5</sd-tag></em> carrying <sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-<sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="gene" role="component" text="apg12" ext_ids="852518" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APG12</sd-tag> <span>(2 µ plasmid) (lane 2) at 30 °C with (lane 4-6) or without (lane 7) 5 mM <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="ATP" ext_ids="CHEBI:15422" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="ATP" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ATP</sd-tag>. Samples were mixed with SDS-sample buffer at the times indicated.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9802"/></sd-panel></fig><fig id="2619"><title></title><label>figf6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2619"/><sd-panel panel_id="9803"><span><sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="cell_type" role="component" text="Spheroplasts" ext_ids="CL:0000524" norm_text="" ext_dbs="CL" in_caption="True" ext_names="spheroplast" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">Spheroplasts</sd-tag> were generated from cells expressing either</span> <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-<span><sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Apg12" ext_ids="852518" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Apg12</sd-tag></span> or <sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-<span><sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Apg5" ext_ids="855954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Apg5</sd-tag></span>. Their lysates were mixed and layered on top of a 10-step (18-54 % w/w) sucrose gradient, and centrifuged at 174,000<em>g</em> for 2.5 h (ref. 29). Fifteen fractions were collected and the positions of free <sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg5" ext_ids="Q12380" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg5</sd-tag>, free <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg12" ext_ids="P38316" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg12</sd-tag> and <sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg5" ext_ids="Q12380" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG5" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg5</sd-tag>/<sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg12" ext_ids="P38316" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg12</sd-tag> <span>conjugate were examined by <sd-tag id="sdTag106" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag>. The peak fractions of <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="protein" role="assayed" text="alcohol dehydrogenase" ext_ids="S5RK20" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ADH1" ext_tax_ids="4932" ext_tax_names="Saccharomyces cerevisiae" ext_urls="https://www.uniprot.org/uniprot/">alcohol dehydrogenase</sd-tag> (ADH)(<sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="cytosol" ext_ids="GO:0005829" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="cytosol" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">cytosol</sd-tag>), <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ALP" ext_ids="P11491" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PHO8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">ALP</sd-tag> (</span><sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="vacuole" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuole</sd-tag><span>), <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Kex2" ext_ids="P13134" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="KEX2" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Kex2</sd-tag> (<sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="Golgi" ext_ids="GO:0005794" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="Golgi apparatus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Golgi</sd-tag>) and <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Sec12" ext_ids="P11655" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SEC12" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Sec12</sd-tag> (<sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="endoplasmic reticulum" ext_ids="GO:0005783" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">endoplasmic reticulum</sd-tag>) are indicated by arrows.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9803"/></sd-panel></fig></article>

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+<article doi="10.1038/35022595" abstract="Lysosome-associated membrane protein-2 (LAMP-2) is a highly glycosylated protein and an important constituent of the lysosomal membrane. Here we show that LAMP-2 deficiency in mice increases mortality between 20 and 40 days of age. The surviving mice are fertile and have an almost normal life span. Ultrastructurally, there is extensive accumulation of autophagic vacuoles in many tissues including liver, pancreas, spleen, kidney and skeletal and heart muscle. In hepatocytes, the autophagic degradation of long-lived proteins is severely impaired. Cardiac myocytes are ultrastructurally abnormal and heart contractility is severely reduced. These findings indicate that LAMP-2 is critical for autophagy. This theory is further substantiated by the finding that human LAMP-2 deficiency causing Danon's disease is associated with the accumulation of autophagic material in striated myocytes."><fig id="2624"><title></title><label>figf1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2624"/><sd-panel panel_id="9045"><strong>a</strong><span>, <sd-tag id="sdTag1" source="sdapi" category="assay" entity_type="" role="" text="Northern blot" ext_ids="OBI_0000860" norm_text="" ext_dbs="OBI" in_caption="True" ext_names="northern blot analysis" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/">Northern blot</sd-tag> analysis of</span> <em><sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="gene" role="assayed" text="lamp-2" ext_ids="16784" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">lamp-2</sd-tag></em> expression. Total RNA was hybridized using a <em><sd-pretag id="sdPretag14329093815770" parent-tag-id="2" class="assayed gene">lamp-2</sd-pretag></em> <span>cDNA2 probe and a murine <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="glyceraldehyde-3-phosphate dehydrogenase" ext_ids="14433" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gapdh" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">glyceraldehyde-3-phosphate dehydrogenase</sd-tag> probe.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9045"/></sd-panel><sd-panel panel_id="9046"><strong>b</strong><span>, <sd-tag id="sdTag9" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis of <sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P17047" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> expression. In control <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="liver" ext_ids="UBERON:0002107" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="liver" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">liver</sd-tag> and <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="kidney" ext_ids="UBERON:0002113" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="kidney" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">kidney</sd-tag> extracts the glycosylated <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P17047" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> molecules were detected. In <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LAMP-2" ext_ids="16784" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LAMP-2</sd-tag>-/- tissues no <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P17047" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> product was found.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9046"/></sd-panel><sd-panel panel_id="9047"><strong>c</strong>, Increased mortality in <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LAMP-2" ext_ids="16784" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LAMP-2</sd-tag> <span>deficient outbred (<sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="organism" role="assayed" text="C57B6/Jx129SV" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">C57B6/Jx129SV</sd-tag>) <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mice" ext_ids="10090///10088" norm_text="" ext_dbs="NCBI taxon///NCBI taxon" in_caption="True" ext_names="Mus musculus///mice" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy////http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>. Forty-two control (closed circles) and</span> <span><sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LAMP-2" ext_ids="16784" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LAMP-2</sd-tag></span><span>-deficient <sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mice" ext_ids="10090///10088" norm_text="" ext_dbs="NCBI taxon///NCBI taxon" in_caption="True" ext_names="Mus musculus///mice" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy////http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> (open circles) were monitored over <sd-tag id="sdTag19" source="sdapi" category="time" entity_type="" role="" text="300 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">300 days</sd-tag>.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9047"/></sd-panel><sd-panel panel_id="9048"><strong>d</strong>, Loss of weight in early dying (<em>n</em> = 7 males) and surviving <span><sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LAMP-2" ext_ids="16784" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LAMP-2</sd-tag></span>-deficient <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> (<em>n</em> = 11 males) in comparison with control <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> ( <em>n</em> <span>= 12 males) monitored for <sd-tag id="sdTag27" source="sdapi" category="time" entity_type="" role="" text="60 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">60 days</sd-tag> after birth.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9048"/></sd-panel></fig><fig id="2625"><title></title><label>figf2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2625"/><sd-panel panel_id="9057"><strong>a</strong><span>, Ultrastructure of <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vacuoles</sd-tag> (arrowheads) in <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="tissue" role="component" text="pancreatic acinar gland cells" ext_ids="UBERON:0001263" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="pancreatic acinus" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">pancreatic acinar gland cells</sd-tag> from a <sd-tag id="sdTag35" source="sdapi" category="time" entity_type="" role="" text="6.5-month-old" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">6.5-month-old</sd-tag></span> <span><sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LAMP-2" ext_ids="16784" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LAMP-2</sd-tag></span>-deficient <span><sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="mouse" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag></span>.<graphic href="https://api.sourcedata.io/file.php?panel_id=9057"/></sd-panel><sd-panel panel_id="9058"><strong>b</strong><span>, <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagic vacuoles</sd-tag> containing <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="glycogen" ext_ids="CHEBI:28087" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="glycogen" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glycogen</sd-tag> (g), <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="cytosol and cellular constituents" ext_ids="GO:0044445" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="cytosolic part" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">cytosol and cellular constituents</sd-tag> in a <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="cell_type" role="component" text="hepatocyte" ext_ids="CL:0000182" norm_text="" ext_dbs="CL" in_caption="True" ext_names="hepatocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">hepatocyte</sd-tag> of an <sd-tag id="sdTag44" source="sdapi" category="time" entity_type="" role="" text="8-day-old" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">8-day-old</sd-tag></span> <span><sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="gene" role="component" text="LAMP-2" ext_ids="16784" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LAMP-2</sd-tag></span>-/- <span><sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="mouse" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag></span><span>. m, <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochrondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochrondria</sd-tag>; bc, <sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="bile canaliculus" ext_ids="GO:0046691" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="intracellular canaliculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">bile canaliculus</sd-tag>.</span> <strong>c</strong>, Accumulation of numerous early <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vacuoles</sd-tag> in cultured <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="gene" role="component" text="LAMP-2" ext_ids="16784" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LAMP-2</sd-tag><span>-/- <sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="cell_type" role="component" text="hepatocytes" ext_ids="CL:0000182" norm_text="" ext_dbs="CL" in_caption="True" ext_names="hepatocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">hepatocytes</sd-tag>. Arrow, large late <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic vacuole" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic <sd-pretag id="sdPretag14329109232920" parent-tag-id="60">vacuole</sd-pretag></sd-tag> containing partially degraded material. Insert, magnification of the region indicated by an asterisk with typical early</span> <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vacuoles</sd-tag> containing undigested cellular constituents. Scale bars: <strong>a</strong>, 3.5 µm; <strong>b</strong>, 0.2 µm; <strong>c</strong>, 1.3 µm; insert, 0.9 µm.<graphic href="https://api.sourcedata.io/file.php?panel_id=9058"/></sd-panel></fig><fig id="2626"><title></title><label>figf3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2626"/><sd-panel panel_id="9052"><p><strong>a</strong>, <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Vacuole" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Vacuole</sd-tag> in a <sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="subcellular" role="component" text="fibre" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">fibre</sd-tag> of the <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="soleus muscle" ext_ids="UBERON:0001389" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="soleus muscle" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">soleus muscle</sd-tag>. <strong>b</strong>, Ultrastructure of a <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vacuole" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuole</sd-tag> in a <sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="cardiomyocyte" ext_ids="CL:0000746" norm_text="" ext_dbs="CL" in_caption="True" ext_names="cardiac muscle cell" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">cardiomyocyte</sd-tag>. Scale bars: <strong>a</strong>, 1 µm; <strong>b</strong>, 1.5 µm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9052"/></sd-panel><sd-panel panel_id="9053"><p><strong>c</strong>, Typical <sd-tag id="sdTag70" source="sdapi" category="assay" entity_type="" role="" text="original twitch recordings" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">original twitch recordings</sd-tag> of developed force of <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="heart muscles" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">heart muscles</sd-tag> from control (thin line) and <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LAMP-2" ext_ids="16784" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LAMP-2</sd-tag>-deficient (thick line) <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>. <strong>d</strong>, Average values of developed force. Preparations of <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LAMP-2" ext_ids="16784" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Lamp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LAMP-2</sd-tag> deficient <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> had a significantly lower baseline developed force at a stimulation frequency of 4 Hz and 10 Hz; <em>P</em>  0.01.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9053"/></sd-panel></fig><fig id="2627"><title></title><label>figf4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2627"/><sd-panel panel_id="9054"><p><strong>a</strong>, <sd-tag id="sdTag71" source="sdapi" category="assay" entity_type="" role="" text="Volume density" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Volume density</sd-tag> of early (Avi) and late (Avd) <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vacuoles</sd-tag> from four independent cultures. Examples of Avi and Avd are shown in <strong>b</strong> and <strong>c</strong>, respectively. Bars represent 0.4 µm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9054"/></sd-panel><sd-panel panel_id="9055"><p><strong>d</strong>, Labelling density of <sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cathepsin-D" ext_ids="P18242" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ctsd" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cathepsin-D</sd-tag> as estimated in two independent experiments. <strong>e</strong>, Labelling density of <sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LAMP-1</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9055"/></sd-panel><sd-panel panel_id="9056"><p><strong>f</strong>, <sd-tag id="sdTag86" source="sdapi" category="assay" entity_type="" role="" text="Degradation of long-lived proteins" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Degradation of long-lived proteins</sd-tag> followed over <sd-tag id="sdTag87" source="sdapi" category="time" entity_type="" role="" text="24 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">24 h</sd-tag> in amino acid and fetal-calf-serum-containing medium. <strong>g</strong>, Effect of <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino-acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino-acid</sd-tag> (AA) deprivation and <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3-methyladenine" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3-methyladenine</sd-tag> (MA) on protein degradation during <sd-tag id="sdTag90" source="sdapi" category="time" entity_type="" role="" text="4 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">4 h</sd-tag> of chase. The error bars in <strong>a</strong>, <strong>d</strong>, <strong>e</strong> and <strong>g</strong> represent s.e.m.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9056"/></sd-panel></fig></article>

token_classification/10-1038_35022604.xml

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+<article doi="10.1038/35022604" abstract="&quot;Lysosomal glycogen storage disease with normal acid maltase&quot; which was originally described by Danon et al., is characterized clinically by cardiomyopathy, myopathy and variable mental retardation. The pathological hallmark of the disease is intracytoplasmic vacuoles containing autophagic material and glycogen in skeletal and cardiac muscle cells. Sarcolemmal proteins and basal lamina are associated with the vacuolar membranes. Here we report ten unrelated patients, including one of the patients from the original case report, who have primary deficiencies of LAMP-2, a principal lysosomal membrane protein. From these results and the finding that LAMP-2-deficient mice manifest a similar vacuolar cardioskeletal myopathy, we conclude that primary LAMP-2 deficiency is the cause of Danon disease. To our knowledge this is the first example of human cardiopathy-myopathy that is caused by mutations in a lysosomal structural protein rather than an enzymatic protein."><fig id="2628"><title></title><label>figf1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2628"/><sd-panel panel_id="9110"><p><strong>a</strong>, The 2-bp deletion identified in exon 9b of patient 1. <strong>b</strong>, The T-to-A nonsense mutation in exon 4 of patient 2 (stop codon is underlined). <strong>c</strong>, Upper panel, intronic mutation in patient 3; lower panel, <sd-tag id="sdTag3" source="sdapi" category="assay" entity_type="" role="" text="sequencing" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">sequencing</sd-tag> of the <sd-tag id="sdTag1" source="sdapi" category="assay" entity_type="" role="" text="RT–PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RT-PCR</sd-tag> product in patient 3, showing exon-6 skipping. <strong>d</strong>, Upper panel, The G-to-A point mutation at the splice-donor site in intron 5 of patient 6; lower panel, <sd-tag id="sdTag2" source="sdapi" category="assay" entity_type="" role="" text="sequencing" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">sequencing</sd-tag> of the <sd-tag id="sdTag4" source="sdapi" category="assay" entity_type="" role="" text="RT–PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RT-PCR</sd-tag> product in patient 6, showing a 6-bp insertion at the junction between exons 5 and 6. The inserted sequence (underlined) is derived from the first six nucleotides of intron 5 (underlined), which creates a stop codon (dotted). Most probably, nucleotides 7 and 8, GT (double underlined), in intron 5 are alternatively recognized as a splice-donor site. <strong>e</strong>, Upper panel, the 10-bp deletion in patient 9. This mutation deletes four nucleotides from intron 5 and six from exon 6. Lower panel, sequence of the <sd-tag id="sdTag5" source="sdapi" category="assay" entity_type="" role="" text="RT–PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RT-PCR</sd-tag> product in patient 9 reveals the deletion of the 10 nucleotides at the 5′ end of exon 6. The 'AG' (double underlined) in exon 6 immediately after the genomic DNA deletion appears to be recognized as an alternative splice-acceptor site.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9110"/></sd-panel></fig><fig id="2629"><title></title><label>figf2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2629"/><sd-panel panel_id="9111"><p class="p1"><strong>Figure 2</strong> Representation of the mutant <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2b" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2b</sd-tag>. 'Normal' represents the <sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2b" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2b</sd-tag> amino-acid sequence. Because patient 1, who developed full DD symptoms, has a mutation in exon 9b, the <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2b" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2b</sd-tag> isoform is most probably responsible for DD. Residue 265, one of the putative disulphide-bond-creating cysteines, and two glycosylation sites are lost by exon-6 skipping in patient 3, which probably results in a significant change in the secondary structure. Black boxes represent the loops created between two cystein residues flanking each of the four loop regions; Y depicts a glycosylation site; hatched boxes show altered amino acids caused by frameshift mutations; dashes represent missing amino acids due to exon-6 skipping in patient 3. All of the other mutant proteins lack the transmembrane domain (grey bar) because of nonsense or frameshift mutations. Thus, those molecules cannot function as lysosomal 'membrane' proteins.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9111"/></sd-panel></fig><fig id="2630"><title></title><label>figf3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2630"/><sd-panel panel_id="9112"><p><strong>a</strong>, <sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="Skeletal muscle" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Skeletal muscle</sd-tag>. Muscle extracts from <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="organism" role="component" text="patients" ext_ids="9606" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Homo sapiens" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">patients</sd-tag> 1-6 and 10 and a control were <sd-tag id="sdTag10" source="sdapi" category="assay" entity_type="" role="" text="blotted" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">blotted</sd-tag> and labelled with antibodies against <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> (top panel) and <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="β-actin" ext_ids="P60709" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ACTB" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">β-actin</sd-tag> (bottom panel). <sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> is deficient in all muscles examined except the sample from patient 1 that showed a trace amount of protein, which is probably the <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2a" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2a</sd-tag> isoform. In support of this idea, <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2b" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2b</sd-tag> is the principal <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> species in skeletal muscle6. Numbers denote <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="organism" role="component" text="patients" ext_ids="9606" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Homo sapiens" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">patients</sd-tag> as in Table 1; C, control. <strong>b</strong>, <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="Heart" ext_ids="UBERON:0000948" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="heart" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Heart</sd-tag>. Protein was extracted from <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cardiac muscle" ext_ids="UBERON:0001133" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cardiac muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cardiac muscle</sd-tag> of patient 4 and a control, <sd-tag id="sdTag20" source="sdapi" category="assay" entity_type="" role="" text="blotted" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">blotted</sd-tag> onto a nitrocellulose membrane, and labelled with the antibodies against <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> (too panel) and <sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="β-actin" ext_ids="P60709" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ACTB" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">β-actin</sd-tag> (bottom panel). <sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> is deficient also in <sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cardiac muscle" ext_ids="UBERON:0001133" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cardiac muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cardiac muscle</sd-tag>. C, control; 4, patient 4.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9112"/></sd-panel></fig><fig id="2631"><title></title><label>figf4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2631"/><sd-panel panel_id="9113"><p><sd-tag id="sdTag25" source="sdapi" category="assay" entity_type="" role="" text="Serial transverse sections" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Serial transverse sections</sd-tag> of the <sd-tag id="sdTag26" source="sdapi" category="assay" entity_type="" role="" text="biopsied" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">biopsied</sd-tag><sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag> from six DD <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="organism" role="component" text="patients" ext_ids="9606" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Homo sapiens" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">patients</sd-tag>, and samples from a XMEA patient and a normal control, were <sd-tag id="sdTag28" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> with antibodies against <sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> and <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="protein" role="assayed" text="limp-I" ext_ids="Q14108" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SCARB2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">limp-I</sd-tag>. <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> is absent in all DD muscles (patient 6 shown here), whereas it is present in the XMEA <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag>. The antibody against <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="protein" role="assayed" text="limp-I" ext_ids="Q14108" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SCARB2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">limp-I</sd-tag> highlighted <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="subcellular" role="component" text="vacuoles" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuoles</sd-tag> in both DD and XMEA muscles. <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="protein" role="component" text="LAMP-1" ext_ids="P11279" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-1</sd-tag> antibody faintly stained both DD and XMEA muscles, suggesting that the expression level of <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="component" text="LAMP-1" ext_ids="P11279" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-1</sd-tag> might be lower in skeletal <sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag> than <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> or <sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="protein" role="assayed" text="limp-I" ext_ids="Q14108" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SCARB2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">limp-I</sd-tag> (data not shown). The <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag> from the patient without a <em>lamp-2</em> mutation also showed <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> deficiency on <sd-tag id="sdTag32" source="sdapi" category="assay" entity_type="" role="" text="immunohistochemistry" ext_ids="BAO_0000415" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunohistochemistry" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunohistochemistry</sd-tag> similar to genetically proven DD <sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="organism" role="component" text="patients" ext_ids="9606" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Homo sapiens" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">patients</sd-tag> with primary <sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag> deficiency (data not shown). The <sd-tag id="sdTag33" source="sdapi" category="assay" entity_type="" role="" text="immunohistochemical stains" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">immunohistochemical stains</sd-tag> of <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAMP-2" ext_ids="P13473" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-2</sd-tag></p>, <sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="protein" role="assayed" text="limp-I" ext_ids="Q14108" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SCARB2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">limp-I</sd-tag>, and <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="protein" role="component" text="LAMP-1" ext_ids="P11279" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAMP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAMP-1</sd-tag> in normal <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="muscle" ext_ids="UBERON:0002385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscle</sd-tag> <span>shows numerous tiny particles and accentuates <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="tissue" role="component" text="type 1 fibres" ext_ids="UBERON:0004057" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle fiber triad" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">type 1 fibres</sd-tag>. H&amp;amp;amp;E, <sd-tag id="sdTag35" source="sdapi" category="assay" entity_type="" role="" text="haematoxylin and eosin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">haematoxylin and eosin</sd-tag>, original magnification ×150.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9113"/></sd-panel></fig></article>

token_classification/10-1038_35044114.xml

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+<?xml version='1.0' encoding='UTF-8'?>
+<article doi="10.1038/35044114" abstract="Autophagy is a dynamic membrane phenomenon for bulk protein degradation in the lysosome/vacuole. Apg8/Aut7 is an essential factor for autophagy in yeast. We previously found that the carboxy-terminal arginine of nascent Apg8 is removed by Apg4/Aut2 protease, leaving a glycine residue at the C terminus. Apg8 is then converted to a form (Apg8-X) that is tightly bound to the membrane. Here we report a new mode of protein lipidation. Apg8 is covalently conjugated to phosphatidylethanolamine through an amide bond between the C-terminal glycine and the amino group of phosphatidylethanolamine. This lipidation is mediated by a ubiquitination-like system. Apg8 is a ubiquitin-like protein that is activated by an E1 protein, Apg7 (refs 7, 8), and is transferred subsequently to the E2 enzymes Apg3/Aut1 (ref. 9). Apg7 activates two different ubiquitin-like proteins, Apg12 (ref. 10) and Apg8, and assigns them to specific E2 enzymes, Apg10 (ref. 11) and Apg3, respectively. These reactions are necessary for the formation of Apg8-phosphatidylethanolamine. This lipidation has an essential role in membrane dynamics during autophagy."><fig id="2632"><title></title><label>figf1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2632"/><sd-panel panel_id="9126"><strong>a</strong><span>, <sd-tag id="sdTag1" source="sdapi" category="assay" entity_type="" role="" text="Phase partitioning" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Phase partitioning</sd-tag> of <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag>. Wild-type and Δ</span><em><sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg4" ext_ids="855498" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg4</sd-tag></em>Δ<em><sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg8</sd-tag></em> cells producing Apg8FG and Δ<em><sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg7</sd-tag></em> cells were subjected to phase partitioning (see Methods).<graphic href="https://api.sourcedata.io/file.php?panel_id=9126"/></sd-panel><sd-panel panel_id="9127"><strong>b</strong>, MALDI mass spectrum of <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="His6" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His<sub>6</sub></sd-tag>-<sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag>. Purified <sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="His6" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His<sub>6</sub></sd-tag>-<sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> (predominantly <span><sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag>FG</span>-X and a small amount of Apg8FG<span>) was extracted with 0.4% <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="molecule" role="component" text="β-octylglycoside" ext_ids="CHEBI:41128" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="B-OCTYLGLUCOSIDE" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">β-octylglycoside</sd-tag> from a polyacrylamide gel and desalted with</span> ZipTip<sub>C4</sub>(Millipore) before mass measurement. The principal MH+ ion signal at <em>m</em>/<em>z</em> 15,003 is shifted in mass by about +635 from the MH+ value corresponding to His<sub>6</sub>-Apg8FG.<graphic href="https://api.sourcedata.io/file.php?panel_id=9127"/></sd-panel><sd-panel panel_id="9129"><strong>c</strong><span>, <sd-tag id="sdTag18" source="sdapi" category="assay" entity_type="" role="" text="MS/MS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MS/MS</sd-tag> spectra of the C-terminal peptides of</span> <span><sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag>FG</span>-X (top) and Apg8FG (bottom). C-terminal fragments were generated from Apg8FG-X and Apg8FG <span>(see Methods). Each fragment that was observed only as non-18O-labelled signals was subjected to <sd-tag id="sdTag24" source="sdapi" category="assay" entity_type="" role="" text="MS/MS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MS/MS</sd-tag>. The <sd-tag id="sdTag25" source="sdapi" category="assay" entity_type="" role="" text="MS/MS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MS/MS</sd-tag> spectra, deconvoluted with MaxEnt3, were interpreted by SeqMS software26. Arrows show the sequences from the N and C terminus based on y″</span><sub><em>m</em></sub> and b<sub><em>l</em></sub> ions, respectively (where <em>m</em> and <em>l</em> <span>denote positions counted from the C and N terminus) that were produced by cleavage of peptide bonds during <sd-tag id="sdTag26" source="sdapi" category="assay" entity_type="" role="" text="MS/MS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MS/MS</sd-tag>. Amino acids shown in three-letter code denote <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="immonium ions" ext_ids="CHEBI:35286" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="iminium ion" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">immonium ions</sd-tag>. The nomenclature of these ions is as in previous work28.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9129"/></sd-panel></fig><fig id="2633"><title></title><label>figf2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2633"/><sd-panel panel_id="9134"><strong>d</strong>, <sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="molecule" role="component" text="Thioester" ext_ids="CHEBI:51277" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="thioester" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Thioester</sd-tag> formation between <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> and <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg7" ext_ids="P38862" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg7</sd-tag>. Cell extracts of Δ<em><sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg7</sd-tag></em>Δ<em><sd-tag id="sdTag137" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg8</sd-tag></em> cells expressing <sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg7" ext_ids="P38862" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg7</sd-tag>-<sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> and/or <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-<sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> from 2µ plasmids were <sd-tag id="sdTag142" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> with anti-<sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> antibody, and <sd-tag id="sdTag144" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> (IB) with anti-<sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> and anti-<sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> antibody. <sd-tag id="sdTag147" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DTT" ext_ids="CHEBI:18320" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="1,4-dithiothreitol" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DTT</sd-tag>-, no <sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DTT" ext_ids="CHEBI:18320" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="1,4-dithiothreitol" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DTT</sd-tag>; <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DTT" ext_ids="CHEBI:18320" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="1,4-dithiothreitol" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DTT</sd-tag>+, 100 mM <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DTT" ext_ids="CHEBI:18320" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="1,4-dithiothreitol" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DTT</sd-tag>; asterisk, <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag>-<sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg7" ext_ids="P38862" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg7</sd-tag> conjugate.<graphic href="https://api.sourcedata.io/file.php?panel_id=9134"/></sd-panel><sd-panel panel_id="9130"><p><strong>b</strong>, Interaction between <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> and <sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg7" ext_ids="P38862" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg7</sd-tag>. Δ<em><sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg7</sd-tag></em>Δ<em><sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg8</sd-tag></em> cells were transformed with <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="gene" role="component" text="APG7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APG7</sd-tag>-<sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> and/or <sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="gene" role="component" text="APG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APG8</sd-tag> on 2µ plasmids. Cell lysates were <sd-tag id="sdTag31" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> with anti-<sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> antibody, and <sd-tag id="sdTag32" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> with anti-<sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> or anti-<sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> antibody. <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> co-<sd-tag id="sdTag40" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> with <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg7" ext_ids="P38862" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg7</sd-tag>-<sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9130"/></sd-panel><sd-panel panel_id="9132"><p><strong>c</strong>, Effect of <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> C-terminal processing on the <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag>-<sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg7" ext_ids="P38862" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg7</sd-tag> interaction. Δ<em><sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="gene" role="component" text="apg4" ext_ids="855498" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg4</sd-tag></em> cells co-expressing <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="gene" role="component" text="Apg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Apg7</sd-tag>-<sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> and <sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-<sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="gene" role="component" text="Apg8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Apg8</sd-tag> (FGR, FG and F) from 2µ plasmids. FGR, wild-type <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag>; FG, <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> lacking C-terminal arginine; F, <sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> lacking C-terminal glycine and arginine. Cell lysates were <sd-tag id="sdTag55" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> with anti-<sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> antibody, and <sd-tag id="sdTag56" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> with anti-<sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> and anti-<sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> antibody.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9132"/></sd-panel></fig><fig id="2634"><title></title><label>figf3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2634"/><sd-panel panel_id="9135"><strong>b</strong>, Interaction between <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> <span>and <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg3" ext_ids="P40344" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg3</sd-tag>. Lysates of Δ</span><em><sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg3" ext_ids="855741" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg3</sd-tag></em> <span>cells expressing <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="protein" role="assayed" text="APG3" ext_ids="P40344" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">APG3</sd-tag> and/or</span> <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>-<span><sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="gene" role="intervention" text="APG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APG8</sd-tag></span> from 2µ plasmids were <sd-tag id="sdTag69" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> <span>with anti-<sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg3" ext_ids="P40344" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg3</sd-tag> antibody, and</span> <sd-tag id="sdTag71" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> <span>with anti-<sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg3" ext_ids="P40344" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg3</sd-tag> and anti-</span><sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> antibody.<graphic href="https://api.sourcedata.io/file.php?panel_id=9135"/></sd-panel><sd-panel panel_id="9136"><strong>c</strong>, Effect of mutated Cys 234 in <span><sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Apg3" ext_ids="855741" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Apg3</sd-tag></span> on the interaction between <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> and <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg3" ext_ids="P40344" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg3</sd-tag>. Lysates of Δ<em><sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg3" ext_ids="855741" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg3</sd-tag></em> cells expressing <sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>-<sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="protein" role="assayed" text="APG8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">APG8</sd-tag> and either wild-type (wt) <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="protein" role="assayed" text="APG3" ext_ids="P40344" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">APG3</sd-tag> or mutant <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="protein" role="assayed" text="APG3" ext_ids="P40344" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">APG3</sd-tag> (C234S and C234A) from 2µ plasmids were <sd-tag id="sdTag83" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> with anti-<sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> antibody, and <sd-tag id="sdTag85" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> with anti-<sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> and anti-<sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg3" ext_ids="P40344" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg3</sd-tag> antibodies.<graphic href="https://api.sourcedata.io/file.php?panel_id=9136"/></sd-panel><sd-panel panel_id="9137"><strong>d</strong><span>, <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="molecule" role="component" text="Thioester" ext_ids="CHEBI:51277" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="thioester" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Thioester</sd-tag> formation between</span> <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> and <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg3" ext_ids="P40344" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg3</sd-tag>. Δ<em><sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg3" ext_ids="855741" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg3</sd-tag></em>, Δ<em><sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg7</sd-tag></em> and Δ<em><sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg10" ext_ids="850684" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG10" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg10</sd-tag></em> cells were transformed with both <sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>-<sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="gene" role="component" text="APG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">APG8</sd-tag> and <sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="gene" role="component" text="Apg3" ext_ids="855741" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Apg3</sd-tag>, or only <sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg3" ext_ids="P40344" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg3</sd-tag>, on 2µ plasmids. Cell extracts were <sd-tag id="sdTag101" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> with anti-<sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> <span>antibody, and subjected to <sd-tag id="sdTag91" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> (IB) using anti-</span><sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> and anti-<sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg3" ext_ids="P40344" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg3</sd-tag> <span>antibody. <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DTT" ext_ids="CHEBI:18320" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="1,4-dithiothreitol" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DTT</sd-tag>-, no <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DTT" ext_ids="CHEBI:18320" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="1,4-dithiothreitol" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DTT</sd-tag>; <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DTT" ext_ids="CHEBI:18320" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="1,4-dithiothreitol" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DTT</sd-tag>+, 100 mM <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="DTT" ext_ids="CHEBI:18320" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="1,4-dithiothreitol" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DTT</sd-tag>; asterisk,</span> <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag>-<sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg3" ext_ids="P40344" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg3</sd-tag> conjugate; diamond, possible <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>-<sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Apg8</sd-tag> dimer.<graphic href="https://api.sourcedata.io/file.php?panel_id=9137"/></sd-panel></fig><fig id="2635"><title></title><label>figf4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2635"/><sd-panel panel_id="9138"><strong>a</strong>, <span><sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Apg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Apg7</sd-tag></span> and <span><sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Apg3" ext_ids="855741" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Apg3</sd-tag></span> are necessary for attachment of <sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182///A6ZKM4" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ATG8///ATG8" ext_tax_ids="307796///559292" ext_tax_names="Saccharomyces cerevisiae YJM789///Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Apg8</sd-tag> <span>to <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="molecule" role="component" text="PE" ext_ids="CHEBI:16038" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phosphatidylethanolamine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PE</sd-tag>. Δ</span><em>apg</em> <span>cell lysates were subjected to <sd-tag id="sdTag113" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-PAGE</sd-tag> containing 6 M <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="molecule" role="component" text="urea" ext_ids="CHEBI:16199" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="urea" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">urea</sd-tag>, and</span> <sd-tag id="sdTag118" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> with anti-<sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Apg8" ext_ids="P38182///A6ZKM4" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ATG8///ATG8" ext_tax_ids="307796///559292" ext_tax_names="Saccharomyces cerevisiae YJM789///Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Apg8</sd-tag> antibody.<graphic href="https://api.sourcedata.io/file.php?panel_id=9138"/></sd-panel><sd-panel panel_id="9139"><strong>b</strong>, Autophagic activity in <em><sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg3" ext_ids="855741" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg3</sd-tag></em> mutants. Wild-type, Δ<em><sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg3" ext_ids="855741" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg3</sd-tag></em> and <em><sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg3" ext_ids="855741" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg3</sd-tag></em><span>C243A cells were grown in rich medium (open bar) and subjected to <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nitrogen" ext_ids="CHEBI:25555" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nitrogen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nitrogen</sd-tag> starvation for <sd-tag id="sdTag125" source="sdapi" category="time" entity_type="" role="" text="4 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">4 h</sd-tag> (filled bar). The autophagic activity of each cell was assessed by measuring the <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="alkaline phosphatase" ext_ids="GO:1903293" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="phosphatase complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">alkaline phosphatase</sd-tag> activity. The</span> <em><sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg3" ext_ids="855741" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG3" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg3</sd-tag></em>C243A mutant showed defective autophagy.<graphic href="https://api.sourcedata.io/file.php?panel_id=9139"/></sd-panel></fig></article>

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+<article doi="10.1038/45257" abstract="The process of autophagy, or bulk degradation of cellular proteins through an autophagosomic-lysosomal pathway, is important in normal growth control and may be defective in tumour cells. However, little is known about the genetic mediators of autophagy in mammalian cells or their role in tumour development. The mammalian gene encoding Beclin 1, a novel Bcl-2-interacting, coiled-coil protein, has structural similarity to the yeast autophagy gene, apg6/vps30, and is mono-allelically deleted in 40-75% of sporadic human breast cancers and ovarian cancers. Here we show, using gene-transfer techniques, that beclin 1 promotes autophagy in autophagy-defective yeast with a targeted disruption of agp6/vps30, and in human MCF7 breast carcinoma cells. The autophagy-promoting activity of beclin 1 in MCF7 cells is associated with inhibition of MCF7 cellular proliferation, in vitro clonigenicity and tumorigenesis in nude mice. Furthermore, endogenous Beclin 1 protein expression is frequently low in human breast epithelial carcinoma cell lines and tissue, but is expressed ubiquitously at high levels in normal breast epithelia. Thus, beclin 1 is a mammalian autophagy gene that can inhibit tumorigenesis and is expressed at decreased levels in human breast carcinoma. These findings suggest that decreased expression of autophagy proteins may contribute to the development or progression of breast and other human malignancies."><fig id="2620"><title></title><label>figf1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2620"/><sd-panel panel_id="9066"><strong>a</strong><span>, <sd-tag id="sdTag1" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis of <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="organism" role="component" text="yeast" ext_ids="4932" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="yeast" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">yeast</sd-tag> cell lysates with polyclonal anti-<sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="protein" role="reporter" text="flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">flag</sd-tag> antibody to detect <sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="protein" role="reporter" text="flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">flag</sd-tag>-tagged human <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Beclin 1" ext_ids="Q14457" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Beclin 1</sd-tag> expression. Two-hundred micrograms of protein per lane was loaded. <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="organism" role="component" text="SEY6210" ext_ids="4932" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Saccharomyces cerevisiae" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">SEY6210</sd-tag>, wild-type <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="organism" role="component" text="yeast" ext_ids="4932" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="yeast" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">yeast</sd-tag>; <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="organism" role="component" text="JCY3000" ext_ids="4932" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Saccharomyces cerevisiae" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">JCY3000</sd-tag>, <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="organism" role="component" text="SEY6210" ext_ids="4932" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Saccharomyces cerevisiae" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">SEY6210</sd-tag> disrupted in</span> <em><sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg6" ext_ids="855983" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VPS30" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg6</sd-tag>/<sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="gene" role="intervention" text="vps30" ext_ids="855983" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VPS30" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">vps30</sd-tag></em><span>; (+) control, lysates of mammalian cells transfected with <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="protein" role="reporter" text="flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">flag</sd-tag>-</span><em><sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin 1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin 1</sd-tag></em>.<graphic href="https://api.sourcedata.io/file.php?panel_id=9066"/></sd-panel><sd-panel panel_id="9067"><strong>b</strong>, Autophagicbody formation in <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="organism" role="assayed" text="yeast" ext_ids="4932" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="yeast" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">yeast</sd-tag> <span>deprived of <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nitrogen" ext_ids="CHEBI:25555" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nitrogen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nitrogen</sd-tag> in the presence (+) and absence (-) of 1 mM <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PMSF" ext_ids="CHEBI:8102" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phenylmethanesulfonyl fluoride" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMSF</sd-tag>. Arrows denote cells that would be scored as positive in the experiment shown in</span> <strong>c</strong>.<graphic href="https://api.sourcedata.io/file.php?panel_id=9067"/></sd-panel><sd-panel panel_id="9068"><strong>c</strong>, Quantitative effects of <em><sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg6" ext_ids="855983" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VPS30" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg6</sd-tag>/<sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="gene" role="intervention" text="vps30" ext_ids="855983" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VPS30" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">vps30</sd-tag></em> and <em><sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin 1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin 1</sd-tag></em> transformation on autophagicbody formation in <em><sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="gene" role="intervention" text="apg6" ext_ids="855983" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VPS30" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">apg6</sd-tag>/<sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="gene" role="intervention" text="vps30" ext_ids="855983" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="VPS30" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">vps30</sd-tag></em>-disrupted <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="organism" role="assayed" text="yeast" ext_ids="4932" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="yeast" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">yeast</sd-tag> in the presence of <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="molecule" role="component" text="PMSF" ext_ids="CHEBI:8102" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phenylmethanesulfonyl fluoride" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PMSF</sd-tag><span>. Cells with one or more <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic bodies" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic bodies</sd-tag> within the <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vacuole" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuole</sd-tag> were scored as positive (see arrows in</span> <strong>b</strong><span>). A minimum of 100 cells was counted for each sample. Results represent the mean (±s.e.m.) percentage of cells with <sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic bodies" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic bodies</sd-tag> within the <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vacuole" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vacuole</sd-tag> for triplicate samples. Similar results were obtained in five independent experiments.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9068"/></sd-panel><sd-panel panel_id="9069"><strong>d</strong><span>, Sorting of vacuolar protein <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="protein" role="assayed" text="carboxypeptidase Y" ext_ids="P00729" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PRC1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">carboxypeptidase Y</sd-tag>, (CPY). p2CPY, precursor form; mCPY, sorted mature form.</span> <em>M</em><sub>r</sub>, relative molecular mass.<graphic href="https://api.sourcedata.io/file.php?panel_id=9069"/></sd-panel></fig><fig id="2621"><title></title><label>figf2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2621"/><sd-panel panel_id="9070"><p><strong>a</strong>-<strong>f</strong>, <sd-tag id="sdTag48" source="sdapi" category="assay" entity_type="" role="" text="Electron micrographs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Electron micrographs</sd-tag> of <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.control (clone 38) (<strong>a</strong>, <strong>b</strong>) and <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.<em><sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin1</sd-tag></em> (clone 17) cells (<strong>c</strong>- <strong>f</strong>) grown in <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag>-rich media (<strong>a</strong>, <strong>c</strong>) or subjected to <sd-tag id="sdTag52" source="sdapi" category="time" entity_type="" role="" text="4 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">4 h</sd-tag> of <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="tissue" role="intervention" text="serum" ext_ids="UBERON:0001977" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="serum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">serum</sd-tag> and <sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino-acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino-acid</sd-tag> deprivation (<strong>b</strong>, <strong>d</strong>-<strong>f</strong>). Asterisks in <strong>e</strong> and <strong>f</strong> denote <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vacuoles</sd-tag> that would be counted in the experiment shown in <strong>g</strong>. <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagic vacuoles</sd-tag> were defined as double-membrane vacuolar structures containing recognizable cytoplasmic contents. Scale bars, 1 µm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=9070"/></sd-panel><sd-panel panel_id="9071"><strong>g</strong>, Quantitative effects of <em><sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin 1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin 1</sd-tag></em> on basal and <sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag>-deprivation-induced autophagy of <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag> cells. Bars indicate mean (±s.e.m.) number of <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vacuoles</sd-tag> per cell for cells growing in normal media (black), for cells subjected to <sd-tag id="sdTag64" source="sdapi" category="time" entity_type="" role="" text="4 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">4 h</sd-tag> of <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="tissue" role="intervention" text="serum" ext_ids="UBERON:0001977" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="serum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">serum</sd-tag> and <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino-acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino-acid</sd-tag> <span>deprivation (grey), and for cells pre-treated for <sd-tag id="sdTag58" source="sdapi" category="time" entity_type="" role="" text="30 min" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">30 min</sd-tag> with 10 mM <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3-MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3-MA</sd-tag> and subjected to</span> <sd-tag id="sdTag67" source="sdapi" category="time" entity_type="" role="" text="4 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">4 h</sd-tag> of <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="tissue" role="intervention" text="serum" ext_ids="UBERON:0001977" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="serum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">serum</sd-tag> and <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino-acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino-acid</sd-tag> <span>deprivation in the presence of <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3-MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3-MA</sd-tag> (open). Mean was determined by counting the total number of</span> <sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vacuoles</sd-tag> in each cell for 100 cells per clone per treatment.<graphic href="https://api.sourcedata.io/file.php?panel_id=9071"/></sd-panel><sd-panel panel_id="9072"><strong>h</strong><span>, Comparison of the rates of <sd-tag id="sdTag73" source="sdapi" category="assay" entity_type="" role="" text="degradation of long-lived proteins" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">degradation of long-lived proteins</sd-tag> in</span> <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.control cells (squares, clone 38), <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.<em><sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin1</sd-tag></em> cells (circles, clone 17) and <sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.<em><sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin1</sd-tag></em><span>stop cells (triangles, clone 70), in <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="undefined" role="intervention" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> + 10%</span> <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="tissue" role="intervention" text="serum" ext_ids="UBERON:0001977" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="serum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">serum</sd-tag> <span>and complete <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino acids" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino acids</sd-tag> (open symbols, solid lines) in <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="undefined" role="intervention" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> alone (closed symbols, solid lines), and in <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="undefined" role="intervention" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> + 10 mM</span> <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3-MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3-MA</sd-tag> (closed symbols, dotted lines). Results are mean (±s.e.m.) of triplicate wells. Similar results were obtained in three independent experiments. Results shown with these clones are representative of results obtained with other clones analysed by electron microscopy in <strong>g</strong>.<graphic href="https://api.sourcedata.io/file.php?panel_id=9072"/></sd-panel></fig><fig id="2622"><title></title><label>figf3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2622"/><sd-panel panel_id="9073"><strong>a</strong>, <sd-tag id="sdTag87" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis of <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="protein" role="reporter" text="flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">flag</sd-tag>-tagged <em><sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin-1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin-1</sd-tag>-</em>transfected <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag> clones. C, <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.control cells (clone 38); St, <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.<em><sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin1</sd-tag></em>stop cells (clone 70). <em>M</em><sub>r</sub>, relative molecular mass.<graphic href="https://api.sourcedata.io/file.php?panel_id=9073"/></sd-panel><sd-panel panel_id="9074"><strong>b</strong>, <sd-tag id="sdTag95" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis of <sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="protein" role="reporter" text="flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">flag</sd-tag>-tagged <em><sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin1</sd-tag></em>stop-transfected <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag> clones. C, MCF.control cells (clone 38); B, <sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.<em><sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin1</sd-tag></em> cells (clone 1).<graphic href="https://api.sourcedata.io/file.php?panel_id=9074"/></sd-panel><sd-panel panel_id="9075"><strong>c</strong><span>, <sd-tag id="sdTag103" source="sdapi" category="assay" entity_type="" role="" text="Photomicrographs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Photomicrographs</sd-tag> of</span> <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.control cells (left panel, clone 38), <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>. <em><sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin1</sd-tag></em> cells (middle panel, clone 17) and <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.<em><sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin1</sd-tag></em><span>stop cells (right panel, clone 70) <sd-tag id="sdTag109" source="sdapi" category="time" entity_type="" role="" text="48 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">48 h</sd-tag> after seeding at similar densities.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9075"/></sd-panel><sd-panel panel_id="9076"><strong>d</strong><span>, <sd-tag id="sdTag110" source="sdapi" category="assay" entity_type="" role="" text="Proliferation" ext_ids="BAO_0002805" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="cell proliferation assay" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Proliferation</sd-tag> of</span> <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.control cells (clones 37 and 38; closed squares and circles, respectively, solid lines), <sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.<em><sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin1</sd-tag></em> cells (clones 1, 6, 17; open squares, circles, triangles, respectively, solid lines) and <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag>.<em><sd-tag id="sdTag115" source="sdapi" category="entity" entity_type="gene" role="intervention" text="beclin1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">beclin1</sd-tag></em>stop cells (clone 70, closed triangles, dotted line). Results represent mean Absorbance (<em>A</em>) (±s.e.m.) for six wells; similar results were obtained in three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=9076"/></sd-panel><sd-panel panel_id="9077"><strong>e</strong><span>, <sd-tag id="sdTag117" source="sdapi" category="assay" entity_type="" role="" text="Cell viability" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cell viability</sd-tag> of</span> <sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag> <span>clones determined by <sd-tag id="sdTag118" source="sdapi" category="assay" entity_type="" role="" text="trypan blue staining" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">trypan blue staining</sd-tag>. Symbols for each clone are as in</span> <strong>d</strong><graphic href="https://api.sourcedata.io/file.php?panel_id=9077"/></sd-panel><sd-panel panel_id="9078"><strong>f</strong><span>, <sd-tag id="sdTag121" source="sdapi" category="assay" entity_type="" role="" text="Clonigenicity" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Clonigenicity</sd-tag> in semisolid medium (<sd-tag id="sdTag122" source="sdapi" category="assay" entity_type="" role="" text="soft agar" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">soft agar</sd-tag>) of</span> <sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag> clones. Results are mean (±s.e.m.) for pooled triplicate wells from 3-4 independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=9078"/></sd-panel><sd-panel panel_id="9079"><strong>g</strong><span>, <sd-tag id="sdTag125" source="sdapi" category="assay" entity_type="" role="" text="Tumour formation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Tumour formation</sd-tag> in NCR nude <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> injected subcutaneously with</span> <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="cell_line" role="intervention" text="MCF7" ext_ids="CVCL_0031" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF7</sd-tag> <span>clones. Numbers on top of bar indicate number of autopsy-confirmed tumours at <sd-tag id="sdTag127" source="sdapi" category="time" entity_type="" role="" text="8 weeks" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">8 weeks</sd-tag> per number of <sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="organism" role="assayed" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> injected with each clone.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9079"/></sd-panel></fig><fig id="2623"><title></title><label>figf4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2623"/><sd-panel panel_id="9080"><strong>a</strong>, <sd-tag id="sdTag132" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> <span>analysis of human <sd-pretag id="sdPretag14331445579400" parent-tag-id="145"><sd-pretag id="sdPretag14331446602080" parent-tag-id="153">breast</sd-pretag> carcinoma</sd-pretag> cell lines. Results are from 8 representative cell lines out of a total of 11 analysed.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9080"/></sd-panel><sd-panel panel_id="9081"><strong>b</strong>, <sd-tag id="sdTag146" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> <span>analysis of matched normal <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="tissue" role="component" text="breast" ext_ids="UBERON:0000310" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="breast" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">breast</sd-tag> and <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="tissue" role="component" text="breast" ext_ids="UBERON:0000310" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="breast" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">breast</sd-tag> carcinoma tissue from <sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="organism" role="component" text="patients" ext_ids="9606" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Homo sapiens" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">patients</sd-tag> with sporadic invasive <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="tissue" role="component" text="breast" ext_ids="UBERON:0000310" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="breast" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">breast</sd-tag> carcinoma. Results are from 7 representative cases out of a total of 17 analysed. N, normal <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="tissue" role="component" text="breast" ext_ids="UBERON:0000310" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="breast" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">breast</sd-tag> tissue; T, tumour tissue;</span> <em>M</em><sub>r</sub>, relative molecular mass.<graphic href="https://api.sourcedata.io/file.php?panel_id=9081"/></sd-panel><sd-panel panel_id="9082"><strong>c</strong><span>, <sd-tag id="sdTag150" source="sdapi" category="assay" entity_type="" role="" text="Immunohistochemical analysis" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Immunohistochemical analysis</sd-tag> of paraffin-embedded sections of <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="breast tissue" ext_ids="UBERON:0000310" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="breast" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">breast tissue</sd-tag> from patient 441 shown in</span> <strong>b</strong>. Adjacent sections are stained with pre-immune 843 rabbit <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="tissue" role="normalizing" text="serum" ext_ids="UBERON:0001977" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="serum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">serum</sd-tag> (left column), 843 anti-<sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Beclin 1" ext_ids="Q14457" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Beclin 1</sd-tag><sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="tissue" role="normalizing" text="serum" ext_ids="UBERON:0001977" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="serum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">serum</sd-tag> <span>(middle column) and anti-<sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="cytokeratin" ext_ids="GO:0045095" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="keratin filament" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">cytokeratin</sd-tag> (right column). Top row shows low power view of region of <sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="breast" ext_ids="UBERON:0000310" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="breast" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">breast</sd-tag> containing tumour (T) and normal <sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="mammary epithelial duct" ext_ids="UBERON:0001765///UBERON:0003244" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="mammary duct///epithelium of mammary gland" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">mammary epithelial duct</sd-tag> (N). Middle row shows higher power view of normal <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="mammary epithelial duct" ext_ids="UBERON:0001765///UBERON:0003244" norm_text="" ext_dbs="Uberon///Uberon" in_caption="True" ext_names="mammary duct///epithelium of mammary gland" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_///https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">mammary epithelial duct</sd-tag>. Bottom row shows higher power view of tumour. Scale bars, 1 mm.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=9082"/></sd-panel></fig></article>

token_classification/10-1038_emboj-2009-113.xml

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+<article doi="10.1038/emboj.2009.113" abstract="Correction to:The EMBO Journal (2009) 28, 677–685. doi:10.1038/emboj.2009.8"><fig id="1840"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1840"/><sd-panel panel_id="4710"><b>(A)</b> <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag>-<sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="protein" role="reporter" text="eGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">eGFP</sd-tag>-<sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> cells were left untreated (Control) or treated with 5 μM <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (Rapa), 500 ng/ml <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> or 10 ng/ml <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TNF" ext_ids="P01375" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNF" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TNF</sd-tag> for 24 h. When indicated, 10 mM <sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag> or 5 μg/ml <sd-tag id="sdTag9">TRAIL‐R2 antagonist</sd-tag> antibody was added 1 h before the drugs. Representative confocal images (20 μm scale bars) and the percentages of cells with <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> translocation are shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=4710"/></sd-panel><sd-panel panel_id="4711"><b>(B)</b> <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag>-<sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="protein" role="reporter" text="eGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">eGFP</sd-tag>-<sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> cells were transfected with the indicated siRNAs for 48 h and analysed by <sd-tag id="sdTag19" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> (left), or stimulated with 500 ng/ml <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> for 24 h and analysed for <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="81631///84557///440738" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3B///MAP1LC3A///MAP1LC3C" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> translocation (right).<graphic href="https://api.sourcedata.io/file.php?panel_id=4711"/></sd-panel><sd-panel panel_id="4712"><b>(C)</b> <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag> cells left untreated (Control) or treated with 500 ng/ml <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> or 5 μM <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (Rapa) for 24 h were analysed for <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐I, <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐II and <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="tubulin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">tubulin</sd-tag> by <sd-tag id="sdTag34" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="molecule" role="component" text="Pepstatin A" ext_ids="CHEBI:7989" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Pepstatin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Pepstatin A</sd-tag> and <sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="molecule" role="component" text="E64d" ext_ids="CHEBI:30270" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="E64" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">E64d</sd-tag> were added to the cells 4 h before harvesting. Similar results were obtained in two independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=4712"/></sd-panel><sd-panel panel_id="4713"><b>(D)</b> <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag> cells were treated with 5 μM <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (Rapa) or indicated concentrations of <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> for 24 h, and the increase in the degradation of long‐lived proteins as compared with the untreated cultures (Control) was measured.<graphic href="https://api.sourcedata.io/file.php?panel_id=4713"/></sd-panel><sd-panel panel_id="4714"><b>(E)</b> <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag>-<sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="protein" role="reporter" text="eGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">eGFP</sd-tag>-<sd-tag id="sdTag47" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> cells transfected with the indicated siRNAs were left untreated 48 h later (Control) or treated with 500 ng/ml <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> for 24 h and analysed for the DNA content by <sd-tag id="sdTag54" source="sdapi" category="assay" entity_type="" role="" text="flow cytometry" ext_ids="BAO_0000005" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="flow cytometry" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">flow cytometry</sd-tag>. The percentage of apoptotic cells with sub‐G1 DNA content is shown. The values represent mean±s.d. for three (A, D) or four (B, E) independent experiments. <sup>*</sup><i>P</i>‐value 0.05, <sup>**</sup><i>P</i>‐value 0.01 and <sup>***</sup><i>P</i>‐value 0.001 as compared with control sample (A-left panel and D), with <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag>‐treated cells without anti‐<sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag>‐R2 (A-right panel) or with <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag>‐treated cells without siRNA (B, E).<graphic href="https://api.sourcedata.io/file.php?panel_id=4714"/></sd-panel></fig><fig id="1841"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1841"/><sd-panel panel_id="4715"><b>(A)</b> Protein lysates from <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag> cells left untreated or treated with 500 ng/ml <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> or 5 μM <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> (Rapa, positive control) for 24 h were analysed by <sd-tag id="sdTag67" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> for phosphorylated p70<sup>S6K</sup> (P‐p70<sup>S6K</sup>), total <sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="protein" role="assayed" text="70S6K" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">p70<sup>S6K</sup></sd-tag> and <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="GAPDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAPDH</sd-tag> (loading control).<graphic href="https://api.sourcedata.io/file.php?panel_id=4715"/></sd-panel><sd-panel panel_id="28538"><p>(<strong>B</strong>) <sd-tag id="sdTag307" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag> analysis of the levels of P‐<sd-tag id="sdTag308" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ACC" ext_ids="O00763///Q13085" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ACACB///ACACA" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ACC</sd-tag> and <sd-tag id="sdTag309" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="tubulin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">tubulin</sd-tag> (loading control) in lysates from <sd-tag id="sdTag310" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag> cells left untreated or treated with 500 ng/ml <sd-tag id="sdTag311" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> for 24 h, 1 mM <sd-tag id="sdTag313" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="AICAR" ext_ids="CHEBI:18406" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="AICA ribonucleotide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">AICAR</sd-tag> for 4 h (positive control) or 5 μM <sd-tag id="sdTag312" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> for 24 h (negative control).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=28538"/></sd-panel><sd-panel panel_id="4717"><b>(C)</b> <sd-tag id="sdTag78" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag> analysis of the level of P‐<sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ACC" ext_ids="Q13085///O00763" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ACACA///ACACB" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ACC</sd-tag> and <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="GAPDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAPDH</sd-tag> (loading control) in lysates from <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag> cells treated with 500 ng/ml <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> for the indicated times.<graphic href="https://api.sourcedata.io/file.php?panel_id=4717"/></sd-panel><sd-panel panel_id="4718"><b>(D)</b> <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag> cells were transfected with indicated siRNAs for 48 h and analysed by <sd-tag id="sdTag85" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> for the indicated proteins immediately (upper panel) or after additional 24 h (middle panel) or 2 h (lower panel) incubation with (+) or without (−) 500 ng/ml <sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=4718"/></sd-panel><sd-panel panel_id="4719"><b>(E)</b> <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag>-<sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="protein" role="reporter" text="eGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">eGFP</sd-tag>-<sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> cells transfected with indicated siRNAs for 48 h and incubated for an additional 24 h with or without 500 ng/ml <sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> were analysed for <sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> translocation (top) and the DNA content (bottom). The values represent mean±s.d. for four independent experiments. <sup>*</sup><i>P</i>‐value 0.05 and <sup>***</sup><i>P</i>‐value 0.001 as compared with <sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag>‐treated cells without siRNA. Similar results were obtained in two (A, B and D) or three (C, D) independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=4719"/></sd-panel></fig><fig id="1842"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1842"/><sd-panel panel_id="4720"><b>(A)</b> <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag>-<sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="reporter" text="eGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">eGFP</sd-tag>-<sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> cells were transfected with indicated siRNAs for 48 h and analysed for the indicated mRNAs (top) and proteins (bottom by <sd-tag id="sdTag106" source="sdapi" category="assay" entity_type="" role="" text="RT–PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RT-PCR</sd-tag> and <sd-tag id="sdTag111" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>, respectively. Similar results were obtained in three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=4720"/></sd-panel><sd-panel panel_id="4721"><b>(B)</b> <span><sd-tag id="sdTag316" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag></span>-<sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="protein" role="reporter" text="eGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">eGFP</sd-tag>-<sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> cells transfected with indicated siRNAs for 48 h, and left untreated or treated with 500 ng/ml <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> for 2 h, 10 μM <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="ionomycin" ext_ids="CHEBI:63954" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="ionomycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ionomycin</sd-tag> for 24 h or starved for <sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino acids" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino acids</sd-tag> and <sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="glucose" ext_ids="CHEBI:17234" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="glucose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glucose</sd-tag> for 24 h (starvation) were analysed for P‐<sd-tag id="sdTag296" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ACC" ext_ids="Q13085///O00763" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ACACA///ACACB" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ACC</sd-tag> and <sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="tubulin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">tubulin</sd-tag> (loading control) expression by <sd-tag id="sdTag130" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. Similar results were obtained in two independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=4721"/></sd-panel><sd-panel panel_id="4722"><b>(C)</b> Cells transfected as in (B) and left untreated or treated with 500 ng/ml <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag>, 10 μM <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="ionomycin" ext_ids="CHEBI:63954" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="ionomycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ionomycin</sd-tag> or starved for <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino acids" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino acids</sd-tag> and <sd-tag id="sdTag137" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="glucose" ext_ids="CHEBI:17234" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="glucose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glucose</sd-tag> for 24 h were analysed for <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9GZQ8///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> translocation. The values represent mean±s.d. of three independent experiments. <sup>***</sup><i>P</i>‐value 0.001 as compared with cells treated in a same way, but transfected without siRNA.<graphic href="https://api.sourcedata.io/file.php?panel_id=4722"/></sd-panel></fig><fig id="1843"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1843"/><sd-panel panel_id="4723"><b>(A)</b> The lysates of <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag> cells treated with 500 ng/ml <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> for the indicated times were analysed by <sd-tag id="sdTag153" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. The control lane (0 min <sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag>) originates from the same blot and has been treated and exposed identically. Similar results were obtained in three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=4723"/></sd-panel><sd-panel panel_id="4724"><b>(B, C)</b> The lysates of <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag>-<sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="protein" role="reporter" text="eGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">eGFP</sd-tag>-<sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> cells transfected with indicated siRNAs for 48 h and left untreated (−) or treated with 500 ng/ml <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> for 2 h were analysed by <sd-tag id="sdTag167" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. (C, lower panel) <sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag>-<sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="protein" role="reporter" text="eGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">eGFP</sd-tag>-<sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> cells were transfected with indicated siRNAs for 48 h and analysed for the indicated mRNAs by <sd-tag id="sdTag172" source="sdapi" category="assay" entity_type="" role="" text="RT–PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RT-PCR</sd-tag>. Similar results were obtained in two independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=4724"/></sd-panel><sd-panel panel_id="4725"><b>(D, E)</b> <span><sd-tag id="sdTag318" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag></span>-<sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="protein" role="reporter" text="eGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">eGFP</sd-tag>-<sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> cells were transfected with indicated siRNAs for 48 h, treated as in Figure 3C and analysed for <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> translocation (left) and sub‐G1 DNA content (right). The values represent mean±s.d. of a minimum of three independent experiments except for the right panel in E (two experiments). <sup>*</sup><i>P</i>‐value 0.05 and <sup>**</sup><i>P</i>‐value 0.01 as compared with cells treated in a same way, but transfected without siRNA.<graphic href="https://api.sourcedata.io/file.php?panel_id=4725"/></sd-panel></fig><fig id="1844"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1844"/><sd-panel panel_id="4726"><b>(A)</b> Protein lysates from <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag> cells left untreated (0) or treated with 50 ng/ml <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TNF" ext_ids="P01375" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNF" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TNF</sd-tag>, 500 ng/ml <sd-tag id="sdTag203" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> (positive control) or 10 ng/ml <sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="protein" role="intervention" text="IL‐1β" ext_ids="P01584" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IL1B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> for indicated times were analysed by <sd-tag id="sdTag204" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> for phosphorylated <sd-tag id="sdTag297" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ACC" ext_ids="O00763///Q13085" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ACACB///ACACA" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ACC</sd-tag> (P‐<sd-tag id="sdTag298" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ACC" ext_ids="O00763///Q13085" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ACACB///ACACA" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ACC</sd-tag><span>), phosphorylated <sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IκB" ext_ids="Q9BYH8///Q8NI38///O00221///Q15653///P25963" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="NFKBIZ///NFKBID///NFKBIE///NFKBIB///NFKBIA" ext_tax_ids="9606///9606///9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">IκB</sd-tag> (</span>P‐IκB) and <sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="GAPDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAPDH</sd-tag> (loading control). The values show the P‐<sd-tag id="sdTag299" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ACC" ext_ids="O00763///Q13085" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ACACB///ACACA" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ACC</sd-tag>/<sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="GAPDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAPDH</sd-tag> and P‐IkB/<sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="GAPDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAPDH</sd-tag> ratios as percentages of the ratios in untreated cells (left lanes) and are representative of two independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=4726"/></sd-panel><sd-panel panel_id="4727"><b>(B, C)</b> <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="MCF10A" ext_ids="CVCL_0598" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="MCF-10A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">MCF10A</sd-tag>-<sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="protein" role="reporter" text="eGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">eGFP</sd-tag>-<sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> cells left untreated or treated with 500 ng/ml <sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag>, 50 ng/ml <sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TNF" ext_ids="P01375" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNF" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TNF</sd-tag> or 10 ng/ml <sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="protein" role="intervention" text="IL‐1β" ext_ids="P01584" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="IL1B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> for 24 h were analysed for <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> translocation (B) and the DNA content (C). The values represent mean±s.d. for two independent experiments. <sup>**</sup><i>P</i>‐value 0.01 and <sup>***</sup><i>P</i>‐value 0.001 as compared with untreated cells.<graphic href="https://api.sourcedata.io/file.php?panel_id=4727"/></sd-panel></fig><fig id="1845"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1845"/><sd-panel panel_id="4728"><b>(A)</b> The lysates of <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="cell_line" role="component" text="hTERT–RPE1" ext_ids="CVCL_4388" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="hTERT-RPE1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">hTERT-RPE1</sd-tag> cells transfected with indicated siRNAs for 48 h and left untreated or treated with 500 ng/ml <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> for 2 h were analysed by <sd-tag id="sdTag222" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=4728"/></sd-panel><sd-panel panel_id="4729"><b>(B)</b> <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="hTERT–RPE1" ext_ids="CVCL_4388" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="hTERT-RPE1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">hTERT-RPE1</sd-tag>-<sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="protein" role="reporter" text="eGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">eGFP</sd-tag>-<sd-tag id="sdTag230" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> cells transfected with indicated siRNAs for 48 h were left untreated or treated with 500 ng/ml <sd-tag id="sdTag232" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> for 24 h and analysed for <sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> translocation (left) and sub‐G1 DNA content (middle) and <sd-tag id="sdTag235" source="sdapi" category="entity" entity_type="protein" role="assayed" text="AMPKα" ext_ids="P54646///Q13131" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="PRKAA2///PRKAA1" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">AMPKα</sd-tag> expression (right).<graphic href="https://api.sourcedata.io/file.php?panel_id=4729"/></sd-panel><sd-panel panel_id="4730"><b>(C)</b> <sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="cell_line" role="component" text="hTERT–RPE1" ext_ids="CVCL_4388" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="hTERT-RPE1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">hTERT-RPE1</sd-tag>-<sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="protein" role="reporter" text="eGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">eGFP</sd-tag>-<sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> cells were transfected with indicated siRNAs for 48 h and analysed for the indicated mRNAs (top). After 48 h, cells were left untreated or treated with 500 ng/ml <sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> for 2 h, and analysed for P‐<sd-tag id="sdTag300" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ACC" ext_ids="O00763///Q13085" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ACACB///ACACA" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ACC</sd-tag> and GAPDH (loading control) expression by <sd-tag id="sdTag251" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. Similar results were obtained in two independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=4730"/></sd-panel><sd-panel panel_id="4731"><b>(D)</b> Cells transfected as described in (C) and left untreated or treated with 500 ng/ml <sd-tag id="sdTag258" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50591" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TNFSF10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag>, 10 μM <sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="ionomycin" ext_ids="CHEBI:63954" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="ionomycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ionomycin</sd-tag> or starved for <sd-tag id="sdTag260" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino acids" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino acids</sd-tag> and <sd-tag id="sdTag261" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="glucose" ext_ids="CHEBI:17234" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="glucose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glucose</sd-tag> for 24 h were analysed for <sd-tag id="sdTag263" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> translocation.<graphic href="https://api.sourcedata.io/file.php?panel_id=4731"/></sd-panel><sd-panel panel_id="4732"><b>(E)</b> Lysates of wild‐type (WT) <sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> and <sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> with an inactive <sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TAK1" ext_ids="26409" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map3k7" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TAK1</sd-tag> knock‐in (<sd-tag id="sdTag282" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TAK1" ext_ids="26409" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map3k7" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TAK1</sd-tag>Δ) treated with 500 ng/ml <sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50592" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Tnfsf10" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> were analysed by <sd-tag id="sdTag284" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. Similar results were obtained in two independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=4732"/></sd-panel><sd-panel panel_id="4733"><b>(F)</b> WT and <sd-tag id="sdTag289" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TAK1" ext_ids="26409" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map3k7" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TAK1</sd-tag>Δ <sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> left untreated and treated with 250 or 500 ng/ml <sd-tag id="sdTag291" source="sdapi" category="entity" entity_type="protein" role="intervention" text="TRAIL" ext_ids="P50592" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Tnfsf10" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">TRAIL</sd-tag> were analysed for cell death by the LDH release assay. Similar results were obtained in two independent experiments (A, C and E). The values represent mean±s.d. for two (D) or a minimum of three independent experiments (B, F). <sup>*</sup><i>P</i>‐value 0.05, <sup>**</sup><i>P</i>‐value 0.01 and <sup>***</sup><i>P</i>‐value 0.001 as compared with cells treated in the same way, but transfected without siRNA (B, D) or the wild‐type cells (F).<graphic href="https://api.sourcedata.io/file.php?panel_id=4733"/></sd-panel></fig><fig id="1846"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1846"/></fig></article>

token_classification/10-1038_emboj-2009-242.xml

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+<article doi="10.1038/emboj.2009.242" abstract="The p53-inducible TIGAR protein functions as a fructose-2,6-bisphosphatase, promoting the pentose phosphate pathway and helping to lower intracellular reactive oxygen species (ROS). ROS functions in the regulation of many cellular responses, including autophagy--a response to stress conditions such as nutrient starvation and metabolic stress. In this study, we show that TIGAR can modulate ROS in response to nutrient starvation or metabolic stress, and functions to inhibit autophagy. The ability of TIGAR to limit autophagy correlates strongly with the suppression of ROS, with no clear effects on the mTOR pathway, and is p53 independent. The induction of autophagy in response to loss of TIGAR can function to moderate apoptotic response by restraining ROS levels. These results reveal a complex interplay in the regulation of ROS, autophagy and apoptosis in response to TIGAR expression, and shows that proteins similar to TIGAR that regulate glycolysis can have a profound effect on the autophagic response through ROS regulation."><fig id="1316"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1316"/><sd-panel panel_id="3036"><p><span><sd-tag id="sdTag388" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> regulates intracellular <sd-tag id="sdTag394" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="ROS" ext_ids="CHEBI:26523" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="reactive oxygen species" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ROS</sd-tag> levels in response to <sd-tag id="sdTag337" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation or metabolic stress. (A) <sd-tag id="sdTag393" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="ROS" ext_ids="CHEBI:26523" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="reactive oxygen species" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ROS</sd-tag> levels in <sd-tag id="sdTag389" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably over-expressing <sd-tag id="sdTag399" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>-tagged-<sd-tag id="sdTag390" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> (clones <sd-tag id="sdTag391" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag>#5 and <sd-tag id="sdTag392" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag>#7) or control cells (clones Cont#1 and Cont#3) left untreated, after 6 h of <sd-tag id="sdTag338" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation or 24 h of metabolic stress. <sd-tag id="sdTag395" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="ROS" ext_ids="CHEBI:26523" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="reactive oxygen species" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ROS</sd-tag> levels were measured by <sd-tag id="sdTag398" source="sdapi" category="assay" entity_type="" role="" text="flow cytometry" ext_ids="BAO_0000005" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="flow cytometry" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">flow cytometry</sd-tag> after <sd-tag id="sdTag397" source="sdapi" category="assay" entity_type="" role="" text="DCF" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DCF</sd-tag> treatment. The results are expressed as the mean <sd-tag id="sdTag396" source="sdapi" category="assay" entity_type="" role="" text="DCF" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DCF</sd-tag> fluorescence (and standard deviation), from three independent experiments.</span></p><graphic href="https://api.sourcedata.io/file.php?panel_id=3036"/></sd-panel><sd-panel panel_id="3037"><sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> regulates intracellular <sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="ROS" ext_ids="CHEBI:26523" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="reactive oxygen species" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ROS</sd-tag> <span>levels in response to <sd-tag id="sdTag324" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation or metabolic stress.(B) Basal, <sd-tag id="sdTag327" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation-induced (</span>5 h) or metabolic stress-induced (18 h) <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="ROS" ext_ids="CHEBI:26523" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="reactive oxygen species" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ROS</sd-tag> levels in <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells in the presence of either scrambled, <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNA1 or <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNA2, measured by <sd-tag id="sdTag15" source="sdapi" category="assay" entity_type="" role="" text="flow cytometry" ext_ids="BAO_0000005" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="flow cytometry" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">flow cytometry</sd-tag> after <sd-tag id="sdTag400" source="sdapi" category="assay" entity_type="" role="" text="DCF" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DCF</sd-tag> treatment. The results are expressed as the mean intensity of cell fluorescence (and standard deviation). <sup>*</sup> <span>represents significant difference from control conditions (P&lt;0.05).</span><graphic href="https://api.sourcedata.io/file.php?panel_id=3037"/></sd-panel></fig><fig id="1317"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1317"/><sd-panel panel_id="3038"><p><sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> expression modulates autophagy in response to <sd-tag id="sdTag328" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation or metabolic stress. (A) (Left panel) <sd-tag id="sdTag411" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag> images of the fluorescence in <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably over-expressing <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>-tagged-<sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> (clone <sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag>#7) or control cells (clone Cont#1) and infected with an <sd-tag id="sdTag332" source="sdapi" category="entity" entity_type="organism" role="component" text="adenovirus" ext_ids="10535" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Adenovirus" ext_tax_ids="10535" ext_tax_names="unidentified adenovirus" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">adenovirus</sd-tag> expressing <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> for 16 h. Cells were then left untreated, exposed to <sd-tag id="sdTag329" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 6 h or to metabolic stress for 24 h. (Right panel) Quantitation of the percentage of <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-positive cells displaying <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> puncta from three independent experiments. The mean values with standard deviation are presented.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3038"/></sd-panel><sd-panel panel_id="3039"><p><sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> expression modulates autophagy in response to <sd-tag id="sdTag333" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation or metabolic stress.(B) (Left panel) <sd-tag id="sdTag414" source="sdapi" category="assay" entity_type="" role="" text="Confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Confocal microscopy</sd-tag> images of the fluorescence in <sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> and transfected with scrambled or <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNAs. After 48 h transfection, cells were then left untreated, exposed to <sd-tag id="sdTag334" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 5 h or to metabolic stress for 18 h. (Right panel) Quantitation of the percentage of <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-positive cells displaying <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> puncta from three independent experiments. The mean values with standard deviation are presented.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3039"/></sd-panel><sd-panel panel_id="3040"><p><sd-tag id="sdTag341" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> expression modulates autophagy in response to <sd-tag id="sdTag342" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation or metabolic stress. (C) (Left panel) <sd-tag id="sdTag87" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> showing the expression levels of endogenous <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-I, <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-II and <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TIGAR" ext_ids="Q9NQ88" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TIGAR</sd-tag> in <sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells transfected with scrambled or <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNAs, and 48 h later exposed to <sd-tag id="sdTag343" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 0, 2.5 and 6 h. (Middle panel) <sd-tag id="sdTag86" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> showing the expression levels of endogenous <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-I, <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-II and <sd-tag id="sdTag344" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> in <sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> stably over-expressing <sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>-tagged-<sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> (clones <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag>#5 and <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag>#7) or control cells (clones Cont#1 and Cont#3) and left untreated. (Right panel) <sd-tag id="sdTag90" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> showing the expression levels of <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag>, <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="protein" role="assayed" text="COX-IV" ext_ids="P13073" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="COX4I1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">COX-IV</sd-tag> and <sd-tag id="sdTag345" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> in <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells transfected with scrambled or <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNAs and left untreated. <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="Actin" ext_ids="P60709" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ACTB" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Actin</sd-tag> expression was examined as a loading control.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3040"/></sd-panel><sd-panel panel_id="3041"><span><sd-tag id="sdTag386" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TIGAR" ext_ids="Q9NQ88" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TIGAR</sd-tag></span> expression modulates autophagy in response to <sd-tag id="sdTag349" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation or metabolic stress.(D) <sd-tag id="sdTag96" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> showing the expression levels of endogenous <span><sd-tag id="sdTag387" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TIGAR" ext_ids="Q9NQ88" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TIGAR</sd-tag></span> in <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells after exposure to <sd-tag id="sdTag350" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation or metabolic stress for 0, 1, 3, 5 and 8 h; <sup>*</sup> <span>represents significant difference from control conditions (P&lt;0.05);</span> <sup>#</sup> represents a lack of significant difference from control conditions (P&gt;0.05).<graphic href="https://api.sourcedata.io/file.php?panel_id=3041"/></sd-panel></fig><fig id="1318"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1318"/><sd-panel panel_id="3042"><sd-tag id="sdTag354" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> expression modulates autophagy independently of p53. (A) Quantitation of the percentage of <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-positive cells displaying <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> puncta. <span><sd-tag id="sdTag417" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag></span> cells stably expressing <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> were transfected with scrambled or <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNAs, and 48 h after transfection, cells were left untreated (t0) or treated with <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bafilomycin A1</sd-tag> (100 nM) for 1 or 2 h (t1 and t2). The percentage of cells with <sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta was calculated at the indicated time points. Data are shown as the mean and standard deviation from three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=3042"/></sd-panel><sd-panel panel_id="3043"><p>(B) Quantitation of the percentage of <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-positive cells displaying <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> puncta. <sd-tag id="sdTag418" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing <sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> were cotransfected with scrambled or <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNAs, and scrambled or <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="gene" role="intervention" text="p53" ext_ids="7157" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TP53" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">p53</sd-tag> siRNA. After 48 h transfection, cells were left untreated or exposed for 5 h to <sd-tag id="sdTag356" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation. The percentage of cells with <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta was calculated, and data are shown as the mean and standard deviation from three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3043"/></sd-panel><sd-panel panel_id="3044"><p>(C) <sd-tag id="sdTag129" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> showing the expression levels of endogenous <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p53" ext_ids="P04637" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TP53" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p53</sd-tag> and <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TIGAR" ext_ids="Q9NQ88" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TIGAR</sd-tag> in <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells cotransfected with scrambled or <sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNAs, and scrambled or <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="gene" role="intervention" text="p53" ext_ids="7157" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TP53" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">p53</sd-tag> siRNA, and 48 h later exposed to <sd-tag id="sdTag357" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 5 h. Actin expression was examined as a loading control.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3044"/></sd-panel><sd-panel panel_id="3045"><p>(D) Quantitation of the percentage of <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-positive cells displaying <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> puncta. <sd-tag id="sdTag419" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing <sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> were cotransfected with scrambled or <sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNAs, and scrambled or <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRAM" ext_ids="55332" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="DRAM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRAM</sd-tag> siRNA1/2. After 48 h transfection, cells were left untreated or exposed for 5 h to <sd-tag id="sdTag358" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation. The percentage of cells with <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta was calculated, and data are shown as the mean and standard deviation from three independent experiments; <sup>*</sup> represents significant difference from starved control conditions (P&lt;0.05); @ represents significant difference from untreated control conditions (P&lt;0.05); <sup>#</sup> represents a lack of significant difference from control conditions (P&gt;0.05).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3045"/></sd-panel></fig><fig id="1319"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1319"/><sd-panel panel_id="3046"><p>(A) <sd-tag id="sdTag420" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells were left untreated, exposed to <sd-tag id="sdTag359" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 6 h or to metabolic stress for 24 h, with or without treatment with <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="AO1" ext_ids="CHEBI:28939///CHEBI:29073" norm_text="" ext_dbs="ChEBI///ChEBI" in_caption="True" ext_names="N-acetyl-L-cysteine///L-ascorbic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=///http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">AO1</sd-tag> (<sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="NAC" ext_ids="CHEBI:28939" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-acetyl-L-cysteine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">NAC</sd-tag> (2 mM) and <sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="L-ascorbic acid" ext_ids="CHEBI:29073" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="L-ascorbic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">L-ascorbic acid</sd-tag> (2 mM)) for 24 h. The percentage of cells with <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta was calculated, and data are shown as the mean and standard deviation from three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3046"/></sd-panel><sd-panel panel_id="3047"><p>(B) (Left panel) <sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="ROS" ext_ids="CHEBI:26523" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="reactive oxygen species" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ROS</sd-tag> levels in <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells left untreated or treated with 0.5 or 1 mM of <sd-tag id="sdTag360" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="H2O2" ext_ids="CHEBI:16240" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="hydrogen peroxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">H2O2</sd-tag> for 24 h. <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="ROS" ext_ids="CHEBI:26523" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="reactive oxygen species" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ROS</sd-tag> levels were measured by <sd-tag id="sdTag167" source="sdapi" category="assay" entity_type="" role="" text="flow cytometry" ext_ids="BAO_0000005" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="flow cytometry" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">flow cytometry</sd-tag> after <sd-tag id="sdTag402" source="sdapi" category="assay" entity_type="" role="" text="DCF" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DCF</sd-tag> treatment. The results are expressed as the mean <sd-tag id="sdTag403" source="sdapi" category="assay" entity_type="" role="" text="DCF" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DCF</sd-tag> fluorescence (and standard deviation) from three independent experiments. (Right panel) Quantitation of the percentage of <sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta positive cells for cells treated as described above. Data are shown as the mean and standard deviation from three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3047"/></sd-panel><sd-panel panel_id="3048"><p>(C) Quantitation of the percentage of <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="protein" role="component" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta positive cells. <sd-tag id="sdTag421" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing <sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag177" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> were transfected with vector pCHER1A expressing the <sd-tag id="sdTag404" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag> gene as control, or expression plasmids for <sd-tag id="sdTag178" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>-tagged-<sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> or <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>-tagged-<sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FBPase-2" ext_ids="114508" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fbp2" ext_tax_ids="10116" ext_tax_names="Rattus norvegicus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FBPase-2</sd-tag>. After 48 h transfection, cells were left untreated, exposed to <sd-tag id="sdTag361" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 6 h or to metabolic stress for 24 h, with or without treatment with <sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="AO1" ext_ids="CHEBI:28939///CHEBI:29073" norm_text="" ext_dbs="ChEBI///ChEBI" in_caption="True" ext_names="N-acetyl-L-cysteine///L-ascorbic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=///http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">AO1</sd-tag> (<sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="NAC" ext_ids="CHEBI:28939" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-acetyl-L-cysteine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">NAC</sd-tag> (2 mM) and <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="L-ascorbic acid" ext_ids="CHEBI:29073" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="L-ascorbic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">L-ascorbic acid</sd-tag> (2 mM)) for 24 h. The percentage of cells with <sd-tag id="sdTag189" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag190" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9GZQ8///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta was calculated, and data are shown as the mean and standard deviation from three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3048"/></sd-panel><sd-panel panel_id="3049"><p>(D) Quantitation of the percentage of <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta positive cells. Cells were left untreated, exposed to <sd-tag id="sdTag364" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 6 h with or without treatment with <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="AO1" ext_ids="CHEBI:28939///CHEBI:29073" norm_text="" ext_dbs="ChEBI///ChEBI" in_caption="True" ext_names="N-acetyl-L-cysteine///L-ascorbic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=///http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">AO1</sd-tag> (<sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="NAC" ext_ids="CHEBI:28939" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-acetyl-L-cysteine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">NAC</sd-tag> (2 mM) and <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="L-ascorbic acid" ext_ids="CHEBI:29073" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="L-ascorbic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">L-ascorbic acid</sd-tag> (2 mM)), <sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="AO2" ext_ids="448288" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="CHEMBL354739" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">AO2</sd-tag> (<sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="glutathione ethyl ester" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">glutathione ethyl ester</sd-tag> (4 mM)) or <sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="AO3" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">AO3</sd-tag> (<sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="ethyl pyruvate" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">ethyl pyruvate</sd-tag> (4 mM)) for 24 h. <sd-tag id="sdTag408" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably expressing <sd-tag id="sdTag204" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> were transfected with vector pCHER1A expressing the <sd-tag id="sdTag407" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag> gene as control, or expression plasmid for <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>-tagged-<sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag>. After 48 h transfection, cells were treated. The percentage of cells with <sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta was calculated, and data are shown as the mean and standard deviation from three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3049"/></sd-panel><sd-panel panel_id="3050"><p>(E) (Left panel) Quantitation of the percentage of <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta positive cells. Cells were left untreated, exposed to <sd-tag id="sdTag367" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 5 h or to metabolic stress for 18 h, with or without treatment with <sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="AO1" ext_ids="CHEBI:28939///CHEBI:29073" norm_text="" ext_dbs="ChEBI///ChEBI" in_caption="True" ext_names="N-acetyl-L-cysteine///L-ascorbic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=///http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">AO1</sd-tag> (<sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="NAC" ext_ids="CHEBI:28939" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-acetyl-L-cysteine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">NAC</sd-tag> (2 mM) and <sd-tag id="sdTag422" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="L-ascorbic acid" ext_ids="CHEBI:29073" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="L-ascorbic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">L-ascorbic acid</sd-tag> (2 mM)) for 24 h. <sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably over-expressing <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> in the presence of either scrambled, <sd-tag id="sdTag230" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNA1 or <sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNA2. (Right panel) Basal or <sd-tag id="sdTag368" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation-induced (5 h) <sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="ROS" ext_ids="CHEBI:26523" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="reactive oxygen species" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ROS</sd-tag> levels in <sd-tag id="sdTag235" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells in the presence of either scrambled, <sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNA1 or <sd-tag id="sdTag237" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNA2 with or without treatment with <sd-tag id="sdTag238" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="AO1" ext_ids="CHEBI:28939///CHEBI:29073" norm_text="" ext_dbs="ChEBI///ChEBI" in_caption="True" ext_names="N-acetyl-L-cysteine///L-ascorbic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=///http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">AO1</sd-tag> (<sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="NAC" ext_ids="CHEBI:28939" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-acetyl-L-cysteine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">NAC</sd-tag> (2 mM) and <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="L-ascorbic acid" ext_ids="CHEBI:29073" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="L-ascorbic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">L-ascorbic acid</sd-tag> (2 mM)) for 24 h, measured by <sd-tag id="sdTag242" source="sdapi" category="assay" entity_type="" role="" text="flow cytometry" ext_ids="BAO_0000005" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="flow cytometry" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">flow cytometry</sd-tag> after <sd-tag id="sdTag405" source="sdapi" category="assay" entity_type="" role="" text="DCF" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DCF</sd-tag> treatment. The results are expressed as the mean intensity of cell fluorescence (and standard deviation). <sup>*</sup> represents significant difference from control conditions (P&lt;0.05); <sup>#</sup> represents a lack of significant difference from control conditions (P&gt;0.05).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3050"/></sd-panel></fig><fig id="1320"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1320"/><sd-panel panel_id="3051"><p>(A) <sd-tag id="sdTag244" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> showing knockdown of <sd-tag id="sdTag245" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG5" ext_ids="Q9H1Y0" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">ATG5</sd-tag> protein expression by <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG5" ext_ids="9474" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG5</sd-tag> siRNA.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3051"/></sd-panel><sd-panel panel_id="3052"><p>(B) <sd-tag id="sdTag247" source="sdapi" category="assay" entity_type="" role="" text="RT–PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RT-PCR</sd-tag> showing knockdown of <sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ATG10" ext_ids="83734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG10</sd-tag> mRNA expression by <sd-tag id="sdTag249" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG10" ext_ids="83734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG10</sd-tag> siRNA.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3052"/></sd-panel><sd-panel panel_id="3053"><p>(C) Quantitation of the percentage of <sd-tag id="sdTag250" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta positive cells. <sd-tag id="sdTag424" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably over-expressing <sd-tag id="sdTag253" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> in the presence of either scrambled, <sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNA1 or <sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNA2, and either scrambled, <sd-tag id="sdTag257" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG5" ext_ids="9474" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG5</sd-tag> siRNA or <sd-tag id="sdTag258" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG10" ext_ids="83734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG10</sd-tag> siRNA. After 48 h, cells were left untreated or exposed to <sd-tag id="sdTag372" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 5 h.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3053"/></sd-panel><sd-panel panel_id="3054"><p>(D) <sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="ROS" ext_ids="CHEBI:26523" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="reactive oxygen species" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ROS</sd-tag> levels in <sd-tag id="sdTag263" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells in the presence of either scrambled, <sd-tag id="sdTag264" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNA1 or <sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNA2, and scrambled, <sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG5" ext_ids="9474" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG5</sd-tag> siRNA or <sd-tag id="sdTag267" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG10" ext_ids="83734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG10</sd-tag> siRNA, measured by <sd-tag id="sdTag268" source="sdapi" category="assay" entity_type="" role="" text="flow cytometry" ext_ids="BAO_0000005" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="flow cytometry" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">flow cytometry</sd-tag> after <sd-tag id="sdTag406" source="sdapi" category="assay" entity_type="" role="" text="DCF" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DCF</sd-tag> treatment. After 48 h, cells were left untreated or exposed to <sd-tag id="sdTag375" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 5 h. The results are expressed as the mean intensity of cell fluorescence (and standard deviation). <sup>*</sup> represents significant difference from control conditions (P&lt;0.05); <sup>#</sup> represents a lack of significant difference from control conditions (P&gt;0.05).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3054"/></sd-panel></fig><fig id="1321"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1321"/><sd-panel panel_id="3055"><p>(A) Quantitation of the percentage of <sd-tag id="sdTag273" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag274" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> puncta positive cells. <sd-tag id="sdTag425" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably over-expressing <sd-tag id="sdTag276" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>-tagged-<sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> (clones <sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag>#5 and <sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag>#7) or control cells (clones Cont#1 and Cont#3) were left untreated or exposed to <sd-tag id="sdTag376" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 6 h, with or without treatment with <sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Z-VAD-FMK" ext_ids="5497174" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="Z-VAD (OMe)-FMK" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">Z-VAD-FMK</sd-tag> for 24 h. The percentage of cells with <sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> puncta was calculated, and data are shown as the mean and standard deviation of the mean from three independent experiments.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3055"/></sd-panel><sd-panel panel_id="3056"><p>(B) Apoptosis in <sd-tag id="sdTag426" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells stably over-expressing <sd-tag id="sdTag287" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>-tagged-<sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> (clones <sd-tag id="sdTag289" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag>#5 and <sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag>#7) or control cells (clones Cont#1 and Cont#3), as measured by cells with a sub-G1 <sd-tag id="sdTag378" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="DNA" ext_ids="CHEBI:16991" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="deoxyribonucleic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DNA</sd-tag> content. Cells were transfected with either scrambled, <sd-tag id="sdTag291" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNA1 or <sd-tag id="sdTag292" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNA2. Cells were left untreated, exposed to <sd-tag id="sdTag377" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 6 h or to metabolic stress for 24 h.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3056"/></sd-panel><sd-panel panel_id="3057"><p>(C) Apoptosis in <sd-tag id="sdTag428" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="U2OS" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS</sd-tag> cells cotransfected with scrambled or <sd-tag id="sdTag300" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TIGAR" ext_ids="57103" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TIGAR" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TIGAR</sd-tag> siRNAs, and scrambled, <sd-tag id="sdTag301" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG5" ext_ids="9474" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG5</sd-tag> siRNA or <sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG10" ext_ids="83734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG10</sd-tag> siRNA, as measured by cells with a sub-G1 <sd-tag id="sdTag381" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="DNA" ext_ids="CHEBI:16991" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="deoxyribonucleic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DNA</sd-tag> content. After 48 h, cells were left untreated, exposed to <sd-tag id="sdTag382" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nutrient" ext_ids="CHEBI:33284" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nutrient" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nutrient</sd-tag> starvation for 6 h or to metabolic stress for 24 h. Data are shown as the mean and standard deviation from three independent experiments. In each case, the increase in apoptosis after knockdown of <sd-tag id="sdTag309" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG5" ext_ids="9474" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG5</sd-tag> or <sd-tag id="sdTag310" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG10" ext_ids="83734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG10</sd-tag>, compared with the matched control, was statistically significant; <sup>*</sup> represents significant difference from control conditions (P&lt;0.05); <sup>#</sup> represents a lack of significant difference from control conditions (P&gt;0.05).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=3057"/></sd-panel></fig></article>

token_classification/10-1038_emboj-2009-366.xml

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+<article doi="10.1038/emboj.2009.366" abstract="The alpha1S subunit has a dual function in skeletal muscle: it forms the L-type Ca(2+) channel in T-tubules and is the voltage sensor of excitation-contraction coupling at the level of triads. It has been proposed that L-type Ca(2+) channels might also be voltage-gated sensors linked to transcriptional activity controlling differentiation. By using the U7-exon skipping strategy, we have achieved long-lasting downregulation of alpha1S in adult skeletal muscle. Treated muscles underwent massive atrophy while still displaying significant amounts of alpha1S in the tubular system and being not paralysed. This atrophy implicated the autophagy pathway, which was triggered by neuronal nitric oxide synthase redistribution, activation of FoxO3A, upregulation of autophagy-related genes and autophagosome formation. Subcellular investigations showed that this atrophy was correlated with the disappearance of a minor fraction of alpha1S located throughout the sarcolemma. Our results reveal for the first time that this sarcolemmal fraction could have a role in a signalling pathway determining muscle anabolic or catabolic state and might act as a molecular sensor of muscle activity."><fig id="2499"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2499"/><sd-panel panel_id="7087"><div><b>(</b>B) <sd-tag id="sdTag3" source="sdapi" category="assay" entity_type="" role="" text="qRT–PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">qRT-PCR</sd-tag> analysis using primers overlapping exons 15 and 16 permitted to quantify the non‐skipped <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="gene" role="assayed" text="α1S" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">α1S</sd-tag> form: 18±6% (<sup>**</sup><i>P</i>⩽0.001, <i>n</i>=19) and 10±7% (<sup>**</sup><i>P</i>⩽0.001 <i>n</i>=19) (black bars) of the total <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="gene" role="assayed" text="α1S" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">α1S</sd-tag> mRNA (grey bars) at 2 and 6 months post injection in <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag> of <sd-tag id="sdTag241" source="sdapi" category="entity" entity_type="organism" role="component" text="AAV1" ext_ids="272636" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Adeno-associated virus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">AAV1</sd-tag>‐(U7‐ESE) and <sd-tag id="sdTag238" source="sdapi" category="entity" entity_type="organism" role="component" text="AAV1" ext_ids="272636" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Adeno-associated virus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">AAV1</sd-tag>‐(U7‐SA):Δ<sd-tag id="sdTag237" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag> or <sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="organism" role="component" text="AAV1" ext_ids="272636" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Adeno-associated virus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">AAV1</sd-tag>‐(U7‐Ctrl): c as a control, respectively.</div><graphic href="https://api.sourcedata.io/file.php?panel_id=7087"/></sd-panel><sd-panel panel_id="7088"><b>(</b>C) Six months post injection, lysates from <span><sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag></span><sup>Δ<sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> (Δ<span><sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></span>) and <span><sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag></span><sup>Ctrl</sup> <span>(c) were <sd-tag id="sdTag245" source="sdapi" category="assay" entity_type="" role="" text="immuno‐blotted" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">immuno‐blotted</sd-tag> for</span> <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="protein" role="assayed" text="α1S" ext_ids="Q02789" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">α1S</sd-tag> or <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="α-actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">α-actin</sd-tag> for four <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>. Graph depicts mean±s.e.m. of relative expression of <sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="protein" role="assayed" text="α1S" ext_ids="Q02789" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">α1S</sd-tag> subunit determined by densitrometry and nomalized to the <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="α-actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">α-actin</sd-tag> expression for each muscle. Results were expressed in protein levels of <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="protein" role="assayed" text="α1S" ext_ids="Q02789" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">α1S</sd-tag> subunit in <span><sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag></span><sup>Δ<sd-tag id="sdTag250" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> normalized to <span><sd-tag id="sdTag249" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag></span><sup>Ctrl</sup> for each <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>, <sup>**</sup><i>P</i>⩽0.001, <i>n</i>=4.<graphic href="https://api.sourcedata.io/file.php?panel_id=7088"/></sd-panel><sd-panel panel_id="25395">(<strong>D</strong>) Longitudinal cryo‐sections from <sd-tag id="sdTag299" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag300" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> (Δ<sd-tag id="sdTag301" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag>) and <sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup> (c) were stained with anti‐<span><sd-tag id="sdTag308" source="sdapi" category="entity" entity_type="protein" role="assayed" text="α1S" ext_ids="Q02789" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">α1S</sd-tag></span> subunit (red) and anti‐<sd-tag id="sdTag304" source="sdapi" category="entity" entity_type="protein" role="assayed" text="laminin" ext_ids="P48678" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lmna" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">laminin</sd-tag> (green) antibodies, <sd-tag id="sdTag305" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nuclei</sd-tag> were visualized by <sd-tag id="sdTag306" source="sdapi" category="assay" entity_type="" role="" text="Dapi" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Dapi</sd-tag> (blue) and imaged by <sd-tag id="sdTag307" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Bars represent 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=25395"/></sd-panel></fig><fig id="2500"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2500"/><sd-panel panel_id="7089"><b>(</b>A) Six months post injection, <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag>s from eight <sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="organism" role="experiment" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> were dissected and weighed.<graphic href="https://api.sourcedata.io/file.php?panel_id=7089"/></sd-panel><sd-panel panel_id="7090"><b>(</b>B) <span>The internal diameters (shortest diameter) from all <sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="fibres" ext_ids="UBERON:0004057" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle fiber triad" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">fibres</sd-tag> throughout the total muscle section were recorded and analysed. Muscles from five different animals were examined. The bar graph presents mean±s.e.m. of the number of <sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="myofibres" ext_ids="UBERON:0004057" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle fiber triad" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">myofibres</sd-tag> by fibre diameter class for</span> <span><sd-tag id="sdTag253" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag></span><sup>Δ<sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> (black) and <span><sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag></span><sup>Ctrl</sup>(grey).<graphic href="https://api.sourcedata.io/file.php?panel_id=7090"/></sd-panel><sd-panel panel_id="7091"><b>(</b>C) Transversal sections of <sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> (Δ<sd-tag id="sdTag257" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag>) and <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup> (c) were stained with <sd-tag id="sdTag41" source="sdapi" category="assay" entity_type="" role="" text="haematoxylin and eosin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">haematoxylin and eosin</sd-tag>, bars represent 100 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7091"/></sd-panel><sd-panel panel_id="12644"><p>(<strong>D</strong>) To quantify fibrosis, transversal sections of total muscle were stained with <sd-tag id="sdTag258" source="sdapi" category="assay" entity_type="" role="" text="Red Sirius" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Red Sirius</sd-tag> and quantified using Histolab Software (marked in blue), data were normalized with total surface of each muscle (orange line surrounding the sections), bars represent 500 μm. (<strong>E</strong>) Quantification is presented in bar graph and showed 4.1±0.1 fold increase of fibrosis in <sd-tag id="sdTag260" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> (Δ<sd-tag id="sdTag261" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag>) compared to <sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup> (c) (<sup>**</sup><em>P</em>0.001, <em>n</em>=4).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=12644"/></sd-panel></fig><fig id="2501"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2501"/><sd-panel panel_id="7094"><b>(</b>A) mRNA from <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag264" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> and <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup> tissues were extracted and <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="gene" role="assayed" text="nNOS" ext_ids="18125" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Nos1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">nNOS</sd-tag> expression was quantified by <sd-tag id="sdTag61" source="sdapi" category="assay" entity_type="" role="" text="qRT–PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">qRT-PCR</sd-tag>. Results are expressed as mean±s.e.m., <sup>**</sup><i>P</i>0.001, <i>n</i>=4.<graphic href="https://api.sourcedata.io/file.php?panel_id=7094"/></sd-panel><sd-panel panel_id="7095"><b>(</b>B) Transversal cryo‐sections of <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> (Δ<sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag>) and <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup> (c) were stained with anti‐<sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="protein" role="assayed" text="nNOS" ext_ids="Q9Z0J4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Nos1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">nNOS</sd-tag> (red), anti‐<sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="protein" role="assayed" text="laminin" ext_ids="P48678" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lmna" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">laminin</sd-tag> (green) antibodies, <sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nuclei</sd-tag> with <sd-tag id="sdTag72" source="sdapi" category="assay" entity_type="" role="" text="Dapi" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Dapi</sd-tag> (blue) and imaged by <sd-tag id="sdTag70" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Bars represent 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7095"/></sd-panel><sd-panel panel_id="7096"><b>(</b>C) The tissues from extracts were analysed by <sd-tag id="sdTag85" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> with <sd-tag id="sdTag235" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FoxO3a" ext_ids="Q9WVH4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FoxO3a</sd-tag>‐P antibody and normalized with <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="α‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">α‐actin</sd-tag> antibody. Graph depicts mean±s.e.m. of relative expression of <sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FoxO3a" ext_ids="Q9WVH4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FoxO3a</sd-tag>‐P determined by densitometry and nomalized to the <sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="α‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">α‐actin</sd-tag> expression for each muscle, <sup>*</sup><i>P</i>⩽0.005, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=7096"/></sd-panel><sd-panel panel_id="7097"><b>(</b>D) Longitudinal cryo‐sections of <sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag267" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> (Δ<sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag>) and <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup> (c) were stained with anti‐<sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FoxO3a" ext_ids="Q9WVH4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FoxO3a</sd-tag> (red), anti‐<sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="protein" role="assayed" text="laminin" ext_ids="P48678" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lmna" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">laminin</sd-tag> (green) antibodies, <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nuclei</sd-tag> with <sd-tag id="sdTag91" source="sdapi" category="assay" entity_type="" role="" text="Dapi" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Dapi</sd-tag> (blue) and imaged by <sd-tag id="sdTag92" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Bars represent 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7097"/></sd-panel><sd-panel panel_id="7098"><p><strong>(</strong>E) mRNA from <sd-tag id="sdTag269" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag270" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> and <sd-tag id="sdTag271" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup> tissues were extracted and regulation of autophagy genes expression was followed by <sd-tag id="sdTag101" source="sdapi" category="assay" entity_type="" role="" text="qRT–PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">qRT-PCR</sd-tag>. <sd-tag id="sdTag233" source="sdapi" category="entity" entity_type="gene" role="assayed" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag>, <sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="gene" role="assayed" text="CathepsinL" ext_ids="13039" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Ctsl" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">CathepsinL</sd-tag>, <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LC3" ext_ids="67443///66734" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> and <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="gene" role="assayed" text="PI3KIII" ext_ids="30955" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Pik3cg" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PI3KIII</sd-tag> expression (noted in red) were significantly increased in <sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag272" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> compared with the controlateral <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup>, <sup>**</sup><em>P</em>0.001, <em>n</em>=4.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=7098"/></sd-panel></fig><fig id="2502"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2502"/><sd-panel panel_id="7099"><b>(</b>A) Ultrathin sections were imaged by <sd-tag id="sdTag120" source="sdapi" category="assay" entity_type="" role="" text="electron microscopy" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">electron microscopy</sd-tag>, M, <sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>; C, <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="collagen fibres" ext_ids="GO:0098644" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="complex of collagen trimers" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">collagen fibres</sd-tag>; T, <sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="T‐tubule" ext_ids="GO:0030315" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="T-tubule" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">T‐tubule</sd-tag>. Arrows show <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="double‐membrane vesicules" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">double‐membrane vesicules</sd-tag> called <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="auphagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">auphagosomes</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7099"/></sd-panel><sd-panel panel_id="7100"><b>(</b>B) Transversal cryo‐sections were stained with anti‐<sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3b" ext_ids="Q9CQV6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Map1lc3b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LC3b</sd-tag> (red), anti‐<sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="protein" role="assayed" text="dystrophin" ext_ids="P11531" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Dmd" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">dystrophin</sd-tag> (green) antibodies, <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nuclei</sd-tag> with <sd-tag id="sdTag131" source="sdapi" category="assay" entity_type="" role="" text="Dapi" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Dapi</sd-tag> (blue) and imaged by <sd-tag id="sdTag132" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Upper panel: <sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup> (Ctrl) and lower panel: <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag274" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> (Δ<sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag>). Bars represent 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7100"/></sd-panel><sd-panel panel_id="7101"><b>(</b>C) <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="tissue" role="component" text="Myofibres" ext_ids="UBERON:0004057" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle fiber triad" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Myofibres</sd-tag> isolated from control (Ctrl) or 6 months post‐injected <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="tissue" role="component" text="FDB" ext_ids="UBERON:0014380" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="flexor digitorum brevis muscle" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">FDB</sd-tag> (Δ<sd-tag id="sdTag276" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag>) muscles were processed for immuno‐fluorescent labelling for <sd-tag id="sdTag147" source="sdapi" category="entity" entity_type="protein" role="assayed" text="P62" ext_ids="Q64337" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Sqstm1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">P62</sd-tag> (green) and <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3b" ext_ids="Q9CQV6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Map1lc3b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">LC3b</sd-tag> (red) and imaged by <sd-tag id="sdTag143" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Scale bars, 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7101"/></sd-panel></fig><fig id="2503"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2503"/><sd-panel panel_id="7102"><b>(</b>A) Ultrathin sections of <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> (Δ<sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag>) and <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup> (c) were imaged by <sd-tag id="sdTag153" source="sdapi" category="assay" entity_type="" role="" text="electron microscopy" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">electron microscopy</sd-tag>. Cis, <sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="terminal cisternae" ext_ids="GO:0014802" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="terminal cisterna" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">terminal cisternae</sd-tag>; T, <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="tubule" ext_ids="GO:0030315" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="T-tubule" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">tubule</sd-tag>; SR, <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="sarcoplasmic reticulum" ext_ids="GO:0016529" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="sarcoplasmic reticulum" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">sarcoplasmic reticulum</sd-tag>. Bars: 500 nm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7102"/></sd-panel><sd-panel panel_id="7103"><b>(</b>B) <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="tissue" role="component" text="Myofibres" ext_ids="UBERON:0004057" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle fiber triad" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Myofibres</sd-tag> isolated from Ctrl or Δ<sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag> <sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="tissue" role="component" text="FDB" ext_ids="UBERON:0014380" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="flexor digitorum brevis muscle" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">FDB</sd-tag> muscles 6 months post injection were processed for immuno‐fluorescent labelling for <sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="protein" role="assayed" text="RyR1" ext_ids="E9PZQ0" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ryr1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">RyR1</sd-tag> (green), <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SERCA" ext_ids="Q64518///O55143///Q8R429" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Atp2a3///Atp2a2///Atp2a1" ext_tax_ids="10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">SERCA</sd-tag> (red), <sd-tag id="sdTag164" source="sdapi" category="assay" entity_type="" role="" text="Dapi" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Dapi</sd-tag> (blue) and imaged by <sd-tag id="sdTag165" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Scale bars, 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7103"/></sd-panel></fig><fig id="2504"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2504"/><sd-panel panel_id="7104"><b>(</b>A) Lysates from <sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> (Δ<sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag>) and <sd-tag id="sdTag178" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup> (c) were <sd-tag id="sdTag282" source="sdapi" category="assay" entity_type="" role="" text="immuno‐blotted" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">immuno‐blotted</sd-tag> for <sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="protein" role="assayed" text="RyR1" ext_ids="E9PZQ0" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ryr1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">RyR1</sd-tag> or <sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="α‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">α‐actin</sd-tag>. (<i>n</i>=4). Graph depicts mean±s.e.m. of relative expression of RyR1 determined by densitometry and nomalized to the <sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="α‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">α‐actin</sd-tag> expression for each muscle. Results were expressed in protein levels of Δ<sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag> in <sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> normalized to <sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup> for each <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>, <sup>*</sup><i>P</i>⩽0.005, <i>n</i>=4.<graphic href="https://api.sourcedata.io/file.php?panel_id=7104"/></sd-panel><sd-panel panel_id="7105"><b>(</b>B) Longitudinal cryo‐sections of <sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Δ<sd-tag id="sdTag286" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag></sup> (Δ<sd-tag id="sdTag287" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag>) and <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag><sup>Ctrl</sup> (c) were stained with anti‐<sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="protein" role="assayed" text="α1S" ext_ids="Q02789" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">α1S</sd-tag> subunit (red), anti‐<sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="protein" role="assayed" text="RyR1" ext_ids="E9PZQ0" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ryr1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">RyR1</sd-tag> (green) antibodies and imaged by <sd-tag id="sdTag202" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Bars=20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7105"/></sd-panel></fig><fig id="2505"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2505"/><sd-panel panel_id="7106"><p><span>Localization of <sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="protein" role="assayed" text="α 1S" ext_ids="Q02789" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">α 1S</sd-tag> subunit. Whole <sd-tag id="sdTag289" source="sdapi" category="entity" entity_type="tissue" role="component" text="skeletal muscle fibres" ext_ids="UBERON:0004057" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle fiber triad" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">skeletal muscle fibres</sd-tag> enzymatically isolated from Ctrl (</span><span>A</span><span>-</span><span>D</span><span>) or Δ<sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DHPR" ext_ids="12292" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DHPR</sd-tag> (</span><span>E</span><span>-</span><span>H</span><span>) <sd-tag id="sdTag291" source="sdapi" category="entity" entity_type="tissue" role="component" text="FDB" ext_ids="UBERON:0014380" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="flexor digitorum brevis muscle" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">FDB</sd-tag> muscles 6 months post injection were processed for immuno‐fluorescent labelling for <sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="protein" role="assayed" text="α1 S" ext_ids="Q02789" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">α1 S</sd-tag> subunit (red) and <sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="protein" role="assayed" text="laminin" ext_ids="P48678" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lmna" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">laminin</sd-tag> (green). Scale bars, 10 μm; Arrows indicate <sd-tag id="sdTag298" source="sdapi" category="entity" entity_type="protein" role="assayed" text="α1 S" ext_ids="Q02789" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cacna1s" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">α1 S</sd-tag> subunit expression on <sd-tag id="sdTag296" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="sarcolemma" ext_ids="GO:0042383" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="sarcolemma" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">sarcolemma</sd-tag>; antibody labelling was visualized by serial <sd-tag id="sdTag297" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag> and represented as movies of the optical sections (Supplementary Movies S5A and S5B). (</span><span>D</span><span>,</span> <span>H</span><span>) Present projections of confocal Z‐series (step between each frame is 1 μm) along</span> <em>XZ</em> <span>and</span> <em>YZ</em> <span>planes as indicated.</span></p><graphic href="https://api.sourcedata.io/file.php?panel_id=7106"/></sd-panel></fig></article>

token_classification/10-1038_emboj-2009-369.xml

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+<article doi="10.1038/emboj.2009.369" abstract="In addition to mitochondria, BCL-2 is located at the endoplasmic reticulum (ER) where it is a constituent of several distinct complexes. Here, we identify the BCL-2-interacting protein at the ER, nutrient-deprivation autophagy factor-1 (NAF-1)-a bitopic integral membrane protein whose defective expression underlies the aetiology of the neurodegenerative disorder Wolfram syndrome 2 (WFS2). NAF-1 contains a two iron-two sulphur coordinating domain within its cytosolic region, which is necessary, but not sufficient for interaction with BCL-2. NAF-1 is displaced from BCL-2 by the ER-restricted BH3-only protein BIK and contributes to regulation of BIK-initiated autophagy, but not BIK-dependent activation of caspases. Similar to BCL-2, NAF-1 is found in association with the inositol 1,4,5-triphosphate receptor and is required for BCL-2-mediated depression of ER Ca(2+) stores. During nutrient deprivation as a physiological stimulus of autophagy, BCL-2 is known to function through inhibition of the autophagy effector and tumour suppressor Beclin 1. NAF-1 is required in this pathway for BCL-2 at the ER to functionally antagonize Beclin 1-dependent autophagy. Thus, NAF-1 is a BCL-2-associated co-factor that targets BCL-2 for antagonism of the autophagy pathway at the ER."><fig id="2570"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2570"/><sd-panel panel_id="7329"><div><b>(A)</b> BH3‐only <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BIK" ext_ids="638" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BIK" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BIK</sd-tag> displaces a subset of <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag> complexes at the <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="subcellular" role="component" text="ER" ext_ids="GO:0005783" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ER</sd-tag>. Purified <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="subcellular" role="component" text="LM" ext_ids="GO:0005789" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">LM</sd-tag> from <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="gene" role="component" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>b5 cells either mock infected or infected with <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Ad" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ad</sd-tag>‐<sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BIK" ext_ids="638" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BIK" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BIK</sd-tag>b5 was subjected to cross‐linking with <sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="BMH" ext_ids="18179261" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="bismaleimidohexane" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">BMH</sd-tag> and visualized by <sd-tag id="sdTag285" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag>. Asterisks (<sup>*</sup>) denote <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag> cross‐linked products, which are displaced by <sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BIK" ext_ids="638" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BIK" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BIK</sd-tag>. Bold arrow denotes region containing cross‐linked <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag>/<sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag>.</div><graphic href="https://api.sourcedata.io/file.php?panel_id=7329"/></sd-panel><sd-panel panel_id="7332"><b>(D)</b> Endogenous <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag> cross‐links with <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag> at the <sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="subcellular" role="component" text="ER" ext_ids="GO:0005783" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ER</sd-tag>. <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="subcellular" role="component" text="LM" ext_ids="GO:0005789" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">LM</sd-tag> purified from <sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> <span><sd-tag id="sdTag292" source="sdapi" category="entity" entity_type="protein" role="reporter" text="neo" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">neo</sd-tag> and</span> <sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>b5 cells were subjected to cross‐linking by <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="molecule" role="component" text="BMH" ext_ids="18179261" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="bismaleimidohexane" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">BMH</sd-tag> and immunoprecipitation with anti‐<sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag> antibody. Precipitates were analysed by <sd-tag id="sdTag291" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> with anti‐<sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7332"/></sd-panel><sd-panel panel_id="7333"><b>(E)</b> <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag> is displaced from <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag> by BH3‐only <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BIK" ext_ids="638" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BIK" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BIK</sd-tag>. <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> <sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="gene" role="component" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>b5 cells were either mock infected or infected with <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Ad" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ad</sd-tag>‐<sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BIK" ext_ids="638" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BIK" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BIK</sd-tag>. Purified <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="subcellular" role="component" text="LM" ext_ids="GO:0005789" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum membrane" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">LM</sd-tag> was treated as in (<b>D</b>).<graphic href="https://api.sourcedata.io/file.php?panel_id=7333"/></sd-panel></fig><fig id="2571"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2571"/><sd-panel panel_id="7334"><b>(A)</b> <sd-tag id="sdTag49" source="sdapi" category="assay" entity_type="" role="" text="Co‐immunoprecipitation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co‐immunoprecipitation</sd-tag> of endogenous <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag> and <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag>. Lysates from <sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="cell_line" role="component" text="SK‐Mel5 cells" ext_ids="CVCL_0527" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="SK-MEL-5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">SK‐Mel5 cells</sd-tag> were collected and immunoprecipitation was performed with anti‐<sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag> antibody. The precipitate was subjected to <sd-tag id="sdTag51" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> with anti‐<sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag> and anti‐<sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7334"/></sd-panel><sd-panel panel_id="7335"><b>(B)</b> <sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> cells were fixed and double stained with anti‐<sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag> and anti‐<sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Calnexin" ext_ids="P27824" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CANX" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Calnexin</sd-tag> or anti‐<sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Cytochrome c" ext_ids="P08574" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CYC1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Cytochrome <i>c</i></sd-tag> antibodies. Scale bar represents 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7335"/></sd-panel><sd-panel panel_id="7336"><b>(C)</b> <sd-tag id="sdTag65" source="sdapi" category="assay" entity_type="" role="" text="Co‐immunoprecipitation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co‐immunoprecipitation</sd-tag> of <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="gene" role="component" text="NAF‐1" ext_ids="493856" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NAF‐1</sd-tag>‐<sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag> and <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag>b5. Lysates from <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="gene" role="component" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>b5 cells infected with <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Ad" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ad</sd-tag>‐<sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag>‐<sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag> were collected and treated as in (<b>A</b>).<graphic href="https://api.sourcedata.io/file.php?panel_id=7336"/></sd-panel><sd-panel panel_id="7337"><b>(D)</b> Mutations in the CDGSH iron‐binding domain of <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag> interfere with <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag> binding to <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag>. <sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> <sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="gene" role="component" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>b5 cells were infected with either <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Ad" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ad</sd-tag>‐<sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="gene" role="component" text="rtTA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rtTA</sd-tag>, <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Ad" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ad</sd-tag>‐<sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NAF‐1" ext_ids="493856" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NAF‐1</sd-tag>‐<sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>, or <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Ad" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ad</sd-tag>‐<sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NAF‐1" ext_ids="493856" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NAF‐1</sd-tag>‐mut‐<sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag> (C99S C101S C110S H114Q). Lysates were treated as in (<b>A</b>). Densitometric analysis was performed using Scion Image software to quantify expression and co‐precipitated levels of <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag>‐<sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag> and <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag>‐mut‐<sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>. Graph depicts the ratio of co‐precipitated protein to expression level.<graphic href="https://api.sourcedata.io/file.php?panel_id=7337"/></sd-panel><sd-panel panel_id="7338"><p><span>(</span><span>E</span><span>) A functional CDGSH iron‐binding domain is necessary, but not sufficient for the interaction between the cytosolic domains of <sd-pretag id="sdPretag14388680794770" parent-tag-id="309">NAF‐1</sd-pretag> and <sd-pretag id="sdPretag14388680335270" parent-tag-id="308">BCL‐2</sd-pretag>. HA‐<sd-pretag id="sdPretag14388680335271" parent-tag-id="308">BCL‐2</sd-pretag> ΔTM was</span> <em>in vitro</em> <span>translated in <sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="organism" role="component" text="rabbit" ext_ids="9986" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="rabbit" ext_tax_ids="9986" ext_tax_names="Oryctolagus cuniculus" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">rabbit</sd-tag> reticulocyte lysate and equivalent aliquots were added to each GST pull‐down reaction. GST‐fusion proteins used were GST alone, GST‐NAF1‐C, GST‐NAF1‐C‐mut (C99S C101S C110S H114Q), and GST‐MitoNEET‐C. The proteins were detected using anti‐HA and anti‐GST</span></p><graphic href="https://api.sourcedata.io/file.php?panel_id=7338"/></sd-panel></fig><fig id="2572"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2572"/><sd-panel panel_id="7339"><b>(A)</b> <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> <sd-tag id="sdTag296" source="sdapi" category="entity" entity_type="protein" role="reporter" text="neo" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">neo</sd-tag> and <sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>b5 cells treated with control (CTRL) or <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NAF‐1" ext_ids="493856" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NAF‐1</sd-tag> shRNA were either mock infected or infected with <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Ad" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ad</sd-tag>‐<sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BIK" ext_ids="638" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BIK" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BIK</sd-tag> in the absence or presence of 50 μM <sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="zVAD‐fmk" ext_ids="5737" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="Z-VAD(OMe)-FMK" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">zVAD‐fmk</sd-tag>. Cell lysates were analysed by <sd-tag id="sdTag297" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7339"/></sd-panel><sd-panel panel_id="7340"><b>(B)</b> Caspase activity was measured using the fluorescent substrate <sd-tag id="sdTag134" source="sdapi" category="assay" entity_type="" role="" text="DEVD‐AMC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DEVD‐AMC</sd-tag>. The results represent the average±s.d. of three independent experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=7340"/></sd-panel><sd-panel panel_id="7341"><b>(C)</b> Prolonged <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BIK" ext_ids="638" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BIK" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BIK</sd-tag> expression and caspase inhibition induces autophagy, which is enhanced by knockdown of <sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag>. <sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> <sd-tag id="sdTag299" source="sdapi" category="entity" entity_type="protein" role="reporter" text="neo" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">neo</sd-tag> and <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>b5 cells treated with CTRL or <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NAF‐1" ext_ids="493856" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NAF‐1</sd-tag> shRNA were infected with <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Ad" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Ad</sd-tag>‐<sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BIK" ext_ids="638" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BIK" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BIK</sd-tag> in the presence of <sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="zVAD‐fmk" ext_ids="5737" norm_text="" ext_dbs="PubChem" in_caption="True" ext_names="Z-VAD(OMe)-FMK" ext_tax_ids="" ext_tax_names="" ext_urls="https://pubchem.ncbi.nlm.nih.gov/compound/">zVAD‐fmk</sd-tag> for the indicated periods of time. Cell lysates were analysed by <sd-tag id="sdTag298" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag>. Levels of <sd-tag id="sdTag300" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> II were normalized to <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> levels by densitometry analysis. Graph depicts normalized <sd-tag id="sdTag301" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> II levels of each lane.<graphic href="https://api.sourcedata.io/file.php?panel_id=7341"/></sd-panel></fig><fig id="2573"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2573"/><sd-panel panel_id="7342"><b>(A)</b> Effect of <sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag> knockdown on starvation‐induced autophagy. <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> cells infected with CTRL or <sd-tag id="sdTag171" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NAF‐1" ext_ids="493856" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NAF‐1</sd-tag> shRNA were starved for 4 h <span>in <sd-tag id="sdTag303" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> with</span> <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> (vehicle) or <sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Baf A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Baf A1</sd-tag> (100 nM). Cell lysates were analysed by <sd-tag id="sdTag169" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7342"/></sd-panel><sd-panel panel_id="7343"><b>(B)</b> Representative images of <sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> staining in <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> <sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> cells transfected with <sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="gene" role="component" text="LUC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LUC</sd-tag> or <sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NAF‐1" ext_ids="493856" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NAF‐1</sd-tag> siRNA, untreated and starved. Scale bar represents 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7343"/></sd-panel><sd-panel panel_id="7344"><b>(C)</b> Quantification of autophagy is expressed as the percentage of <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag189" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag>‐expressing cells displaying punctate <sd-tag id="sdTag190" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag191" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9H492///Q9BXW4///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3A///MAP1LC3C///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>. A minimum of 100 cells per sample were counted; results represent the average±s.d. of three independent experiments. Cell lysates were analysed by <sd-tag id="sdTag192" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7344"/></sd-panel></fig><fig id="2574"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2574"/><sd-panel panel_id="7345"><b>(A)</b> <sd-tag id="sdTag204" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag> contributes to the interaction between <sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag> and <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="gene" role="component" text="Beclin 1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Beclin 1</sd-tag>. <sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="gene" role="component" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>b5 cells were transfected with <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="gene" role="component" text="Beclin 1" ext_ids="8678" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Beclin 1</sd-tag> and either <sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="gene" role="component" text="LUC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LUC</sd-tag> or <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NAF‐1" ext_ids="493856" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NAF‐1</sd-tag> siRNA. Cells were lysed and subjected to immunoprecipitation with anti‐<sd-tag id="sdTag203" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag> antibody. Precipitates were subjected to analysis by <sd-tag id="sdTag211" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> using anti‐<sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Beclin 1" ext_ids="Q14457" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BECN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Beclin 1</sd-tag> and anti‐<sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="gene" role="component" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>. All lanes are derived from the same gel and of the same exposure. Thin white lines indicate where lanes have been removed.<graphic href="https://api.sourcedata.io/file.php?panel_id=7345"/></sd-panel><sd-panel panel_id="7346"><b>(B)</b> Loss of <span><sd-tag id="sdTag310" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag></span> prevents <span><sd-tag id="sdTag311" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BCL‐2" ext_ids="P10415" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BCL‐2</sd-tag></span>b5 from antagonizing starvation‐induced autophagy. <sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> GFP‐<span><sd-tag id="sdTag312" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag></span> <span>and <sd-tag id="sdTag308" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>b5/</span><sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="440738///81631///84557" norm_text="" ext_dbs="NCBI gene///NCBI gene///NCBI gene" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> cells were transfected with either <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="gene" role="component" text="LUC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LUC</sd-tag> <span>or <sd-tag id="sdTag309" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NAF‐1" ext_ids="493856" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NAF‐1</sd-tag> siRNA and starved for</span> 4 h. Cells were analysed as in Figure 4C.<graphic href="https://api.sourcedata.io/file.php?panel_id=7346"/></sd-panel><sd-panel panel_id="7347"><p>(<b>C</b>) Representative electron micrographs of <sd-tag id="sdTag237" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> <sd-tag id="sdTag313" source="sdapi" category="entity" entity_type="protein" role="reporter" text="neo" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">neo</sd-tag> and <sd-tag id="sdTag238" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag232" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>b5 cells treated with either <sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="gene" role="component" text="LUC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">LUC</sd-tag> or <sd-tag id="sdTag233" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NAF‐1" ext_ids="493856" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NAF‐1</sd-tag> siRNA, with or without subsequent starvation. Scale bar represents 10 μm. Cell lysates were analysed by <sd-tag id="sdTag235" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag>. All lanes are derived from the same gel and of the same exposure. Thin white line indicates where lanes have been removed. Autophagy levels observed by <sd-tag id="sdTag315" source="sdapi" category="assay" entity_type="" role="" text="electron microscopy" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">electron microscopy</sd-tag> (<b>C</b>) were quantified and expressed as either the percentage of cells containing <sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vacuoles</sd-tag> (<b>D</b>) or the number of <sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> per cell (<b>E</b>). A minimum of 100 cells per sample were counted; results represent the average±s.e.m.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=7347"/></sd-panel></fig><fig id="2575"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2575"/><sd-panel panel_id="7348"><b>(A)</b> <sd-tag id="sdTag245" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> <span><sd-tag id="sdTag317" source="sdapi" category="entity" entity_type="protein" role="reporter" text="neo" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">neo</sd-tag></span> and <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>b5 cells treated with either CTRL or <sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NAF‐1" ext_ids="493856" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NAF‐1</sd-tag> shRNA were loaded with <sd-tag id="sdTag249" source="sdapi" category="assay" entity_type="" role="" text="Fura‐2AM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Fura‐2AM</sd-tag>, and <sd-tag id="sdTag250" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="ER" ext_ids="GO:0005783" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ER</sd-tag> Ca<sup>2+</sup> stores were measured as the difference in cytoplasmic Ca<sup>2+</sup> concentration before and after addition of <sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="TG" ext_ids="CHEBI:9516" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="thapsigargin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">TG</sd-tag> (2 μM). Shown are representative traces of <sd-tag id="sdTag256" source="sdapi" category="assay" entity_type="" role="" text="Fura‐2AM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Fura‐2AM</sd-tag> fluorescence measured at 340/380 nm excitation wavelength ratio at 510 nm wavelength emission. Arrow indicates time at which <sd-tag id="sdTag257" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="TG" ext_ids="CHEBI:9516" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="thapsigargin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">TG</sd-tag> was added, delta values indicate <sd-tag id="sdTag258" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="TG" ext_ids="CHEBI:9516" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="thapsigargin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">TG</sd-tag>‐sensitive <sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="ER" ext_ids="GO:0005783" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ER</sd-tag> <sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="Ca2+" ext_ids="CHEBI:22984" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="calcium atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Ca<sup>2+</sup></sd-tag> stores.<graphic href="https://api.sourcedata.io/file.php?panel_id=7348"/></sd-panel><sd-panel panel_id="7349"><b>(B)</b> Differences in <sd-tag id="sdTag318" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="ER" ext_ids="GO:0005783" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="endoplasmic reticulum" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ER</sd-tag> <sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="Ca2+" ext_ids="CHEBI:22984" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="calcium atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Ca<sup>2+</sup></sd-tag> stores are shown as the average±s.e.m. of three independent experiments as described in (<b>A</b>).<graphic href="https://api.sourcedata.io/file.php?panel_id=7349"/></sd-panel><sd-panel panel_id="7350"><b>(C)</b> <sd-tag id="sdTag274" source="sdapi" category="assay" entity_type="" role="" text="Co‐immunoprecipitation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co‐immunoprecipitation</sd-tag> of endogenous <sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NAF‐1" ext_ids="Q8N5K1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CISD2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NAF‐1</sd-tag> and endogenous <sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IP3 receptor type I" ext_ids="Q14643" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ITPR1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IP3 receptor type I</sd-tag>. Lysate from <sd-tag id="sdTag276" source="sdapi" category="entity" entity_type="cell_line" role="component" text="H1299" ext_ids="CVCL_0060" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="NCI-H1299" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">H1299</sd-tag> <sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="gene" role="component" text="BCL‐2" ext_ids="596" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BCL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BCL‐2</sd-tag>b5 cells was collected and immunoprecipitation was performed with anti‐<sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IP3R1" ext_ids="Q14643" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ITPR1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">IP3R1</sd-tag> antibody. The resulting precipitate was analysed by <sd-tag id="sdTag278" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7350"/></sd-panel></fig></article>

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+<article doi="10.1038/emboj.2009.390" abstract=""><fig id="1847"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1847"/><sd-panel panel_id="4734"><b>(A)</b> <span><sd-tag id="sdTag472" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag> analysis of</span> <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG1" ext_ids="Q99933" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG1</sd-tag>, <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag>, <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Hsc/Hsp70" ext_ids="P11142///P17066" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="HSPA8///HSPA6" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Hsc/Hsp70</sd-tag> and <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Hsp90" ext_ids="P08238///P07900" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="HSP90AB1///HSP90AA1" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Hsp90</sd-tag> in young and old <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells. For detection of BAG proteins, an antibody directed against the conserved BAG domain was used.<graphic href="https://api.sourcedata.io/file.php?panel_id=4734"/></sd-panel><sd-panel panel_id="4735"><b>(B)</b> <sd-tag id="sdTag11" source="sdapi" category="assay" entity_type="" role="" text="Real‐time PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Real‐time PCR</sd-tag> analysis of human BAG family members and <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="gene" role="assayed" text="Hsc70" ext_ids="3312///10722" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="HSPA8///HSPA10" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">Hsc70</sd-tag> and <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="gene" role="assayed" text="Hsp90" ext_ids="3320" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HSP90AA1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Hsp90</sd-tag> in young and old <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells. Depicted is the expression ratio (log2) of target genes in old cells relative to young cells. <sup>*</sup><i>P</i>0.05 and <sup>**</sup><i>P</i>0.01 versus young, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4735"/></sd-panel><sd-panel panel_id="4736"><b>(C)</b> <sd-tag id="sdTag22" source="sdapi" category="assay" entity_type="" role="" text="Co‐IP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co‐IP</sd-tag> analysis of <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Hsc/Hsp70" ext_ids="P11142///P17066" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="HSPA8///HSPA6" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Hsc/Hsp70</sd-tag> interaction with <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG1" ext_ids="Q99933" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG1</sd-tag> and <sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag> in young (Y) and old (O) <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells. Upper panel shows relative amounts of proteins in cell lysates used for <sd-tag id="sdTag29" source="sdapi" category="assay" entity_type="" role="" text="Co‐IP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co‐IP</sd-tag> (Input). Middle panel shows levels of <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG1" ext_ids="Q99933" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG1</sd-tag> and <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag> found in <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Hsc/Hsp70" ext_ids="P11142///P17066" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="HSPA8///HSPA6" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Hsc/Hsp70</sd-tag> <sd-tag id="sdTag23" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitates" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">immunoprecipitates</sd-tag>. Lower panel shows levels of <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Hsc/Hsp70" ext_ids="P11142///P17066" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="HSPA8///HSPA6" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Hsc/Hsp70</sd-tag> co‐sedimented upon <sd-tag id="sdTag24" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitation" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitation</sd-tag> of <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=4736"/></sd-panel><sd-panel panel_id="4737"><b>(D, E)</b> <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">293</sd-tag> cells were treated with the indicated agents for 8 h <span>followed by <sd-tag id="sdTag477" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis of indicated proteins.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=4737"/></sd-panel></fig><fig id="1848"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1848"/><sd-panel panel_id="4738"><b>(A)</b> <sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">293</sd-tag> cells were transfected with <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="gene" role="intervention" text="bag1" ext_ids="573" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bag1</sd-tag>, <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="gene" role="intervention" text="bag3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bag3</sd-tag> or nonsense (nons) siRNAs, as indicated. After 48 h, cells were transfected with <sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="protein" role="reporter" text="d2GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">d2GFP</sd-tag> expression plasmid together with half the amounts of the indicated siRNAs. After additional 24 h, levels of indicated proteins were detected by <sd-tag id="sdTag478" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis.<graphic href="https://api.sourcedata.io/file.php?panel_id=4738"/></sd-panel><sd-panel panel_id="4739"><b>(B)</b> <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">293</sd-tag> cells were transfected with indicated siRNAs for 48 h followed by <sd-tag id="sdTag59" source="sdapi" category="assay" entity_type="" role="" text="real‐time PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">real‐time PCR</sd-tag> analysis of <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="gene" role="assayed" text="BAG1" ext_ids="573" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BAG1</sd-tag> and <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="gene" role="assayed" text="BAG3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BAG3</sd-tag> mRNA levels. Depicted is the mean relative expression ratio (log2) ±s.e.m. <sup>*</sup><i>P</i>0.05 and <sup>***</sup><i>P</i>0.001 versus nons, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4739"/></sd-panel><sd-panel panel_id="4740"><b>(C)</b> <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BAG1" ext_ids="573" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BAG1</sd-tag> knockdown was performed in <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">293</sd-tag> cells for 48 h. Thereafter, cells were transfected with <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> or <sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐based UPS reporter genes as indicated. After additional 24 h, levels of <sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐positive proteins were detected by <sd-tag id="sdTag67" source="sdapi" category="assay" entity_type="" role="" text="western‐blot" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">western‐blot</sd-tag> analysis using a <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> antibody.<graphic href="https://api.sourcedata.io/file.php?panel_id=4740"/></sd-panel><sd-panel panel_id="4741"><b>(D, E)</b> <sd-tag id="sdTag515" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag> analysis of indicated proteins from <sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="cell_line" role="component" text="d2HEK" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">d2HEK</sd-tag> cells treated with different concentrations of <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> for 5 h (<b>D</b>) or transfected with indicated amounts of <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG1S" ext_ids="Q99933" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG1S</sd-tag> plasmid for 24 h (<b>E</b>).<graphic href="https://api.sourcedata.io/file.php?panel_id=4741"/></sd-panel></fig><fig id="1849"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1849"/><sd-panel panel_id="4742"><b>(A)</b> <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">293</sd-tag> cells were transfected with nonsense (nons), <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="gene" role="intervention" text="bag1" ext_ids="573" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bag1</sd-tag> or <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="gene" role="intervention" text="bag3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bag3</sd-tag> siRNAs for 48 h and then treated for 2 h with the lysosomal inhibitors <sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="pepstatinA" ext_ids="CHEBI:7989" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Pepstatin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">pepstatinA</sd-tag> and <sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="E64" ext_ids="CHEBI:30270" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="E64" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">E64</sd-tag> (both 10 μg/ml; <sd-tag id="sdTag460" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Pep.A" ext_ids="CHEBI:7989" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Pepstatin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Pep.A</sd-tag>/<sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="E64" ext_ids="CHEBI:30270" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="E64" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">E64</sd-tag>) or <sd-tag id="sdTag461" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> as control, followed by <sd-tag id="sdTag479" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis of the indicated proteins.<graphic href="https://api.sourcedata.io/file.php?panel_id=4742"/></sd-panel><sd-panel panel_id="4743"><b>(B)</b> <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">293</sd-tag> cells were transfected for 48 h with the indicated siRNAs and <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag> expression plasmid (<sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BAG3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BAG3</sd-tag>‐<sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="gene" role="component" text="N1" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">N1</sd-tag>) or vector control (<sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="gene" role="component" text="N1" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">N1</sd-tag>) followed by the same analysis as in (A).<graphic href="https://api.sourcedata.io/file.php?panel_id=4743"/></sd-panel><sd-panel panel_id="4744">(C) Diagram shows the autophagic flux of <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="cell_line" role="component" text="293" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">293</sd-tag> cells with differently modulated <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BAG1" ext_ids="573" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BAG1</sd-tag> and <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BAG3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BAG3</sd-tag> levels as described in (A) and (B). Autophagic flux was determined by the strength of <sd-tag id="sdTag480" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9GZQ8///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐II accumulation in a 2‐h treatment period with <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Pep.A" ext_ids="CHEBI:7989" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Pepstatin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Pep.A</sd-tag>/<sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="E64" ext_ids="CHEBI:30270" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="E64" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">E64</sd-tag>. Therefore, normalised <sd-tag id="sdTag481" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9GZQ8///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3B///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐II levels in the absence of inhibitors were subtracted from corresponding levels obtained in the presence of <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Pep.A" ext_ids="CHEBI:7989" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Pepstatin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Pep.A</sd-tag>/<sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="E64" ext_ids="CHEBI:30270" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="E64" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">E64</sd-tag>. Values are expressed as mean±s.e.m. *P0.05 versus control‐transfected cells, n=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4744"/></sd-panel><sd-panel panel_id="4745"><b>(D)</b> <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells were transfected with <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> fused to <sd-tag id="sdTag137" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="84557" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> (<sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="protein" role="reporter" text="pGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pGFP</sd-tag>.<sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="84557" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag>) and co‐transfected either with <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BAG3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BAG3</sd-tag>‐N1 or N1. After transfection for 48 h, cells were treated as in (A) and levels of indicated proteins were detected by <sd-tag id="sdTag483" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis.<graphic href="https://api.sourcedata.io/file.php?panel_id=4745"/></sd-panel><sd-panel panel_id="4746"><b>(E)</b> <sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells, transfected as in (D) for 24 h, were microscopically analysed for <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="84557" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> fluorescence. Representative pictures are shown. Bar: 20 μm. Values expressed in diagram are mean±s.e.m. from three independent experiments (50 cells were counted per experiment). <sup>*</sup><i>P</i>0.05 versus N1, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4746"/></sd-panel></fig><fig id="1850"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1850"/><sd-panel panel_id="4747"><b>(A)</b> <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells were transfected with <sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag> (<sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BAG3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BAG3</sd-tag>‐N1) or vector control. After transfection for 48 h, levels of indicated proteins were detected by <sd-tag id="sdTag166" source="sdapi" category="assay" entity_type="" role="" text="western‐blot" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">western‐blot</sd-tag> analysis.<graphic href="https://api.sourcedata.io/file.php?panel_id=4747"/></sd-panel><sd-panel panel_id="4748"><b>(B)</b> Transcript levels of <sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="gene" role="assayed" text="SQSTM1" ext_ids="8878" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SQSTM1</sd-tag> in <sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells transfected as in (A) were compared by <sd-tag id="sdTag171" source="sdapi" category="assay" entity_type="" role="" text="real���time PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">real‐time PCR</sd-tag> analysis. Depicted is the fold‐increase of <sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="gene" role="assayed" text="SQSTM1" ext_ids="8878" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SQSTM1</sd-tag> mRNA levels in <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BAG3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BAG3</sd-tag>‐N1‐transfected cells relative to control (N1)‐transfected cells. Values are expressed as mean±s.e.m. <sup>**</sup><i>P</i>0.01 versus N1 cells, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4748"/></sd-panel><sd-panel panel_id="4749"><b>(C)</b> <sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells were transfected with a <sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="gene" role="component" text="BAG3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BAG3</sd-tag>‐<sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> fusion plasmid for 48 h <span>followed by indirect <sd-pretag id="sdPretag14389337434580" parent-tag-id="504">immunofluorescence</sd-pretag> staining of endogenous</span> <sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQSTM1" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SQSTM1</sd-tag>. (a) Direct fluorescence of <sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag>‐<sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> <span>(green), (b) indirect <sd-pretag id="sdPretag14389337574640" parent-tag-id="504">immunofluorescence</sd-pretag> of</span> <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQSTM1" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SQSTM1</sd-tag> (red) and (c) the stainings of (a) and (b) overlapped. <sd-tag id="sdTag178" source="sdapi" category="assay" entity_type="" role="" text="DAPI" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAPI</sd-tag> (blue) was used to stain DNA. Representative pictures are shown. Bar: 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=4749"/></sd-panel><sd-panel panel_id="4750"><b>(D)</b> <sd-tag id="sdTag191" source="sdapi" category="assay" entity_type="" role="" text="Co‐IP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co‐IP</sd-tag> studies testing the interaction of <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQSTM1" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SQSTM1</sd-tag> and <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag>. <sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells were transfected as in (A). After 24 h, <sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQSTM1" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SQSTM1</sd-tag> and <sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag> were <sd-tag id="sdTag189" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> followed by analysis of co‐sedimented proteins, as indicated. As negative control purified rabbit (rb) and mouse (ms) <sd-tag id="sdTag190" source="sdapi" category="entity" entity_type="subcellular" role="component" text="IgG" ext_ids="GO:0071735" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="IgG immunoglobulin complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">IgG</sd-tag> was used. Left panel shows relative amounts of proteins in lysates used for <sd-tag id="sdTag198" source="sdapi" category="assay" entity_type="" role="" text="Co‐IP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Co‐IP</sd-tag> (Input).<graphic href="https://api.sourcedata.io/file.php?panel_id=4750"/></sd-panel></fig><fig id="1851"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1851"/><sd-panel panel_id="4751"><b>(A)</b> Proteasomal <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="protein" role="assayed" text="chymotrypsin" ext_ids="Q99895" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CTRC" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">chymotrypsin</sd-tag> and <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cathepsin" ext_ids="O60911///P07711" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="CTSV///CTSL" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">cathepsin</sd-tag> activity in lysates from young (Y) and old (O) <sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells was determined using specific fluorescence probes, as described in the Material and methods section. Values are expressed are mean±s.e.m. <sup>*</sup><i>P</i>0.05 and <sup>**</sup><i>P</i>0.01 versus young, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4751"/></sd-panel><sd-panel panel_id="4752"><b>(B)</b> <sd-tag id="sdTag216" source="sdapi" category="assay" entity_type="" role="" text="Real‐time PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Real‐time PCR</sd-tag> analysis of <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="gene" role="assayed" text="LC3" ext_ids="84557" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag>, <sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="gene" role="assayed" text="WIPI1" ext_ids="55062" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WIPI1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WIPI1</sd-tag> and <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="gene" role="assayed" text="SQSTM1" ext_ids="8878" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SQSTM1</sd-tag> mRNA levels in young and old <sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells. Depicted is the mean expression ratio (log2) ±s.e.m. of target genes in old cells relative to young cells. <sup>**</sup><i>P</i>0.01 and <sup>***</sup><i>P</i>0.001 versus young, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4752"/></sd-panel><sd-panel panel_id="4753"><b>(C)</b> <sd-tag id="sdTag489" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag> analysis of <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and <sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQSTM1" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SQSTM1</sd-tag> in young and old <sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells.<graphic href="https://api.sourcedata.io/file.php?panel_id=4753"/></sd-panel><sd-panel panel_id="4754"><b>(D)</b> Young and old <sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells were treated for 2 h with <sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (BafA1, 2 μM) or <sd-tag id="sdTag230" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> as control followed by <sd-tag id="sdTag491" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis of indicated proteins.<graphic href="https://api.sourcedata.io/file.php?panel_id=4754"/></sd-panel><sd-panel panel_id="4755"><b>(E)</b> <sd-tag id="sdTag237" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot analysis" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14389320535500" parent-tag-id="472">Immunoblot</sd-pretag> analysis</sd-tag> of <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI1" ext_ids="Q5MNZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI1</sd-tag> expression in young and old <sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells.<graphic href="https://api.sourcedata.io/file.php?panel_id=4755"/></sd-panel><sd-panel panel_id="4756"><b>(F)</b> <span>Indirect <sd-tag id="sdTag496" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence staining" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14389337054680" parent-tag-id="504">immunofluorescence</sd-pretag> staining</sd-tag> of endogenous</span> <sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (green), <sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQSTM1" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SQSTM1</sd-tag> (red) and <sd-tag id="sdTag245" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI1" ext_ids="Q5MNZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI1</sd-tag> (white) in <sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells of young and old age. <sd-tag id="sdTag248" source="sdapi" category="assay" entity_type="" role="" text="DAPI" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAPI</sd-tag> (blue) was used to stain <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="DNA" ext_ids="CHEBI:16991" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="deoxyribonucleic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DNA</sd-tag>. Representative pictures are shown. Bar: 20 μm. Diagrams show percentage of cells with indicated characteristics counted as in Figure 3E.<graphic href="https://api.sourcedata.io/file.php?panel_id=4756"/></sd-panel><sd-panel panel_id="4757"><b>(G)</b> Old and young <sd-tag id="sdTag258" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells were treated for 1 h with <sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> as control (C), <sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="lactacystin" ext_ids="CHEBI:52722" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lactacystin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">lactacystin</sd-tag> (L, 2 μM) or <sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="NH4Cl" ext_ids="CHEBI:31206" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="ammonium chloride" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">NH<sub>4</sub>Cl</sd-tag> (20 mM) plus <sd-tag id="sdTag253" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="leupeptin" ext_ids="CHEBI:6426" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Leupeptin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">leupeptin</sd-tag> (<sd-tag id="sdTag464" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Leu" ext_ids="CHEBI:25017" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="leucine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Leu</sd-tag>, 5 μM) (N, <sd-tag id="sdTag466" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="NH4Cl" ext_ids="CHEBI:31206" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="ammonium chloride" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">NH<sub>4</sub>Cl</sd-tag>/<sd-tag id="sdTag465" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Leu" ext_ids="CHEBI:25017" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="leucine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Leu</sd-tag>). <sd-tag id="sdTag254" source="sdapi" category="assay" entity_type="" role="" text="Western‐blot" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Western‐blot</sd-tag> analyses were performed for detection of indicated proteins. In the diagram (right panel), levels of <sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="protein" role="assayed" text="polyUb" ext_ids="P42677///P62987///P0CG48///P0CG47" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="RPS27///UBA52///UBC///UBB" ext_tax_ids="9606///9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">polyUb</sd-tag>‐proteins and <sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SQSTM1" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SQSTM1</sd-tag> are depicted after normalisation to corresponding <sd-tag id="sdTag257" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="Tubulin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Tubulin</sd-tag> levels. Values are expressed as mean±s.e.m. <sup>*</sup><i>P</i>0.05 versus old control, <sup>#</sup><i>P</i>0.05 versus young control, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4757"/></sd-panel><sd-panel panel_id="4758"><b>(H)</b> <sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells of old (upper panel) and young (lower panel) age were transfected with <sd-tag id="sdTag260" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg7" ext_ids="10533" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg7</sd-tag> or nonsense (nons) siRNA. After transfection for 4 days , the cells were treated with <sd-tag id="sdTag263" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="NH4Cl" ext_ids="CHEBI:31206" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="ammonium chloride" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">NH<sub>4</sub>Cl</sd-tag>/<sd-tag id="sdTag264" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Leu" ext_ids="CHEBI:25017" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="leucine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Leu</sd-tag> or <sd-tag id="sdTag269" source="sdapi" category="entity" entity_type="molecule" role="component" text="DMSO" ext_ids="CHEBI:28262" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="dimethyl sulfoxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DMSO</sd-tag> for 1 h followed by fractioning of cell lysates in <sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="molecule" role="component" text="TritonX‐100" ext_ids="CHEBI:9750" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="Triton X-100" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">TritonX‐100</sd-tag> (TX‐100) soluble and insoluble material. Equal protein amounts of both fractions were directed to <sd-tag id="sdTag498" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis for analysis of indicated proteins. <sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="Gapdh" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Gapdh</sd-tag> and <sd-tag id="sdTag267" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="Histone H3" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Histone H3</sd-tag> were used as loading controls of soluble and insoluble fractions, respectively.<graphic href="https://api.sourcedata.io/file.php?panel_id=4758"/></sd-panel><sd-panel panel_id="4759"><b>(I)</b> <span><sd-tag id="sdTag501" source="sdapi" category="assay" entity_type="" role="" text="Transmission electron microscopic analysis" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Transmission electron microscopic analysis</sd-tag></span> of young (a) and old (b) <sd-tag id="sdTag282" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells. Magnifications of marked areas in (a) and (b) are shown in (c) and (d), respectively. An arrow indicates an <sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autolysosome" ext_ids="GO:0044754" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autolysosome</sd-tag>, and arrow heads indicate <sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag>. M, <sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondrion" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondrion</sd-tag>. N, <sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="nucleus" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nucleus</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=4759"/></sd-panel></fig><fig id="1852"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1852"/><sd-panel panel_id="4760"><b>(A)</b> <sd-tag id="sdTag503" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag> analysis of indicated proteins of young (Y) and old (O) <sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells upon fractionation as described in Figure 5H.<graphic href="https://api.sourcedata.io/file.php?panel_id=4760"/></sd-panel><sd-panel panel_id="4761"><b>(B, C)</b> After transfection for 96 h of old <sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells with <sd-tag id="sdTag296" source="sdapi" category="entity" entity_type="gene" role="intervention" text="bag3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bag3</sd-tag> or nonsense (nons) siRNA, <sd-tag id="sdTag298" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG1" ext_ids="Q99933" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG1</sd-tag> and <sd-tag id="sdTag299" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag> protein and mRNA levels were analysed by <sd-tag id="sdTag294" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> (B) and <sd-tag id="sdTag300" source="sdapi" category="assay" entity_type="" role="" text="real‐time PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">real‐time PCR</sd-tag> (C) analysis, respectively. Transcript levels in <sd-tag id="sdTag301" source="sdapi" category="entity" entity_type="gene" role="intervention" text="bag3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bag3</sd-tag> siRNA cells are depicted as the mean log2 expression ratio ±s.e.m. relative to nons siRNA cells. <sup>*</sup><i>P</i>0.05 and <sup>***</sup><i>P</i>0.001 versus nons, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4761"/></sd-panel><sd-panel panel_id="4762"><b>(D)</b> <span>Indirect <sd-tag id="sdTag504" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunofluorescence</sd-tag></span> analysis of endogenous <sd-tag id="sdTag313" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (green) and <sd-tag id="sdTag314" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WIPI1" ext_ids="Q5MNZ9" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WIPI1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WIPI1</sd-tag> (white) in old <sd-tag id="sdTag308" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells transfected with nons (a, b) and <sd-tag id="sdTag310" source="sdapi" category="entity" entity_type="gene" role="intervention" text="bag3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">bag3</sd-tag> siRNA (c, d) for 96 h. <sd-tag id="sdTag312" source="sdapi" category="assay" entity_type="" role="" text="DAPI" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAPI</sd-tag> (blue) was used as a nuclear marker. Representative pictures are shown. Bar: 20 μm. Diagrams show percentage of cells counted as in Figure 3E.<graphic href="https://api.sourcedata.io/file.php?panel_id=4762"/></sd-panel><sd-panel panel_id="4763"><b>(E)</b> Same analysis as in Figure 5D but old cells transfected as in (A) were used. Values expressed in the diagram are mean±s.e.m. <sup>*</sup><i>P</i>0.05 versus nons, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4763"/></sd-panel><sd-panel panel_id="4764"><b>(F)</b> Same analysis as in Figure 5G but old <sd-tag id="sdTag328" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells transfected as in (A) were used. C, control; L, <sd-tag id="sdTag329" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="lactacystin" ext_ids="CHEBI:52722" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lactacystin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">lactacystin</sd-tag>, N, <sd-tag id="sdTag506" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="NH4Cl" ext_ids="CHEBI:31206" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="ammonium chloride" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">NH<sub>4</sub>Cl</sd-tag>/<sd-tag id="sdTag330" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Leu" ext_ids="CHEBI:25017" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="leucine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Leu</sd-tag>. Values are expressed as mean±s.e.m. <sup>*</sup><i>P</i>0.05 versus nons control, or as indicated, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4764"/></sd-panel><sd-panel panel_id="4765"><b>(G, H)</b> Same analysis as in (F) but young <sd-tag id="sdTag343" source="sdapi" category="entity" entity_type="cell_line" role="component" text="I90" ext_ids="CVCL_0347" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="IMR-90" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">I90</sd-tag> cells 48 h after transfection with a <sd-tag id="sdTag345" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag> expression plasmid (<sd-tag id="sdTag346" source="sdapi" category="entity" entity_type="gene" role="intervention" text="BAG3" ext_ids="9531" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">BAG3</sd-tag>‐N1) or vector control (N1) together with nons or <sd-tag id="sdTag342" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sqstm1" ext_ids="8878" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sqstm1</sd-tag> siRNA (G) and nons or <sd-tag id="sdTag351" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg7" ext_ids="10533" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg7</sd-tag> siRNA (H), as indicated, were used. <sup>*</sup>, <sup>#</sup>, ∼ and <sup>+</sup>, <i>P</i>0.05 versus C N1, C <sd-tag id="sdTag353" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag>‐N1, C <sd-tag id="sdTag355" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="O95817" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="BAG3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag>‐N1 <sd-tag id="sdTag357" source="sdapi" category="entity" entity_type="protein" role="assayed" text="sqstm1" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">sqstm1</sd-tag> or <sd-tag id="sdTag358" source="sdapi" category="entity" entity_type="protein" role="assayed" text="atg7" ext_ids="O95352" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">atg7</sd-tag> and C N1 <sd-tag id="sdTag360" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sqstm1" ext_ids="8878" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sqstm1</sd-tag> or <sd-tag id="sdTag361" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg7" ext_ids="10533" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg7</sd-tag>, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4765"/></sd-panel></fig><fig id="1853"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1853"/><sd-panel panel_id="4766"><b>(A)</b> Protein extracts from <sd-tag id="sdTag379" source="sdapi" category="entity" entity_type="tissue" role="component" text="cerebellum" ext_ids="UBERON:0002037" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebellum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cerebellum</sd-tag> (CER) of young (Y, 3 months) and old (O, 24 months) <sd-tag id="sdTag383" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> were analysed for <sd-tag id="sdTag385" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG1" ext_ids="Q60739" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Bag1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">BAG1</sd-tag> and <sd-tag id="sdTag386" source="sdapi" category="entity" entity_type="protein" role="assayed" text="BAG3" ext_ids="Q9JLV1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Bag3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">BAG3</sd-tag> expression by <sd-tag id="sdTag507" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> analysis.<graphic href="https://api.sourcedata.io/file.php?panel_id=4766"/></sd-panel><sd-panel panel_id="4767"><b>(B)</b> <sd-tag id="sdTag389" source="sdapi" category="assay" entity_type="" role="" text="Real‐time PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Real‐time PCR</sd-tag> analysis of indicated mRNA levels in <sd-tag id="sdTag390" source="sdapi" category="entity" entity_type="tissue" role="component" text="cerebellum" ext_ids="UBERON:0002037" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebellum" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cerebellum</sd-tag> of young and old <sd-tag id="sdTag391" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>. Depicted is the log2 expression ratio of target genes in old <sd-tag id="sdTag392" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> relative to young <sd-tag id="sdTag393" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>. Values are expressed as mean±s.e.m. <sup>*</sup><i>P</i>0.05 and <sup>**</sup><i>P</i>0.01 versus young, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4767"/></sd-panel><sd-panel panel_id="4768"><b>(C)</b> <sd-tag id="sdTag510" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag> analysis as in (A) but in <sd-tag id="sdTag398" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cortex" ext_ids="UBERON:0000956" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebral cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> (CTX), <sd-tag id="sdTag399" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="hippocampus" ext_ids="UBERON:0002305" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="layer of hippocampus" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">hippocampus</sd-tag> (HIP) and <sd-tag id="sdTag400" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="mid‐brain" ext_ids="UBERON:0001891" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="midbrain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">mid‐brain</sd-tag> (MB).<graphic href="https://api.sourcedata.io/file.php?panel_id=4768"/></sd-panel><sd-panel panel_id="4769"><b>(D)</b> <sd-tag id="sdTag411" source="sdapi" category="assay" entity_type="" role="" text="Western‐blot" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Western‐blot</sd-tag> analysis of indicated proteins in different brain regions of young and old <sd-tag id="sdTag412" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=4769"/></sd-panel><sd-panel panel_id="4770"><b>(E)</b> Total <sd-tag id="sdTag431" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cathepsin" ext_ids="P06797" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ctsl" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cathepsin</sd-tag> and specific <sd-tag id="sdTag428" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cathepsin B" ext_ids="P10605" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ctsb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cathepsin B</sd-tag> activity in brain extracts from young and old <sd-tag id="sdTag432" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> was determined using fluorescence probes <sd-tag id="sdTag429" source="sdapi" category="assay" entity_type="" role="" text="Z‐FR‐AMC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Z‐FR‐AMC</sd-tag> and <sd-tag id="sdTag430" source="sdapi" category="assay" entity_type="" role="" text="Z‐RR‐AMC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Z‐RR‐AMC</sd-tag>, respectively, as described in the Material and methods section. Values are expressed as mean±s.e.m. <sup>*</sup><i>P</i>0.05 versus young, <i>n</i>=3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4770"/></sd-panel><sd-panel panel_id="4771"><b>(F)</b> Expression analysis of indicated proteins in primary hippocampal astrocytic and neuronal cell cultures from young (2 months) and old (24 months) <sd-tag id="sdTag439" source="sdapi" category="entity" entity_type="organism" role="component" text="rats" ext_ids="10114" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Rattus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">rats</sd-tag>. Detection of <sd-tag id="sdTag440" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GLT1" ext_ids="P31596" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Slc1a2" ext_tax_ids="10116" ext_tax_names="Rattus norvegicus" ext_urls="https://www.uniprot.org/uniprot/">GLT1</sd-tag> and <sd-tag id="sdTag441" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeuN" ext_ids="D4A2H6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rbfox3" ext_tax_ids="10116" ext_tax_names="Rattus norvegicus" ext_urls="https://www.uniprot.org/uniprot/">NeuN</sd-tag> served as <sd-tag id="sdTag453" source="sdapi" category="entity" entity_type="cell_type" role="experiment" text="astrocyte" ext_ids="CL:0000127" norm_text="" ext_dbs="CL" in_caption="True" ext_names="astrocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">astrocyte</sd-tag> and neuron markers, respectively. Note the <sd-tag id="sdTag446" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NeuN" ext_ids="D4A2H6" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rbfox3" ext_tax_ids="10116" ext_tax_names="Rattus norvegicus" ext_urls="https://www.uniprot.org/uniprot/">NeuN</sd-tag> signals in astrocytic cultures. We attributed these signals to the presence of resting <sd-tag id="sdTag443" source="sdapi" category="entity" entity_type="subcellular" role="component" text="nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">nuclei</sd-tag> of dead neurons, which we observed under the microscope.<graphic href="https://api.sourcedata.io/file.php?panel_id=4771"/></sd-panel></fig></article>

token_classification/10-1038_emboj-2009-405.xml

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+<article doi="10.1038/emboj.2009.405" abstract="Autophagy is primarily considered a non-selective degradation process induced by starvation. Nutrient-independent basal autophagy, in contrast, imposes intracellular QC by selective disposal of aberrant protein aggregates and damaged organelles, a process critical for suppressing neurodegenerative diseases. The molecular mechanism that distinguishes these two fundamental autophagic responses, however, remains mysterious. Here, we identify the ubiquitin-binding deacetylase, histone deacetylase-6 (HDAC6), as a central component of basal autophagy that targets protein aggregates and damaged mitochondria. Surprisingly, HDAC6 is not required for autophagy activation; rather, it controls the fusion of autophagosomes to lysosomes. HDAC6 promotes autophagy by recruiting a cortactin-dependent, actin-remodelling machinery, which in turn assembles an F-actin network that stimulates autophagosome-lysosome fusion and substrate degradation. Indeed, HDAC6 deficiency leads to autophagosome maturation failure, protein aggregate build-up, and neurodegeneration. Remarkably, HDAC6 and F-actin assembly are completely dispensable for starvation-induced autophagy, uncovering the fundamental difference of these autophagic modes. Our study identifies HDAC6 and the actin cytoskeleton as critical components that define QC autophagy and uncovers a novel regulation of autophagy at the level of autophagosome-lysosome fusion."><fig id="2492"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2492"/><sd-panel panel_id="7057"><p><span><sd-tag id="sdTag325" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO MEF cells are defective in aggregate clearance but not in autophagosome induction or targeting. (</span><span>A</span><span>) <sd-tag id="sdTag327" source="sdapi" category="assay" entity_type="" role="" text="Filter‐trap analysis" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Filter‐trap analysis</sd-tag> of <sd-tag id="sdTag328" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag>‐induced, <sd-tag id="sdTag329" source="sdapi" category="entity" entity_type="molecule" role="component" text="SDS" ext_ids="CHEBI:8984" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sodium dodecyl sulfate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">SDS</sd-tag>‐insoluble ubiquitinated aggregates generated in wild‐type (WT), <sd-tag id="sdTag335" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO, and KO <sd-tag id="sdTag331" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> reconstituted with different <sd-tag id="sdTag336" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> constructs as indicated. The signal intensity from the <sd-tag id="sdTag330" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P0CG50///P0CG49///Q6ZWU9///P62984" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="//////Rps27///Uba52" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag><sd-tag id="sdTag332" source="sdapi" category="assay" entity_type="" role="" text="immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblot</sd-tag> (bottom panel) was quantified and presented as the average of the means from three independent experiments along with the standard deviation (top). Note the significant accumulation of <sd-tag id="sdTag337" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P0CG50///P0CG49///Q6ZWU9///P62984" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="//////Rps27///Uba52" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive aggregates in <sd-tag id="sdTag338" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag339" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> and KO <sd-tag id="sdTag340" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> stably expressing <sd-tag id="sdTag341" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>‐CD and ΔBUZ mutants. WT, <sd-tag id="sdTag342" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO, and <sd-tag id="sdTag343" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag344" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> stably expressing human <sd-tag id="sdTag345" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> (hHDAC6 WT), <sd-tag id="sdTag346" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> CD (catalytically inactive mutant), or <sd-tag id="sdTag347" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> ΔBUZ (<sd-tag id="sdTag348" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P0CG50///P0CG49///Q6ZWU9///P62984" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="//////Rps27///Uba52" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐binding‐deficient mutant) were analysed for the level of <sd-tag id="sdTag349" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> using an anti‐human <sd-tag id="sdTag350" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> antibody. Mouse endogenous <sd-tag id="sdTag351" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> (m<sd-tag id="sdTag334" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HDAC6" ext_ids="Q9Z2V5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">HDAC6</sd-tag>) and <sd-tag id="sdTag333" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> levels were determined by each corresponding antibody.</span></p><graphic href="https://api.sourcedata.io/file.php?panel_id=7057"/></sd-panel><sd-panel panel_id="7058"><b>(B)</b> WT and <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were treated with <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> and subjected to <sd-tag id="sdTag35" source="sdapi" category="assay" entity_type="" role="" text="Western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Western blot</sd-tag> analysis for <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>, <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag>, and <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HDAC6" ext_ids="Q9Z2V5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">HDAC6</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7058"/></sd-panel><sd-panel panel_id="7059"><b>(C)</b> Cells were treated with <sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> as described under Materials and methods and <sd-pretag id="sdPretag14389602041840" parent-tag-id="352">immunostained</sd-pretag> with antibodies to <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> (green) and <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (red). Arrows indicate <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive aggregates that colocalize with <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐positive <sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0044754" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag>. Scale bar, 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7059"/></sd-panel><sd-panel panel_id="7060"><b>(D)</b> WT and <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG5</sd-tag> KO <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> are treated with 2.5 μM <sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> for 1 day and incubated with normal growth media for 18 h. <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> <span>are <sd-tag id="sdTag352" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> with anti‐</span><sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (red) and anti‐<sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> antibody (green).<graphic href="https://api.sourcedata.io/file.php?panel_id=7060"/></sd-panel></fig><fig id="2493"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2493"/><sd-panel panel_id="7061"><b>(A)</b> Wild‐type and <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transfected with pcDNA, pcDNA‐HDAC6WT, HDAC6CD, or <sd-tag id="sdTag353" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>ΔBuz, along with <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="66734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map1lc3a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> as indicated. Yellow signals indicate non‐acidic <sd-tag id="sdTag354" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> and red signals indicate acidic <sd-tag id="sdTag355" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagolysosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagolysosomes</sd-tag>. Scale bar, 10 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7061"/></sd-panel><sd-panel panel_id="7062"><b>(B)</b> The total number of yellow <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> was quantified from three independent experiments (&gt;12 cells each) and presented as the percentage of total <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> dots (red plus yellow) along with the standard deviation.<graphic href="https://api.sourcedata.io/file.php?panel_id=7062"/></sd-panel><sd-panel panel_id="7063"><b>(C)</b><sd-tag id="sdTag86" source="sdapi" category="assay" entity_type="" role="" text="In vitro fusion assays" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><i>In vitro</i> fusion assays</sd-tag>. <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosomes</sd-tag> (APGs) and <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (Lys) purified from wild type and <sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag><sup>−/−</sup> <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were subjected to heterotypic and homotypic <i>in vitro</i> fusion assays (representative fields are shown in Supplementary Figure S3). Values are means+s.e. of the percentages of fusion from three independent experiments (more than 10 images per each experiment).<graphic href="https://api.sourcedata.io/file.php?panel_id=7063"/></sd-panel><sd-panel panel_id="7064"><b>(D)</b> <sd-tag id="sdTag91" source="sdapi" category="assay" entity_type="" role="" text="EM" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">EM</sd-tag> images of wild‐type and <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> in normal growth conditions. Yellow arrows, <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag>; red arrows, <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagolysosomes" ext_ids="GO:0005776///GO:0044754" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="autophagic vacuole///autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">autophagolysosomes</sd-tag>; green arrowheads, <sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="multilamellar bodies" ext_ids="GO:0005771" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="multivesicular body" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">multilamellar bodies</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7064"/></sd-panel><sd-panel panel_id="7065"><b>(E)</b> Quantification of <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> and <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagolysosomes" ext_ids="GO:0005776///GO:0044754" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="autophagic vacuole///autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">autophagolysosomes</sd-tag>. The error bar represents the standard error.<graphic href="https://api.sourcedata.io/file.php?panel_id=7065"/></sd-panel></fig><fig id="2494"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2494"/><sd-panel panel_id="7066"><b>(A)</b> <sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosome" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosome</sd-tag>-<sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosome" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosome</sd-tag> fusion is analysed in wild‐type and <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> with or without starvation (6 h) using <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="66734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map1lc3a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> as described in Figure 2A.<graphic href="https://api.sourcedata.io/file.php?panel_id=7066"/></sd-panel><sd-panel panel_id="7067"><b>(B)</b> Wild‐type and <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were cultured in <sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="undefined" role="component" text="Hank's solution" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Hank's solution</sd-tag> for 3 h <span>followed by <sd-pretag id="sdPretag14389612905050" parent-tag-id="368">immunoblotting</sd-pretag> with an antibody for</span> <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>, <sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HDAC6" ext_ids="Q9Z2V5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">HDAC6</sd-tag>, and <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="GAPDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAPDH</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7067"/></sd-panel><sd-panel panel_id="7068"><b>(C)</b> <sd-tag id="sdTag131" source="sdapi" category="assay" entity_type="" role="" text="Long‐lived protein degradation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Long‐lived protein degradation</sd-tag> in wild‐type and <sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEF cells" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEF cells</sd-tag>. The degradation of <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="[14C]‐valine" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">[<sup>14</sup>C]‐valine</sd-tag> <span>labelled long‐lived <sd-tag id="sdTag324" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="protein" ext_ids="CHEBI:36080" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="protein" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">protein</sd-tag> was measured in the presence or absence of 3‐methyl adenine (</span><sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3MA</sd-tag>, inhibits the formation of <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="subcellular" role="component" text="autophagic vacuoles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagic vacuoles</sd-tag>). The average of percentage degradation from three independent experiments is presented. The error bar represents the standard deviation.<graphic href="https://api.sourcedata.io/file.php?panel_id=7068"/></sd-panel></fig><fig id="2495"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2495"/><sd-panel panel_id="7069"><b>(A)</b> Wild‐type and <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag137" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were treated with <sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> and <sd-tag id="sdTag358" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> with antibodies to <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Lamp‐1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Lamp‐1</sd-tag> (a <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="subcellular" role="component" text="lysosome" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosome</sd-tag> marker, red) and <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> (green) as indicated. <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="protein" role="assayed" text="F‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">F‐actin</sd-tag> was detected by <sd-tag id="sdTag133" source="sdapi" category="assay" entity_type="" role="" text="phalloidin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">phalloidin</sd-tag> (blue). The arrows indicate <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive aggregates that are surrounded by <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="protein" role="assayed" text="F‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">F‐actin</sd-tag> and <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Lamp‐1" ext_ids="P11438" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Lamp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Lamp‐1</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7069"/></sd-panel><sd-panel panel_id="7070"><b>(B, C)</b> Wild‐type and <sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transfected with <sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag147" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="66734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map1lc3a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag>, followed by treatment with <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LatA" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LatA</sd-tag> (100 nM) or <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nocodazole" ext_ids="CHEBI:34892" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nocodazole" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nocodazole</sd-tag> (250 nM) for 6 h and analysed as described in Figure 3A.<graphic href="https://api.sourcedata.io/file.php?panel_id=7070"/></sd-panel><sd-panel panel_id="7071"><b>(D)</b> <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosomes</sd-tag> (APGs) and <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (Lys) isolated from fed <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag> <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="cell_type" role="component" text="hepatocytes" ext_ids="CL:0000182" norm_text="" ext_dbs="CL" in_caption="True" ext_names="hepatocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">hepatocytes</sd-tag> were treated or not with <sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="latrunculin" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">latrunculin</sd-tag> (<sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LatA" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LatA</sd-tag>) as indicated, extensively washed to remove traces of the inhibitor, and then labelled with the antibody and subjected to <sd-tag id="sdTag163" source="sdapi" category="assay" entity_type="" role="" text="in vitro fusion assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><i>in vitro</i> fusion assay</sd-tag> in the presence or absence of purified <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="protein" role="intervention" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag>. The number of total fusion events/total number of <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> for each condition was as follows: 176/880; 233/1110; 84/930; and 180/950. The differences with untreated samples were significant at <sup>**</sup><i>P</i>0.01.<graphic href="https://api.sourcedata.io/file.php?panel_id=7071"/></sd-panel><sd-panel panel_id="7072"><b>(E)</b> <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosomes</sd-tag> (APGs) and <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (Lys) isolated from fed or starved <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag> <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="cell_type" role="component" text="hepatocytes" ext_ids="CL:0000182" norm_text="" ext_dbs="CL" in_caption="True" ext_names="hepatocyte" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">hepatocytes</sd-tag> were treated or not with <sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="latrunculin" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">latrunculin</sd-tag> (<sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LatA" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LatA</sd-tag>) as labelled and subjected to <sd-tag id="sdTag171" source="sdapi" category="assay" entity_type="" role="" text="in vitro fusion assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><i>in vitro</i> fusion assay</sd-tag>. The differences with untreated samples were significant at <sup>*</sup><i>P</i>0.05. The number of total fusion events/total number of <sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> for each condition was as follows: 169/1250; 87/972; 190/1120; and 175/1165.<graphic href="https://api.sourcedata.io/file.php?panel_id=7072"/></sd-panel><sd-panel panel_id="7073"><b>(F)</b> <sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosomes</sd-tag> (APGs) and <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (Lys) isolated from <sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="gene" role="component" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were treated or not with <sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="latrunculin" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">latrunculin</sd-tag> (<sd-tag id="sdTag177" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LatA" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LatA</sd-tag>) as indicated and subjected to <sd-tag id="sdTag178" source="sdapi" category="assay" entity_type="" role="" text="in vitro fusion assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><i>in vitro</i> fusion assay</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7073"/></sd-panel></fig><fig id="2496"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2496"/><sd-panel panel_id="7074"><b>(A)</b> Biochemical characterization of autophagic compartments isolated from <sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="gene" role="component" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO cells. Different subcellular fractions (75 μg protein) isolated from the wild type (WT) were subjected to <sd-tag id="sdTag184" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-PAGE</sd-tag> <span>and <sd-pretag id="sdPretag14389612949370" parent-tag-id="368">immunoblotting</sd-pretag> for the indicated proteins. Hom, homogenate; APG,</span> <sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag>; APL, <sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="autophagolysosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagolysosomes</sd-tag>; Lys, <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7074"/></sd-panel><sd-panel panel_id="7075"><b>(B)</b> <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosomes</sd-tag> (APGs) and <sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> (Lys) isolated from fed cells were treated or not with <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="latrunculin" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">latrunculin</sd-tag> (<sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="LatA" ext_ids="CHEBI:69136" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="latrunculin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LatA</sd-tag>) as labelled and subjected to <sd-tag id="sdTag197" source="sdapi" category="assay" entity_type="" role="" text="in vitro fusion assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><i>in vitro</i> fusion assay</sd-tag>. The differences with untreated samples were significant at <sup>**</sup><i>P</i>0.01.<graphic href="https://api.sourcedata.io/file.php?panel_id=7075"/></sd-panel><sd-panel panel_id="7076"><b>(C)</b> WT and <sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG5</sd-tag> KO <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were treated with <sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> and <sd-tag id="sdTag359" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> with antibodies to <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> (green) as indicated. <sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="protein" role="assayed" text="F‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">F‐actin</sd-tag> was detected by <sd-tag id="sdTag203" source="sdapi" category="assay" entity_type="" role="" text="phalloidin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">phalloidin</sd-tag> (red). The arrows indicated <sd-tag id="sdTag204" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive protein aggregates.<graphic href="https://api.sourcedata.io/file.php?panel_id=7076"/></sd-panel></fig><fig id="2497"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2497"/><sd-panel panel_id="7077"><b>(A)</b> Wild‐type and <sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were treated with <sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> and <sd-tag id="sdTag360" source="sdapi" category="assay" entity_type="" role="" text="immunostained" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostained</sd-tag> with antibodies against <sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cortactin" ext_ids="Q60598" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cortactin</sd-tag> (red), <sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> (green), and <sd-tag id="sdTag214" source="sdapi" category="assay" entity_type="" role="" text="phalloidin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">phalloidin</sd-tag> for <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="protein" role="assayed" text="F‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">F‐actin</sd-tag> (blue) as indicated. The arrows indicated <sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive aggregates that were colocalized with <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="protein" role="assayed" text="F‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">F‐actin</sd-tag> and <sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cortactin" ext_ids="Q60598" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cortactin</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7077"/></sd-panel><sd-panel panel_id="7078"><b>(B)</b> Wild‐type <sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transfected with control or <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cortactin" ext_ids="13043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cortactin</sd-tag> siRNA, treated with <sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag>, and stained with antibodies for <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Lap‐1" ext_ids="P97449" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Anpep" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Lap‐1</sd-tag> (red, to label <sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosome" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosome</sd-tag>), or <sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52///Ubc///Ubb" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> (green) and <sd-tag id="sdTag224" source="sdapi" category="assay" entity_type="" role="" text="phalloidin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">phalloidin</sd-tag> for <sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="protein" role="assayed" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> (blue). Note that <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="protein" role="assayed" text="F‐actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">F‐actin</sd-tag> staining at protein aggregates was lost, but <sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosomes</sd-tag> remained concentrated in <sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cortactin" ext_ids="13043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cortactin</sd-tag> knockdown cells (arrow).<graphic href="https://api.sourcedata.io/file.php?panel_id=7078"/></sd-panel><sd-panel panel_id="7079"><p><span>(</span><span>C</span><span>) Wild‐type <sd-tag id="sdTag361" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag> were transfected with control or <sd-tag id="sdTag362" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cortactin" ext_ids="13043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cortactin</sd-tag> siRNA, treated <sd-tag id="sdTag363" source="sdapi" category="entity" entity_type="molecule" role="component" text="MG132" ext_ids="CHEBI:75142" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">MG132</sd-tag> 2.5 μM for 18 h, and subjected to <sd-tag id="sdTag365" source="sdapi" category="assay" entity_type="" role="" text="filter‐trap assay" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">filter‐trap assay</sd-tag> using a <sd-tag id="sdTag366" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P0CG49///Q6ZWU9///P62984///P0CG50" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="///Rps27///Uba52///" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> antibody. The knockdown level of endogenous <sd-tag id="sdTag367" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cortactin" ext_ids="Q60598" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cortactin</sd-tag> was confirmed by <sd-tag id="sdTag368" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> using an antibody against <sd-tag id="sdTag370" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cortactin" ext_ids="13043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cortactin</sd-tag> and <sd-tag id="sdTag369" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="GAPDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAPDH</sd-tag> in the right panel.</span></p><graphic href="https://api.sourcedata.io/file.php?panel_id=7079"/></sd-panel><sd-panel panel_id="7080"><b>(D)</b> <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="cell_line" role="component" text="U2OS cells" ext_ids="CVCL_0042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="U2OS" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">U2OS cells</sd-tag> were transfected with control siRNA and <sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cortactin" ext_ids="13043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cortactin</sd-tag> siRNA. <sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosome" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosome</sd-tag>-<sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosome" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosome</sd-tag> fusion was analysed with or without starvation (6 h) using the <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="66734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map1lc3a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> reporter as described in Figure 3A.<graphic href="https://api.sourcedata.io/file.php?panel_id=7080"/></sd-panel><sd-panel panel_id="7081"><b>(E)</b> The <sd-tag id="sdTag250" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag>‐<sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="66734" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Map1lc3a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> plasmid was cotransfected with wild type, 9KQ (acetylation‐mimic), or 9KR (deacetylation‐mimic) <sd-tag id="sdTag253" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cortactin" ext_ids="13043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Cttn" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cortactin</sd-tag>‐expressing plasmids into wild‐type <sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEFs" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEFs</sd-tag>. <sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Autophagosome" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Autophagosome</sd-tag>-<sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="lysosome" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">lysosome</sd-tag> fusion was analysed as described in Figure 3A.<graphic href="https://api.sourcedata.io/file.php?panel_id=7081"/></sd-panel></fig><fig id="2498"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2498"/><sd-panel panel_id="7082"><p><span>(</span><span>A</span><span>) <sd-tag id="sdTag372" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag373" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> accumulate <sd-tag id="sdTag374" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52//////" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive protein aggregates in the <sd-tag id="sdTag375" source="sdapi" category="entity" entity_type="tissue" role="component" text="brain" ext_ids="UBERON:0000955" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="brain" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">brain</sd-tag>. The <sd-tag id="sdTag376" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="hippocampus" ext_ids="UBERON:0001954" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="Ammon's horn" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">hippocampus</sd-tag> and <sd-tag id="sdTag377" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="cerebral cortex" ext_ids="UBERON:0000956" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebral cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cerebral cortex</sd-tag> regions from 6‐month‐old wild‐type and <sd-tag id="sdTag382" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52//////" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> KO littermates were subjected to <sd-tag id="sdTag379" source="sdapi" category="assay" entity_type="" role="" text="immunostaining" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunostaining</sd-tag> with a <sd-tag id="sdTag390" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52//////" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> antibody and counterstained with <sd-tag id="sdTag380" source="sdapi" category="assay" entity_type="" role="" text="hematoxylin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">hematoxylin</sd-tag>. The red arrows indicate <sd-tag id="sdTag384" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P62984///P0CG49///P0CG50///Q6ZWU9" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Uba52/////////Rps27" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive neuritic aggregates and black arrows indicate cytoplasmic aggregates. These <sd-tag id="sdTag383" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="Q6ZWU9///P62984///P0CG50///P0CG49" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Rps27///Uba52//////" ext_tax_ids="10090///10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive structures were rarely observed in control littermates. Scale bar, 50 μm</span></p><graphic href="https://api.sourcedata.io/file.php?panel_id=7082"/></sd-panel><sd-panel panel_id="7083"><b>(B)</b> Apoptotic cell death in the <sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="cortex" ext_ids="UBERON:0000956" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="cerebral cortex" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">cortex</sd-tag> and <sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="hippocampus" ext_ids="UBERON:0001954" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="Ammon's horn" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">hippocampus</sd-tag> region of <sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> as determined by <sd-tag id="sdTag276" source="sdapi" category="assay" entity_type="" role="" text="TUNEL" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TUNEL</sd-tag> staining. Apoptotic cells were only observed in <sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="15185" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Hdac6" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> KO <sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>. Scale bar, 100 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7083"/></sd-panel><sd-panel panel_id="7084"><b>(C)</b> <sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="32461" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HDAC6" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> depletion in the <i>Drosophila</i> <sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> leads to <sd-tag id="sdTag291" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P15357///P18101///P0CG69" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="RpS27A///RpL40///Ubi-p63E" ext_tax_ids="7227///7227///7227" ext_tax_names="Drosophila melanogaster///Drosophila melanogaster///Drosophila melanogaster" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐positive pathology. <sd-tag id="sdTag299" source="sdapi" category="assay" entity_type="" role="" text="Immunostaining" ext_ids="BAO_0002426" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunofluorescent labeling" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunostaining</sd-tag> for <sd-tag id="sdTag292" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P15357///P18101///P0CG69" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="RpS27A///RpL40///Ubi-p63E" ext_tax_ids="7227///7227///7227" ext_tax_names="Drosophila melanogaster///Drosophila melanogaster///Drosophila melanogaster" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag> (green) in frontal <sd-tag id="sdTag293" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> sections of 1‐day‐old (d1) and 30‐day‐old (d30) fly eyes. The eyes of <sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="32461" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HDAC6" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>‐depleted flies (GMR:<sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="gene" role="component" text="GAL4" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAL4</sd-tag>/UAS‐<sd-tag id="sdTag289" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="32461" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HDAC6" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>RNAi) developed <sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ubiquitin" ext_ids="P15357///P18101///P0CG69" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="RpS27A///RpL40///Ubi-p63E" ext_tax_ids="7227///7227///7227" ext_tax_names="Drosophila melanogaster///Drosophila melanogaster///Drosophila melanogaster" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ubiquitin</sd-tag>‐ positive cytoplasmic inclusions that become more prominent at day 30 (d30). Blue, <span><sd-tag id="sdTag386" source="sdapi" category="assay" entity_type="" role="" text="DAPI" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAPI</sd-tag></span>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7084"/></sd-panel><sd-panel panel_id="7085"><b>(D)</b> Depletion of <sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="32461" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HDAC6" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag> in the <i>Drosophila</i> <sd-tag id="sdTag303" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> leads to age‐dependent degeneration. <sd-tag id="sdTag300" source="sdapi" category="assay" entity_type="" role="" text="Light micrographs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Light micrographs</sd-tag> (left) and corresponding <sd-tag id="sdTag301" source="sdapi" category="assay" entity_type="" role="" text="Richardson‐stained" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Richardson‐stained</sd-tag> <span>frontal <sd-tag id="sdTag389" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> sections (right) of 1‐day‐old and 30‐day‐old fly eyes. The eyes of control flies (GMR:</span><sd-tag id="sdTag307" source="sdapi" category="entity" entity_type="gene" role="component" text="GAL4" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAL4</sd-tag>/+) and <sd-tag id="sdTag308" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="32461" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HDAC6" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>‐depleted flies (GMR:<sd-tag id="sdTag309" source="sdapi" category="entity" entity_type="gene" role="component" text="GAL4" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GAL4</sd-tag>/UAS‐HDAC6RNAi) show normal highly organized ommatidial array at day 1; 30‐day‐old control animals also show no defects, but 30‐day‐old <sd-tag id="sdTag312" source="sdapi" category="entity" entity_type="gene" role="intervention" text="HDAC6" ext_ids="32461" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="HDAC6" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">HDAC6</sd-tag>‐depleted flies show degeneration with disorganization of the ommatidial array and loss of normal <sd-tag id="sdTag313" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> architecture ( × 40 and × 80).<graphic href="https://api.sourcedata.io/file.php?panel_id=7085"/></sd-panel></fig></article>

token_classification/10-1038_emboj-2009-80.xml

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+<?xml version='1.0' encoding='UTF-8'?>
+<article doi="10.1038/emboj.2009.80" abstract="Atg8 is conjugated to phosphatidylethanolamine (PE) by ubiquitin-like conjugation reactions. Atg8 has at least two functions in autophagy: membrane biogenesis and target recognition. Regulation of PE conjugation and deconjugation of Atg8 is crucial for these functions in which Atg4 has a critical function by both processing Atg8 precursors and deconjugating Atg8-PE. Here, we report the crystal structures of catalytically inert human Atg4B (HsAtg4B) in complex with processed and unprocessed forms of LC3, a mammalian orthologue of yeast Atg8. On LC3 binding, the regulatory loop and the N-terminal tail of HsAtg4B undergo large conformational changes. The regulatory loop masking the entrance of the active site of free HsAtg4B is lifted by LC3 Phe119, so that a groove is formed along which the LC3 tail enters the active site. At the same time, the N-terminal tail masking the exit of the active site of HsAtg4B in the free form is detached from the enzyme core and a large flat surface is exposed, which might enable the enzyme to access the membrane-bound LC3-PE."><fig id="1854"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1854"/><sd-panel panel_id="4772"><b>(A)</b> Ribbon diagram of the Hs<sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>-<sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(1-120) complex. Hs<sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> is coloured salmon red, and <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> is coloured green.<graphic href="https://api.sourcedata.io/file.php?panel_id=4772"/></sd-panel><sd-panel panel_id="4773"><b>(B)</b> Structural comparison between free and Hs<sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>‐bound <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>. Crystal structure of free <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(1-120) (PDB code 1UGM) is superimposed on the Hs<sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>‐bound <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>. Hs<sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>‐bound <sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> is coloured green, and free <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> is coloured grey.<graphic href="https://api.sourcedata.io/file.php?panel_id=4773"/></sd-panel><sd-panel panel_id="4774"><b>(C)</b> Structural comparison between free and <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐bound Hs<sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>. Crystal structure of free Hs<sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> (PDB code 2CY7) is superimposed on the <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐bound Hs<sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>. <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐bound Hs<sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> is coloured salmon red, and free Hs<sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> is coloured grey. The regions with large conformational differences between free and <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐bound forms are coloured black (free) and red (<sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> bound). All the figures representing molecular structures were generated with PyMOL ( DeLano, 2002).<graphic href="https://api.sourcedata.io/file.php?panel_id=4774"/></sd-panel></fig><fig id="1855"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1855"/><sd-panel panel_id="4775"><b>(A)</b> Interaction between Hs<sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> and the ubiquitin core of <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>. Hs<sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> is coloured salmon red, and <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> is coloured green. The side chains of the residues involved in the Hs<sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>-<sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> interaction are shown as stick models. Possible hydrophilic interactions are shown as broken lines.<graphic href="https://api.sourcedata.io/file.php?panel_id=4775"/></sd-panel><sd-panel panel_id="4776"><b>(B)</b> Interaction between Hs<sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> and the C‐terminal tail of <sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>. Trp142 and the regulatory loop of Hs<sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> are coloured blue, whereas the remainder is coloured as in (A). As the side chain of Cys74 has two conformations, both conformations are shown. Possible hydrophilic interactions are shown as broken lines.<graphic href="https://api.sourcedata.io/file.php?panel_id=4776"/></sd-panel><sd-panel panel_id="4777"><b>(C)</b> <i>In vitro</i> proteolysis assay. Left, <sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> mutants fused to <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag> were incubated with Hs<sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg4B" ext_ids="23192" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg4B</sd-tag>. Right, <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-<sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag> was incubated with Hs<sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> mutants. Procedures are described in detail in Materials and methods.<graphic href="https://api.sourcedata.io/file.php?panel_id=4777"/></sd-panel></fig><fig id="1856"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1856"/><sd-panel panel_id="4778"><b>(A)</b> Annealed <i>F</i><sub>o</sub>−<i>F</i><sub>c</sub> electron density map for the C‐terminal region (residues 119-122) of <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(1-124). Left, <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(1-124) bound to the Hs<sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> H280A mutant; right, <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(1-124) bound to the Hs<sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> C74S mutant. Structure of the C‐terminal region of <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> <span>is also shown as a stick model, in which <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="carbon" ext_ids="CHEBI:27594" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbon atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">carbon</sd-tag>,</span> <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="nitrogen" ext_ids="CHEBI:25555" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nitrogen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nitrogen</sd-tag> and <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="oxygen" ext_ids="CHEBI:25805" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oxygen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">oxygen</sd-tag> atoms are coloured green, blue and red, respectively.<graphic href="https://api.sourcedata.io/file.php?panel_id=4778"/></sd-panel><sd-panel panel_id="4779"><b>(B)</b> Structure of the C‐terminal tail of <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(1-124) and the catalytic site of Hs<sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>. Left, <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(1-124) bound to Hs<sd-pretag id="sdPretag14267591738510" parent-tag-id="88" class="component protein">Atg4B</sd-pretag> H280A mutant, right, <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(1-124) bound to the Hs<sd-pretag id="sdPretag14267592251290" parent-tag-id="88" class="component protein">Atg4B</sd-pretag> C74S mutant. Hs<sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> is shown as a ribbon model, whereas <sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> is shown as a stick model. The side chains of the residues comprising the catalytic triad and Tyr54 of Hs<sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> are also shown as a stick model. <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="Carbon" ext_ids="CHEBI:27594" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbon atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Carbon</sd-tag>, <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="nitrogen" ext_ids="CHEBI:25555" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nitrogen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nitrogen</sd-tag>, <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="oxygen" ext_ids="CHEBI:25805" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oxygen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">oxygen</sd-tag> and <sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="sulphur" ext_ids="CHEBI:26833" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sulfur atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">sulphur</sd-tag> atoms are coloured green, blue, red and yellow, respectively. Mutated catalytic residues are coloured cyan.<graphic href="https://api.sourcedata.io/file.php?panel_id=4779"/></sd-panel><sd-panel panel_id="4780"><b>(C)</b> Structural comparison between the Hs<sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>-<sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> precursor and <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP2" ext_ids="Q9HC62" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP2</sd-tag>-<sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO‐3" ext_ids="P55854" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO‐3</sd-tag> precursor complexes. Left, structure of the Hs<sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>-<sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> precursor complex; right, structure of the <sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP2" ext_ids="Q9HC62" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP2</sd-tag>-<sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO‐3" ext_ids="P55854" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO‐3</sd-tag> precursor complex. Hs<sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> and <sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP2" ext_ids="Q9HC62" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP2</sd-tag> are shown as a ribbon model, whereas <sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and <sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO‐3" ext_ids="P55854" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO‐3</sd-tag> precursors are shown as a stick model. The side chains of the important residues at the catalytic site are also shown as a stick model. Atom colouring is the same as in (A, B).<graphic href="https://api.sourcedata.io/file.php?panel_id=4780"/></sd-panel></fig><fig id="1857"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1857"/><sd-panel panel_id="4781"><b>(A)</b> Surface model of free (left) and <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(1-124)‐bound (right) Hs<sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>. W142 and the regulatory loop are coloured blue, and the N‐terminal tail is coloured cyan. The catalytic Cys74 is coloured red. <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(1-124) is shown as a ribbon model.<graphic href="https://api.sourcedata.io/file.php?panel_id=4781"/></sd-panel><sd-panel panel_id="4782"><b>(B)</b> <i>In vitro</i> proteolysis assay using N‐terminal tail‐deleted Hs<sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg4B" ext_ids="23192" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg4B</sd-tag>. <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>-<sd-tag id="sdTag115" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GST" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GST</sd-tag> was incubated with either wild‐type or N‐terminally truncated <span>Hs<sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag></span> <span>and was subjected to <sd-tag id="sdTag162" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS–PAGE</sd-tag> analysis.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=4782"/></sd-panel><sd-panel panel_id="4783"><b>(C)</b> Structural comparison between free and <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag><span>(1-124)‐bound Hs<sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> and</span> <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP2" ext_ids="Q9HC62" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP2</sd-tag>-<sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO‐3" ext_ids="P55854" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO‐3</sd-tag> precursor complexes. Left, free HsAtg4B; middle, the HsAtg4B-<sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> precursor complex; right, the <sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP2" ext_ids="Q9HC62" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP2</sd-tag>-<sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO‐3" ext_ids="P55854" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO‐3</sd-tag> precursor complex. The three structures are shown in the same orientation. Model colouring is the same as in Figure 3.<graphic href="https://api.sourcedata.io/file.php?panel_id=4783"/></sd-panel><sd-panel panel_id="4784"><b>(D)</b> urface model of <sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(1-120) bound to Hs<sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>. Atom colouring is the same as in (A).<graphic href="https://api.sourcedata.io/file.php?panel_id=4784"/></sd-panel></fig><fig id="1858"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1858"/><sd-panel panel_id="4785"><b>(A)</b> Overall structure of Hs bound to both substrate and non‐substrate <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>. Substrate <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> is designated as <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(S) and coloured green, whereas non‐substrate <sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> is designated as <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>(N) and coloured blue.<graphic href="https://api.sourcedata.io/file.php?panel_id=4785"/></sd-panel><sd-panel panel_id="4786"><p><span>(</span><span>B</span><span>) Stereo‐view of the N‐terminal tail of Hs<sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> bound to the WXXL‐binding site of <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>. The side chains of the residues involved in the interaction between Hs<sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag> and <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> are labelled and shown with a stick model. Model colouring is the same as in (A).</span></p><graphic href="https://api.sourcedata.io/file.php?panel_id=4786"/></sd-panel><sd-panel panel_id="4787"><b>(C)</b> Structural comparison of the N‐terminal tail-<span><sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag></span> interaction with the <span><sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag></span>-<span><sd-tag id="sdTag171" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag></span> interaction. The structure of <span><sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag></span> complexed with a <span><sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag></span> peptide is superimposed on that complexed with the N‐terminal tail peptide. As the structure of <span><sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9BXW4///Q9H492///Q9GZQ8" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3C///MAP1LC3A///MAP1LC3B" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag></span> is almost identical to each other, only that bound to the N‐terminal tail peptide of Hs is shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=4787"/></sd-panel><sd-panel panel_id="4788"><b>(D)</b> Chemical shift perturbations of the <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> backbone amide groups upon complex formation with the N‐terminal‐tail peptide. The combined <sup>1</sup>H and <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="15N" ext_ids="CHEBI:25555" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nitrogen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId="><sup>15</sup>N</sd-tag> chemical shift differences, calculated using the equation Δp.p.m.=[(ΔδH<sub>N</sub>)<sup>2</sup>+(ΔδN/5)<sup>2</sup>]<sup>1/2</sup> were plotted against residue numbers.<graphic href="https://api.sourcedata.io/file.php?panel_id=4788"/></sd-panel><sd-panel panel_id="4789"><b>(E)</b> Mapping of chemical shift perturbation results on the crystal structure of <sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9GZQ8///Q9BXW4///Q9H492" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="MAP1LC3B///MAP1LC3C///MAP1LC3A" ext_tax_ids="9606///9606///9606" ext_tax_names="Homo sapiens///Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> bound to Hs<sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg4B" ext_ids="Q9Y4P1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG4B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg4B</sd-tag>. The residues with Δp.p.m. &gt;0.4 are shown in blue, 0.4&gt;Δp.p.m.&gt;0.3 in cyan and 0.3&gt;Δp.p.m. &gt;0.2 in green.<graphic href="https://api.sourcedata.io/file.php?panel_id=4789"/></sd-panel></fig></article>

token_classification/10-1038_emboj-2010-60.xml

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+<article doi="10.1038/emboj.2010.60" abstract="Mitochondria are crucial organelles in the production of energy and in the control of signalling cascades. A machinery of pro-fusion and fission proteins regulates their morphology and subcellular localization. In muscle this results in an orderly pattern of intermyofibrillar and subsarcolemmal mitochondria. Muscular atrophy is a genetically controlled process involving the activation of the autophagy-lysosome and the ubiquitin-proteasome systems. Whether and how the mitochondria are involved in muscular atrophy is unknown. Here, we show that the mitochondria are removed through autophagy system and that changes in mitochondrial network occur in atrophying muscles. Expression of the fission machinery is per se sufficient to cause muscle wasting in adult animals, by triggering organelle dysfunction and AMPK activation. Conversely, inhibition of the mitochondrial fission inhibits muscle loss during fasting and after FoxO3 overexpression. Mitochondrial-dependent muscle atrophy requires AMPK activation as inhibition of AMPK restores muscle size in myofibres with altered mitochondria. Thus, disruption of the mitochondrial network is an essential amplificatory loop of the muscular atrophy programme."><fig id="2588"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2588"/><sd-panel panel_id="7405"><div><strong>(A)</strong> Adult <sd-tag id="sdTag409" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> were transfected with <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>‐<sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and with <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="protein" role="reporter" text="pDsRed2" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pDsRed2</sd-tag>‐<sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Mito" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Mito</sd-tag>. Animals were starved for 24 h or denervated for 7 days. <sd-tag id="sdTag410" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="Muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Muscles</sd-tag> were exposed and observed <em>in situ</em> using <sd-tag id="sdTag3" source="sdapi" category="assay" entity_type="" role="" text="confocal in vivo microscopy" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">confocal <em>in vivo</em> microscopy</sd-tag>. At least five animals per condition have been studied. Scale bar, 20 μm.</div><graphic href="https://api.sourcedata.io/file.php?panel_id=7405"/></sd-panel><sd-panel panel_id="7406"><b>(B)</b> Adult <sd-tag id="sdTag456" source="sdapi" category="entity" entity_type="tissue" role="intervention" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> were transfected with <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>‐<sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and with <sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="protein" role="reporter" text="pDsRed2" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pDsRed2</sd-tag>‐<sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Mito" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Mito</sd-tag>. <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Lysosomes" ext_ids="GO:0005764" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="lysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Lysosomes</sd-tag> were inhibited by treating <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> <span>with 50 mg/kg of <sd-tag id="sdTag453" source="sdapi" category="entity" entity_type="molecule" role="component" text="chloroquine" ext_ids="CHEBI:3638" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="chloroquine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">chloroquine</sd-tag> for</span> 7 days<span>. <sd-tag id="sdTag452" source="sdapi" category="entity" entity_type="molecule" role="component" text="Chloroquine" ext_ids="CHEBI:3638" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="chloroquine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Chloroquine</sd-tag> treatment started at the day of denervation and lasted for</span> 7 days, whereas for fasting experiments at the 6th day of <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="molecule" role="component" text="chloroquine" ext_ids="CHEBI:3638" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="chloroquine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">chloroquine</sd-tag> injection food was removed for 24 h. <sd-tag id="sdTag457" source="sdapi" category="entity" entity_type="tissue" role="intervention" text="Muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Muscles</sd-tag> were exposed and observed <i>in situ</i> using <sd-tag id="sdTag34" source="sdapi" category="assay" entity_type="" role="" text="confocal in vivo microscopy" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">confocal <i>in vivo</i> microscopy</sd-tag>. At least five animals per condition have been studied. Scale bar, 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7406"/></sd-panel></fig><fig id="2589"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2589"/><sd-panel panel_id="7407"><b>(A)</b> Imaging of <sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag>‐mediated modification of the mitochondrial network in <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="soleus muscle" ext_ids="UBERON:0001389" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="soleus muscle" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">soleus muscle</sd-tag> of living <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>. Adult <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="soleus muscles" ext_ids="UBERON:0001389" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="soleus muscle" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">soleus muscles</sd-tag> were transfected with <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="reporter" text="pDsRed2" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pDsRed2</sd-tag>‐<sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Mito" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Mito</sd-tag> and either c.a.<sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag> or mock vector (control). Two weeks later, muscles were exposed and observed <i>in situ</i> using two‐photon microscopy. At least five animals per condition were studied.<graphic href="https://api.sourcedata.io/file.php?panel_id=7407"/></sd-panel><sd-panel panel_id="7408"><b>(B)</b> Overexpression of c.a.<sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag> induces mitochondrial changes and removal through autophagy. <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="Muscle fibres" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Muscle fibres</sd-tag> were transfected by electroporation with <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>‐<sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>, <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="protein" role="reporter" text="pDsRed2" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">pDsRed2</sd-tag>‐<sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Mito" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Mito</sd-tag> and either c.a.<sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag> or mock vector. Two weeks later, fluorescent fibres were analysed for mitochondrial distribution by <sd-tag id="sdTag59" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. A higher magnification of the square is depicted on the right panels. White arrows point <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> engulfing the <sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7408"/></sd-panel><sd-panel panel_id="7409"><b>(C)</b> Overexpression of c.a.<sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag> induces reduction in <sd-tag id="sdTag415" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="myofibre" ext_ids="GO:0030016" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="myofibril" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">myofibre</sd-tag> size and decrease in <span><sd-tag id="sdTag461" source="sdapi" category="assay" entity_type="" role="" text="SDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDH</sd-tag> staining</span>. Left image: immunostaining for <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FoxO3" ext_ids="Q9WVH4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FoxO3</sd-tag> shows atrophic fibres, which over‐expressed <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag> (red) and are labelled by asterisks. <sd-tag id="sdTag412" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Nuclei</sd-tag> are stained by <sd-tag id="sdTag413" source="sdapi" category="assay" entity_type="" role="" text="Hoechst" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Hoechst</sd-tag> (blue). Right image: <sd-tag id="sdTag414" source="sdapi" category="assay" entity_type="" role="" text="histochemistry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">histochemistry</sd-tag> <span>for <sd-tag id="sdTag459" source="sdapi" category="entity" entity_type="protein" role="assayed" text="succinate dehydrogenase" ext_ids="Q8K2B3///Q9CQA3///Q9CZB0" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Sdha///Sdhb///Sdhc" ext_tax_ids="10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">succinate dehydrogenase</sd-tag> (<sd-tag id="sdTag460" source="sdapi" category="assay" entity_type="" role="" text="SDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDH</sd-tag>) on serial section. Note that fibres positive for</span> <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag> <span>are negative for <sd-tag id="sdTag462" source="sdapi" category="assay" entity_type="" role="" text="SDH" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDH</sd-tag> staining (asterisks).</span><graphic href="https://api.sourcedata.io/file.php?panel_id=7409"/></sd-panel><sd-panel panel_id="7410"><b>(D)</b> Electron micrograph of a control and c.a.<sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag>‐expressing fibres. <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="tissue" role="component" text="Muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Muscles</sd-tag> were processed with standard fixation‐embedding procedure. Black and white arrows indicate subsarcolemmal and intermyofibrillar <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>, respectively. Note that subsarcolemmal <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> are reduced in <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag> overexpressing fibres, whereas intermyofibrillar <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> are smaller and paler than control ones. Red arrowheads show a <sd-tag id="sdTag418" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicle" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicle</sd-tag> containing <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>. The image is representative of the <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag>‐transfected fibres.<graphic href="https://api.sourcedata.io/file.php?panel_id=7410"/></sd-panel></fig><fig id="2590"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2590"/><sd-panel panel_id="7411"><div><b>(A)</b> RNAi‐mediated knockdown of <sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> showed by <sd-tag id="sdTag88" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> assay. <sd-tag id="sdTag489" source="sdapi" category="entity" entity_type="cell_line" role="component" text="MEF" ext_ids="CL:2000042" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="embryonic fibroblast" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">MEF</sd-tag> cells were transfected with vectors expressing four different <sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Fis" ext_ids="Q9CQ92" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Fis</sd-tag> shRNAs. For <i>in vivo</i> experiments <sd-pretag id="sdPretag14587471355280" parent-tag-id="484" class="component gene">Fis</sd-pretag> (4) was used. Efficiency of protein knockdown is indicated in Supplementary Table S2.</div><graphic href="https://api.sourcedata.io/file.php?panel_id=7411"/></sd-panel><sd-panel panel_id="7412"><b>(B)</b> Blockade of <sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> and of <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag> by RNAi reduces muscle loss during fasting. Adult <sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="skeletal muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">skeletal muscles</sd-tag> were transfected with specific shRNAs for <sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag> <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> (oligo 4) and <sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="organism" role="component" text="mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mouse</sd-tag> <sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag> or co‐transfected and 8 days later <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> were starved for 48 h. Cross‐sectional area (CSA) of transfected fibres, identified by <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>, was measured as described earlier (<sup>*</sup><i>P</i>0.01) <i>n</i>=450.<graphic href="https://api.sourcedata.io/file.php?panel_id=7412"/></sd-panel><sd-panel panel_id="7413"><b>(C)</b> RNAi of <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> and <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag> significantly prevents <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="gene" role="assayed" text="MuRF‐1" ext_ids="433766" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Trim63" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">MuRF‐1</sd-tag> and <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="gene" role="assayed" text="atrogin‐1" ext_ids="67731" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fbxo32" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atrogin‐1</sd-tag> promoters activation during starvation. <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA muscles" ext_ids="UBERON:0004499" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA muscles</sd-tag> were transfected with either 5 kb of the <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="gene" role="assayed" text="MuRF‐1" ext_ids="433766" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Trim63" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">MuRF‐1</sd-tag> promoter (left panel) or 3.5 kb of <sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="gene" role="assayed" text="atrogin‐1" ext_ids="67731" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fbxo32" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atrogin‐1</sd-tag> promoter (right panel) with or without shRNAs vectors against Fis and <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag>. In fasting experiments, after 7 days from transfection <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> were starved for 24 h. A <sd-tag id="sdTag423" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="renilla" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">renilla</sd-tag><span>‐<sd-tag id="sdTag486" source="sdapi" category="assay" entity_type="" role="" text="luciferase" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">luciferase</sd-tag> construct (pRL‐TK) was co‐transfected to normalized for transfection efficiency. The activation of</span> <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="gene" role="assayed" text="MuRF‐1" ext_ids="433766" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Trim63" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">MuRF‐1</sd-tag> and <sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="gene" role="assayed" text="atrogin‐1" ext_ids="67731" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fbxo32" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atrogin‐1</sd-tag> promoters was determined by <sd-tag id="sdTag425" source="sdapi" category="entity" entity_type="gene" role="reporter" text="firefly" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">firefly</sd-tag> activity and normalize for the renilla. Each condition represents the average of at least three independent experiments±s.e.m. (<sup>*</sup><i>P</i>0.05).<graphic href="https://api.sourcedata.io/file.php?panel_id=7413"/></sd-panel><sd-panel panel_id="7414"><b>(D)</b> Muscle atrophy induced by <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag> is reduced by d.n.<sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>. Adult <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="skeletal muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">skeletal muscles</sd-tag> were transfected with <sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐tagged c.a.<sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FoxO3" ext_ids="Q9WVH4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FoxO3</sd-tag> with or without d.n.<sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag> and examined after 2 weeks. CSA of transfected fibres, identified by anti‐<sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> <span><sd-pretag id="sdPretag14587464714120" parent-tag-id="471">immunofluorescence</sd-pretag>, was measured as described earlier (</span><sup>*</sup><i>P</i>0.001) <i>n</i>=400.<graphic href="https://api.sourcedata.io/file.php?panel_id=7414"/></sd-panel><sd-panel panel_id="7415"><b>(E)</b> Blockade of the fission machinery by d.n.<sd-tag id="sdTag138" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag> or <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag> inhibition by RNAi reduces <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag>‐mediated <sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosome" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosome</sd-tag> formation. Animals were transfected with <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>‐<sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>, c.a.<sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag> in presence or absence of d.n.<sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag> or shRNAs against <sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag>. Twelve days later, <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> were collected and analysed for fluorescent <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> formation (<sup>*</sup><i>P</i>0.001) <i>n</i>=450.<graphic href="https://api.sourcedata.io/file.php?panel_id=7415"/></sd-panel><sd-panel panel_id="7416"><b>(F)</b> <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag>‐dependent activation of <sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="gene" role="assayed" text="MuRF‐1" ext_ids="433766" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Trim63" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">MuRF‐1</sd-tag> and <sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="gene" role="assayed" text="atrogin‐1" ext_ids="67731" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fbxo32" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atrogin‐1</sd-tag> is significantly reduced by inhibition of the fission machinery. <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="gene" role="assayed" text="MuRF‐1" ext_ids="433766" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Trim63" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">MuRF‐1</sd-tag> promoter (left panel) or <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="gene" role="assayed" text="atrogin‐1" ext_ids="67731" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fbxo32" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atrogin‐1</sd-tag> promoter (right panel) was co‐transfected into adult <span><sd-tag id="sdTag468" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag> muscle</span> with or without c.a.<sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag> and in the presence or absence of d.n.<sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>. A <span><sd-tag id="sdTag466" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="renilla" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">renilla</sd-tag></span><span>‐<sd-tag id="sdTag467" source="sdapi" category="assay" entity_type="" role="" text="luciferase" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">luciferase</sd-tag> vector was co‐transfected to normalize for transfection efficiency. Eight days later,</span> <span><sd-tag id="sdTag463" source="sdapi" category="entity" entity_type="gene" role="reporter" text="firefly" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">firefly</sd-tag> and <sd-tag id="sdTag464" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="renilla" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">renilla</sd-tag>‐<sd-tag id="sdTag465" source="sdapi" category="assay" entity_type="" role="" text="luciferase" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">luciferase</sd-tag> activity</span> was determined. Each condition represents the average of at least three independent experiments±s.e.m. (<sup>*</sup><i>P</i>0.05).<graphic href="https://api.sourcedata.io/file.php?panel_id=7416"/></sd-panel></fig><fig id="2591"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2591"/><sd-panel panel_id="7434"><p>Overexpression of <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>/<sd-tag id="sdTag207" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> and <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag> proteins induces changes in the mitochondrial network <em>in vivo</em>. <em>In vivo</em> imaging of the mitochondrial network was performed in <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> expressing <sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag>, an atrophy‐related gene under <sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="gene" role="component" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag> control, and <sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>/<sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> proteins. Adult <sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> were transfected with plasmids encoding mitochondrially targeted yellow fluorescent protein (<sd-tag id="sdTag469" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mtM13" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mtM13</sd-tag>‐<sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>) and either mock vector, <sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag>, <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>, <sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> or <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>/<sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag>. Seven days later (for <sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag>) or 12 days later (for <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag> and <sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag>), <sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> were observed <em>in vivo</em> with <sd-tag id="sdTag227" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. <sd-tag id="sdTag235" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag> was injected into the <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> to monitor <sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>, which retain membrane potential. <sd-tag id="sdTag230" source="sdapi" category="entity" entity_type="tissue" role="component" text="Muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">Muscles</sd-tag> transfected with <sd-tag id="sdTag470" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mtM13" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mtM13</sd-tag>‐<sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag> and mock vector showed the orderly pattern of intermyofibrillar and subsarcolemmal <sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> (upper panel‐IMF). Scale bar: 20 μm.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=7434"/></sd-panel></fig><fig id="2592"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2592"/><sd-panel panel_id="7417"><b>(A)</b> Adult <sd-tag id="sdTag472" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag> muscles were transfected with either <sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>, <sd-tag id="sdTag169" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag>, <sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag> and <sd-tag id="sdTag171" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> or mock vector. Muscles were collected 12 or 21 days after transfection and cross‐sectional area of transfected fibres, identified by <span><sd-tag id="sdTag471" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunofluorescence</sd-tag></span>, was measured as described earlier (<sup>*</sup><i>P</i>0.001) <i>n</i>=400.<graphic href="https://api.sourcedata.io/file.php?panel_id=7417"/></sd-panel><sd-panel panel_id="7418"><b>(B)</b> <sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag> or <sd-tag id="sdTag192" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3 l" ext_ids="12177" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3 l</sd-tag> expression for 7 days causes a 20% reduction of the cross‐sectional area. <span><sd-tag id="sdTag476" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA muscles" ext_ids="UBERON:0004499" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_"><sd-pretag id="sdPretag14587470201670" parent-tag-id="483">TA</sd-pretag> muscles</sd-tag></span> were transfected with <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag>, <sd-tag id="sdTag190" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3l" ext_ids="12177" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3l</sd-tag> or mock vector. Cross‐sectional area of transfected fibres, identified by <sd-tag id="sdTag433" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunofluorescence</sd-tag>, was analysed (<sup>*</sup><i>P</i>0.001) <i>n</i>=500.<graphic href="https://api.sourcedata.io/file.php?panel_id=7418"/></sd-panel><sd-panel panel_id="7419"><b>(C)</b> Quantification of <sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐positive autophagic <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> in adult <sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> co‐tranfected with <sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>‐<sd-pretag id="sdPretag14682274809880" parent-tag-id="243">LC3</sd-pretag> and <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>, <sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> or <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>/<sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> expression plasmids or mock vector.<graphic href="https://api.sourcedata.io/file.php?panel_id=7419"/></sd-panel><sd-panel panel_id="7420"><b>(D)</b> Mutations in BH3 domain of <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag> (Bnip3BH3mut) do not affect BNIP3‐mediated autophagy. Adult <sd-tag id="sdTag241" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> were co‐transfected with <sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>‐<sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="67443///66734" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> and <sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag> or Bnip3BH3mut expression plasmids and <sd-tag id="sdTag245" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐positive <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0031982" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vesicle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> were quantified.<graphic href="https://api.sourcedata.io/file.php?panel_id=7420"/></sd-panel><sd-panel panel_id="7421"><b>(E)</b> <sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag>‐mediated atrophy is not modified by mutating the BH3 domain (Bnip3BH3mut). Adult <sd-tag id="sdTag477" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA muscles" ext_ids="UBERON:0004499" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue of tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_"><sd-pretag id="sdPretag14587470214810" parent-tag-id="483">TA</sd-pretag> muscles</sd-tag> were transfected with <sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag> or Bnip3BH3mut expression plasmids and cross‐sectional area was quantified 7 days later and plotted as % of controls (<sup>*</sup><i>P</i>0.001) <i>n</i>=440.<graphic href="https://api.sourcedata.io/file.php?panel_id=7421"/></sd-panel></fig><fig id="2593"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2593"/><sd-panel panel_id="7422"><b>(A)</b><i>In vivo</i> imaging of the mitochondrial network was performed in <sd-tag id="sdTag264" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> expressing Fis1<sup>K148R</sup>. Adult <sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> were transfected with plasmids encoding mitochondrially targeted yellow fluorescent protein (<sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mtM13" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mtM13</sd-tag>‐<sd-tag id="sdTag267" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>) and <sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="gene" role="component" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag><sup>K148R</sup>. Twelve days later <sd-tag id="sdTag270" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> were observed <i>in vivo</i> with <sd-tag id="sdTag271" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. <sd-tag id="sdTag272" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag> was injected into the <sd-tag id="sdTag273" source="sdapi" category="entity" entity_type="tissue" role="component" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> to monitor <sd-tag id="sdTag274" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag>, which retain membrane potential. Mitochondrial network was greatly altered but mitochondrial membrane potential was conserved.<graphic href="https://api.sourcedata.io/file.php?panel_id=7422"/></sd-panel><sd-panel panel_id="7423"><p><strong>(B)</strong> <sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="tissue" role="component" text="FDB muscle fibres" ext_ids="UBERON:0014380" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="flexor digitorum brevis muscle" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">FDB muscle fibres</sd-tag> were transfected by electroporation <em>in vivo</em>. Eight days later adult fibres were isolated and placed in cell culture. Adult fibres were loaded with <sd-tag id="sdTag284" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag> (5 nM) for 30 min at 37°C. <sd-tag id="sdTag285" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag> accumulates in the <sd-tag id="sdTag286" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> that maintain mitochondrial membrane potential. <sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Oligomycin" ext_ids="CHEBI:25675" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oligomycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Oligomycin</sd-tag> (Olm, 5 μM) and the protonophore <sd-tag id="sdTag282" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="FCCP" ext_ids="CHEBI:75458" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="carbonyl cyanide p-trifluoromethoxyphenylhydrazone" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">FCCP</sd-tag> (4 μM) were added at the indicated time points. <sd-tag id="sdTag287" source="sdapi" category="assay" entity_type="" role="" text="TMRM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TMRM</sd-tag> staining were monitored in at least 10 fibres per construct (<sup>*</sup><em>P</em>0.001).</p><graphic href="https://api.sourcedata.io/file.php?panel_id=7423"/></sd-panel><sd-panel panel_id="7424"><b>(C)</b> h<span><sd-tag id="sdTag484" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis" ext_ids="51024" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="FIS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis</sd-tag></span><sup>K148R</sup>‐transfected <sd-tag id="sdTag292" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="muscles" ext_ids="UBERON:0001134" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="skeletal muscle tissue" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">muscles</sd-tag> were collected 12 and 21 days after transfection. Cross‐sectional area of transfected fibres, identified by anti‐<sd-tag id="sdTag291" source="sdapi" category="entity" entity_type="protein" role="reporter" text="myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">myc</sd-tag> <sd-tag id="sdTag290" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunofluorescence</sd-tag>, was quantified (<i>n</i>=550).<graphic href="https://api.sourcedata.io/file.php?panel_id=7424"/></sd-panel><sd-panel panel_id="7425"><b>(D)</b> <sd-tag id="sdTag297" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag>‐dependent activation of <sd-tag id="sdTag298" source="sdapi" category="entity" entity_type="gene" role="assayed" text="MuRF‐1" ext_ids="433766" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Trim63" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">MuRF‐1</sd-tag>. <sd-tag id="sdTag299" source="sdapi" category="entity" entity_type="gene" role="assayed" text="MuRF‐1" ext_ids="433766" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Trim63" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">MuRF‐1</sd-tag> promoter was co‐transfected into adult <sd-tag id="sdTag479" source="sdapi" category="entity" entity_type="tissue" role="component" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag> muscle with or without <sd-tag id="sdTag300" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> or <span><sd-tag id="sdTag482" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Fis1" ext_ids="Q9CQ92" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Fis1</sd-tag></span><sup>K148R</sup>. A <sd-tag id="sdTag439" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="renilla" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">renilla</sd-tag>‐<sd-tag id="sdTag480" source="sdapi" category="assay" entity_type="" role="" text="luciferase" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">luciferase</sd-tag> vector was co‐transfected to normalize for transfection efficiency. Eight days later, <sd-tag id="sdTag440" source="sdapi" category="entity" entity_type="gene" role="reporter" text="firefly" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">firefly</sd-tag> and <span><sd-pretag id="sdPretag14587471685470" parent-tag-id="423">renilla</sd-pretag></span>‐<sd-tag id="sdTag481" source="sdapi" category="assay" entity_type="" role="" text="luciferase" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">luciferase</sd-tag> activity was determined. Each condition represents the average of at least five independent experiments±s.e.m. (<sup>*</sup><i>P</i>0.05).<graphic href="https://api.sourcedata.io/file.php?panel_id=7425"/></sd-panel></fig><fig id="2594"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2594"/><sd-panel panel_id="7426"><b>(A)</b> Left panel: mitochondrial fission activates <sd-tag id="sdTag327" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="AMPK" ext_ids="GO:0031588" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="AMP-activated protein kinase complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AMPK</sd-tag>. <span><sd-tag id="sdTag490" source="sdapi" category="entity" entity_type="cell_line" role="experiment" text="HEK293" ext_ids="CVCL_0045" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HEK293" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HEK293</sd-tag> cells</span> were transfected with a mock vector (control), <sd-tag id="sdTag314" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="664" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BNIP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag>, <sd-tag id="sdTag315" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="10059" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="DNM1L" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>, <sd-tag id="sdTag316" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="51024" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="FIS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> or co‐transfected with <sd-tag id="sdTag317" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="10059" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="DNM1L" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag> and <sd-tag id="sdTag318" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="51024" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="FIS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag>. Cells were collected 24 h later and lysates were analysed by <sd-tag id="sdTag323" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. Right panel: <sd-tag id="sdTag328" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> analysis shows <sd-tag id="sdTag329" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="AMPK" ext_ids="GO:0031588" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="AMP-activated protein kinase complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AMPK</sd-tag> phosphorylation in <sd-tag id="sdTag312" source="sdapi" category="entity" entity_type="tissue" role="experiment" text="EDL" ext_ids="UBERON:0001386" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="extensor digitorum longus" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">EDL</sd-tag> and <sd-tag id="sdTag311" source="sdapi" category="entity" entity_type="tissue" role="intervention" text="soleus muscles" ext_ids="UBERON:0001389" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="soleus muscle" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">soleus muscles</sd-tag> during muscle atrophy. P‐AMPK/<sd-tag id="sdTag326" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="AMPK" ext_ids="GO:0031588" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="AMP-activated protein kinase complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AMPK</sd-tag> ratio analysed by densitometric analysis is indicated below the panels. (<b>B</b>-<b>E</b>) Inhibition of <sd-tag id="sdTag330" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="AMPK" ext_ids="GO:0031588" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="AMP-activated protein kinase complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AMPK</sd-tag> blocks <sd-tag id="sdTag320" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="664" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="BNIP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag>‐ and <sd-tag id="sdTag321" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="10059" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="DNM1L" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>/<sd-tag id="sdTag322" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="51024" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="FIS1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag>‐mediated atrophy.<graphic href="https://api.sourcedata.io/file.php?panel_id=7426"/></sd-panel><sd-panel panel_id="7427"><b>(B)</b> Adult <sd-tag id="sdTag338" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA muscles" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_"><sd-pretag id="sdPretag14587469926390" parent-tag-id="483">TA</sd-pretag> muscles</sd-tag> were transfected with <sd-tag id="sdTag340" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag> together with d.n.<sd-tag id="sdTag343" source="sdapi" category="entity" entity_type="gene" role="intervention" text="AMPK" ext_ids="108079///105787" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="Prkaa2///Prkaa1" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">AMPK</sd-tag> or mock vector and cross‐sectional area was measured (<sup>*</sup><i>P</i>0.001) <i>n</i>=480.<graphic href="https://api.sourcedata.io/file.php?panel_id=7427"/></sd-panel><sd-panel panel_id="7428"><b>(C)</b> Adult <sd-tag id="sdTag344" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA muscles" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_"><sd-pretag id="sdPretag14587469947280" parent-tag-id="483">TA</sd-pretag> muscles</sd-tag> were transfected with <sd-tag id="sdTag345" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag> and <sd-tag id="sdTag346" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> together with d.n.<sd-tag id="sdTag347" source="sdapi" category="entity" entity_type="gene" role="intervention" text="AMPK" ext_ids="108079///105787" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="Prkaa2///Prkaa1" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">AMPK</sd-tag> or mock vector. Twelve days later muscles were collected and cross‐sectional area was quantified (<sup>*</sup><i>P</i>0.001) <i>n</i>=400.<graphic href="https://api.sourcedata.io/file.php?panel_id=7428"/></sd-panel><sd-panel panel_id="7429"><b>(D, E)</b> RNAi‐mediated knockdown of <sd-tag id="sdTag352" source="sdapi" category="entity" entity_type="gene" role="intervention" text="AMPK α 1" ext_ids="105787" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Prkaa1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">AMPK α 1</sd-tag> and α 2 inhibits <sd-tag id="sdTag360" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag>‐ and <sd-tag id="sdTag361" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>/<sd-tag id="sdTag362" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag>‐dependent atrophy. <sd-tag id="sdTag444" source="sdapi" category="entity" entity_type="organism" role="component" text="Mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Mouse</sd-tag> <sd-tag id="sdTag357" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA muscles" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_"><sd-pretag id="sdPretag14587470432910" parent-tag-id="483">TA</sd-pretag> muscles</sd-tag> were co‐transfected with <sd-tag id="sdTag363" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Bnip3" ext_ids="12176" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Bnip3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Bnip3</sd-tag> or <sd-tag id="sdTag364" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag> and <sd-tag id="sdTag365" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> and pSuper vectors expressing shRNAs against lacZ (control) or <sd-tag id="sdTag358" source="sdapi" category="entity" entity_type="gene" role="intervention" text="AMPK" ext_ids="108079///105787" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="Prkaa2///Prkaa1" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">AMPK</sd-tag>. Twelve days later, <sd-tag id="sdTag354" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA muscles" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_"><sd-pretag id="sdPretag14587470279420" parent-tag-id="483">TA</sd-pretag> muscles</sd-tag> were collected and the cross‐sectional area was quantified (<sup>*</sup><i>P</i>0.001) <i>n</i>=450.<graphic href="https://api.sourcedata.io/file.php?panel_id=7429"/></sd-panel></fig><fig id="2595"><title></title><label>Figure 8</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2595"/><sd-panel panel_id="7430"><b>(A)</b> <sd-tag id="sdTag368" source="sdapi" category="assay" entity_type="" role="" text="Quantitative PCR" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Quantitative PCR</sd-tag> analysis was performed in triplicates using specific oligonucleotides (see Supplementary Table 1) (<sup>*</sup><i>P</i>0.01).<graphic href="https://api.sourcedata.io/file.php?panel_id=7430"/></sd-panel><sd-panel panel_id="7431"><b>(B)</b> <sd-tag id="sdTag378" source="sdapi" category="assay" entity_type="" role="" text="Immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblotting</sd-tag> analysis shows that <sd-tag id="sdTag379" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="AICAR" ext_ids="CHEBI:18406" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="AICA ribonucleotide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">AICAR</sd-tag> treatment causes phosphorylation of <sd-tag id="sdTag382" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="AMPK" ext_ids="GO:0031588" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="AMP-activated protein kinase complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AMPK</sd-tag> and the downstream target <sd-tag id="sdTag380" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ACC" ext_ids="E9Q4Z2" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Acacb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">ACC</sd-tag> but does not affect phosphorylation of <sd-tag id="sdTag381" source="sdapi" category="entity" entity_type="protein" role="assayed" text="AKT" ext_ids="Q60823///Q9WUA6///P31750" norm_text="" ext_dbs="Uniprot///Uniprot///Uniprot" in_caption="True" ext_names="Akt2///Akt3///Akt1" ext_tax_ids="10090///10090///10090" ext_tax_names="Mus musculus///Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">AKT</sd-tag> and <sd-tag id="sdTag383" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FoxO3" ext_ids="Q9WVH4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FoxO3</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=7431"/></sd-panel><sd-panel panel_id="7432"><b>(C)</b> <sd-tag id="sdTag391" source="sdapi" category="entity" entity_type="protein" role="assayed" text="FoxO3" ext_ids="Q9WVH4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">FoxO3</sd-tag> binding to <sd-tag id="sdTag392" source="sdapi" category="entity" entity_type="gene" role="assayed" text="atrogin‐1" ext_ids="67731" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fbxo32" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atrogin‐1</sd-tag> and <sd-tag id="sdTag393" source="sdapi" category="entity" entity_type="gene" role="assayed" text="MuRF‐1" ext_ids="433766" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Trim63" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">MuRF‐1</sd-tag> promoters, as determined by <sd-tag id="sdTag395" source="sdapi" category="assay" entity_type="" role="" text="ChIP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">ChIP</sd-tag>, is induced by <sd-tag id="sdTag394" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="AICAR" ext_ids="CHEBI:18406" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="AICA ribonucleotide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">AICAR</sd-tag> treatment.<graphic href="https://api.sourcedata.io/file.php?panel_id=7432"/></sd-panel><sd-panel panel_id="7433"><b>(D)</b> RNAi‐mediated knockdown of <sd-tag id="sdTag398" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag> inhibits <sd-tag id="sdTag399" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag>/<sd-tag id="sdTag400" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag>‐dependent atrophy. <sd-tag id="sdTag408" source="sdapi" category="entity" entity_type="organism" role="component" text="Mouse" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">Mouse</sd-tag> <sd-tag id="sdTag483" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="TA" ext_ids="UBERON:0001385" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="tibialis anterior" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">TA</sd-tag> muscles were co‐transfected with <sd-tag id="sdTag401" source="sdapi" category="entity" entity_type="gene" role="intervention" text="DRP1" ext_ids="74006" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Dnm1l" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">DRP1</sd-tag> and <sd-tag id="sdTag402" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Fis1" ext_ids="66437" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Fis1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Fis1</sd-tag> and pSuper vectors expressing shRNAs against either lacZ (control) or <sd-tag id="sdTag403" source="sdapi" category="entity" entity_type="gene" role="intervention" text="FoxO3" ext_ids="56484" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Foxo3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">FoxO3</sd-tag>. Twelve days later, muscles were collected and the cross‐sectional area was quantified (<sup>*</sup><i>P</i>0.001) <i>n</i>=450.<graphic href="https://api.sourcedata.io/file.php?panel_id=7433"/></sd-panel></fig></article>

token_classification/10-1038_emboj-2010-74.xml

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+<?xml version='1.0' encoding='UTF-8'?>
+<article doi="10.1038/emboj.2010.74" abstract="Autophagy, a critical process for bulk degradation of proteins and organelles, requires conjugation of Atg8 proteins to phosphatidylethanolamine on the autophagic membrane. At least eight different Atg8 orthologs belonging to two subfamilies (LC3 and GATE-16/GABARAP) occur in mammalian cells, but their individual roles and modes of action are largely unknown. In this study, we dissect the activity of each subfamily and show that both are indispensable for the autophagic process in mammalian cells. We further show that both subfamilies act differently at early stages of autophagosome biogenesis. Accordingly, our results indicate that LC3s are involved in elongation of the phagophore membrane whereas the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation."><fig id="1924"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1924"/><sd-panel panel_id="5015"><b>(A)</b> <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3<sub>B</sub></sd-tag> (left panel) or <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> (right panel) were transfected with either non‐targeting siRNA (control siRNA) or a pool of LC3 siRNAs (A, B, C), using DharmaFect reagent. After 72 h interval, the cells were incubated for 2 h in <sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> medium in the absence or presence of 0.1 μM <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Baf A" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Baf A</sd-tag> and subjected to <span><sd-tag id="sdTag264" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> analysis</span> after lysis with RIPA extraction buffer.<graphic href="https://api.sourcedata.io/file.php?panel_id=5015"/></sd-panel><sd-panel panel_id="5016"><b>(B)</b> Quantification of relative <sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> and <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GATE‐16" ext_ids="P60520" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GATE‐16</sd-tag> level (upper panel) and degradation (lower panel) was performed as described in 'Materials and methods'. Mean±s.d. of three independent experiments is presented.<graphic href="https://api.sourcedata.io/file.php?panel_id=5016"/></sd-panel><sd-panel panel_id="5017"><b>(C)</b> <sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="gene" role="component" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> were transfected with non‐targeting siRNA or a pool of LC3 siRNAs and treated as in (<b>A</b>). The cells were subjected to immunostaining with anti‐<sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> after fixation, and analysed by <sd-tag id="sdTag24" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. The <sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> intensity of three independent experiments was measured as described in 'Materials and methods' (right panel). Scale bar: 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=5017"/></sd-panel></fig><fig id="1925"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1925"/><sd-panel panel_id="5018"><b>(A)</b> <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> (left panel) or <sd-tag id="sdTag39" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3<sub>B</sub></sd-tag> (right panel) were transfected with either non‐targeting siRNA (control siRNA) or a pool of <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAP" ext_ids="11337" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAP</sd-tag> siRNAs (<sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAP" ext_ids="11337" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAP</sd-tag>, <sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAPL1" ext_ids="11337" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAPL1</sd-tag>, and <sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag>) using DharmaFect reagent. After 72 h interval, the cells were incubated for 2 h in <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> medium in the absence or presence of 0.1 μM <sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Baf A" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Baf A</sd-tag> and subjected to <sd-tag id="sdTag265" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> analysis after lysis with RIPA extraction buffer.<graphic href="https://api.sourcedata.io/file.php?panel_id=5018"/></sd-panel><sd-panel panel_id="5019"><b>(B)</b> Quantification of relative <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> and <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3<sub>B</sub></sd-tag> level (upper panel) and degradation (lower panel) were performed as described in 'Materials and methods'. Mean±s.d. of three independent experiments is presented.<graphic href="https://api.sourcedata.io/file.php?panel_id=5019"/></sd-panel><sd-panel panel_id="5020"><b>(C)</b> <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3<sub>B</sub></sd-tag> were transfected with non‐targeting siRNA or a pool of <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAP" ext_ids="11337" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAP</sd-tag> siRNAs and treated as in (<b>A</b>). The cells were subjected to immunostaining with anti‐<sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> after fixation, and analysed by <sd-tag id="sdTag67" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. The <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> intensity of three independent experiments was measured as described in 'Materials and methods' (right panel). Scale bar: 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=5020"/></sd-panel></fig><fig id="1926"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1926"/><sd-panel panel_id="5021"><b>(A)</b> Bulk protein degradation was tested in <sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells that were transfected with non‐targeting siRNA (control siRNA), a pool of <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAP" ext_ids="11337" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAP</sd-tag>/<sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> siRNAs, or a pool of LC3 siRNAs. The rate of long‐lived protein degradation was measured in cells incubated in either <sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="undefined" role="component" text="αMEM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">αMEM</sd-tag> (control) or <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="undefined" role="intervention" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> (starvation) medium, in the presence or absence of 10 mM of <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="3‐MA" ext_ids="CHEBI:38635" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="3-methyladenine" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">3‐MA</sd-tag>, 72 h after siRNA transfection. Values expressing the protein degradation percentage are represented as the mean±s.d. of three determinations.<graphic href="https://api.sourcedata.io/file.php?panel_id=5021"/></sd-panel><sd-panel panel_id="5022"><b>(B)</b> <sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3<sub>B</sub></sd-tag> (left panel) or <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag90" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> (right panel) were transfected with a pool of <sd-tag id="sdTag91" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAP" ext_ids="11337" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAP</sd-tag>/<sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> siRNAs or a pool of LC3, respectively, and with non‐targeting siRNA. Seventy‐two hours after transfection, the cells were collected after 5 h of starvation and the relative level of <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3B" ext_ids="Q9GZQ8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LC3<sub>B</sub></sd-tag> or <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GATE‐16" ext_ids="P60520" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">GATE‐16</sd-tag> was measured using <sd-tag id="sdTag96" source="sdapi" category="assay" entity_type="" role="" text="flow cytometry" ext_ids="BAO_0000005" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="flow cytometry" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">flow cytometry</sd-tag>. Values represent the mean±s.d. of three experiments.<graphic href="https://api.sourcedata.io/file.php?panel_id=5022"/></sd-panel></fig><fig id="1927"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1927"/><sd-panel panel_id="5023"><b>(A)</b> <sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>‐<sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="gene" role="component" text="Atg5" ext_ids="9474" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag> were transfected with non‐targeting siRNA (control siRNA), a pool of LC3 siRNAs, or a pool of <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAP" ext_ids="11337" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAP</sd-tag>/<sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> siRNAs using DharmaFect reagent. Seventy‐two hours after transfection, the cells were incubated for 2 h in <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> medium, fixed, and immunostained with anti‐<sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag> antibodies. Quantification of <sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg5" ext_ids="Q9H1Y0" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg5</sd-tag> and <sd-tag id="sdTag108" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag>‐labelled puncta structures from three independent experiments is presented on the right panel. Scale bar: 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=5023"/></sd-panel><sd-panel panel_id="5024"><b>(B)</b> <sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>‐<sd-tag id="sdTag115" source="sdapi" category="entity" entity_type="gene" role="component" text="Atg5" ext_ids="9474" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag> were treated as in (<b>A</b>) and monitored by <sd-tag id="sdTag112" source="sdapi" category="assay" entity_type="" role="" text="live microscopy" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">live microscopy</sd-tag>. Quantification of the lifespan of <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg5" ext_ids="Q9H1Y0" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg5</sd-tag>‐labelled puncta structures is presented. Mean±s.d. of three independent experiments is presented. <sup>*</sup><i>P</i>0.05, <sup>**</sup><i>P</i>0.001.<graphic href="https://api.sourcedata.io/file.php?panel_id=5024"/></sd-panel><sd-panel panel_id="5025"><b>(C)</b> <sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>‐<sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="gene" role="component" text="Atg5" ext_ids="9474" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag> cells were transfected with siRNA pool and starved as in (<b>A</b>). Cryo sections of fixed cells were immunolabelled using anti‐<sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> antibodies and analysed by <sd-tag id="sdTag137" source="sdapi" category="assay" entity_type="" role="" text="TEM" ext_ids="BAO_0000455" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="transmission electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">TEM</sd-tag> as described in 'Materials and methods'. Quantification of the <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="gene" role="component" text="Atg5" ext_ids="9474" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG5" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag>‐labelled structures size is presented at the right panel. <sup>*</sup><i>P</i>0.05, <sup>**</sup><i>P</i>0.001.<graphic href="https://api.sourcedata.io/file.php?panel_id=5025"/></sd-panel></fig><fig id="1928"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1928"/><sd-panel panel_id="5026"><b>(A)</b> Control <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells and <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3<sub>B</sub></sd-tag> or <sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> were starved for 2 h in <sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> medium fixed and immunostained with anti‐<sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag> antibodies. Quantification of <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag>‐labelled puncta structures from three independent experiments is presented at the right panel. Arrowheads represent <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg‐16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg‐16</sd-tag>‐labelled puncta. Scale bar: 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=5026"/></sd-panel><sd-panel panel_id="5027"><b>(B)</b> <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3<sub>B</sub></sd-tag> (left panel) or <sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> (middle panel) were starved for 2 h in <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> medium. The cells were fixed and their cryo sections were immunolabelled as in ( Figure 4B). Quantification of the size of <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐labelled structures (right panel) from three independent experiments is presented. <sup>*</sup><i>P</i>0.05, <sup>**</sup><i>P</i>0.001.<graphic href="https://api.sourcedata.io/file.php?panel_id=5027"/></sd-panel></fig><fig id="1929"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1929"/><sd-panel panel_id="5028"><b>(A, B)</b> Control <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells and <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag177" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3<sub>B</sub></sd-tag> (<b>A</b>) or <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag168" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> (<b>B</b>) were transfected with the reciprocal siRNA pools using DharmaFect reagent. After 72 h interval, the cells were incubated for 2 h in <sd-tag id="sdTag171" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag>, subjected to immunostaining with anti‐<sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag> after fixation, and analysed by <sd-tag id="sdTag174" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Quantification of cells containing <sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag> structures larger than 2 μm (<b>A</b>) or <sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag>‐labelled puncta structures (<b>B</b>) from three independent experiments in comparison to control and to G to A mutants (<b>D</b>) is presented at the lower panel. Scale bar: 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=5028"/></sd-panel><sd-panel panel_id="5029"><b>(C)</b> <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing silent <sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3<sub>B</sub></sd-tag> or <sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> were transfected with their siRNA pools using DharmaFect reagent. After 72‐h interval, the cells were incubated for 2 h in <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> medium and subjected to immunostaining with anti‐<sd-tag id="sdTag190" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag> and anti‐<sd-tag id="sdTag191" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> antibodies followed by fixation. The cells were analysed by <sd-tag id="sdTag192" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag>. Arrows represent cells, which do not express <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> proteins whereas arrowheads represent cells, which express <sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐proteins. Quantification of <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag>‐labelled puncta structures from three independent experiments is presented at the right panel. Scale bar: 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=5029"/></sd-panel><sd-panel panel_id="5030"><b>(D)</b> <sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag267" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3<sub>B</sub></sd-tag><sup>G120A</sup> or <sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<span><sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag></span><sup>G116A</sup>were transfected with either pool of <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GABARAP" ext_ids="11337" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAP" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GABARAP</sd-tag>/<sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> siRNAs or LC3 siRNAs, respectively, and a non‐targeting siRNA. The cells were starved for 2 h, fixed, and immunostained with anti‐<sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag> and anti‐<sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="Q13501" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SQSTM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> antibodies. Quantification is presented in (<b>A</b>, <b>B</b>) at the lower panels. Scale bar: 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=5030"/></sd-panel><sd-panel panel_id="5031"><b>(E)</b> <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3<sub>B</sub></sd-tag> (left panel) or <sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> (right panel) were transfected with the reciprocal siRNA pool or with non‐targeting siRNA and starved for 2 h in <sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> medium. The cells were fixed and their cryo sections were immuno‐labelled using anti‐<sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> antibodies and analysed by <sd-tag id="sdTag216" source="sdapi" category="assay" entity_type="" role="" text="TEM" ext_ids="BAO_0000455" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="transmission electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">TEM</sd-tag> as described in 'Materials and methods'. Quantification of cells containing <sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag> structures larger than 2 μm (left panel) or the size of <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag>‐labelled structures (right panel) is presented.<graphic href="https://api.sourcedata.io/file.php?panel_id=5031"/></sd-panel></fig><fig id="1930"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1930"/><sd-panel panel_id="5032"><b>(A)</b> Control <sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells and <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells stably expressing <sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="gene" role="intervention" text="LC3B" ext_ids="81631" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MAP1LC3B" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">LC3<sub>B</sub></sd-tag> or <sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GATE‐16" ext_ids="11345" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GABARAPL2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GATE‐16</sd-tag> were transfected with <sd-tag id="sdTag260" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Hs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Hs</sd-tag><span><sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg4A" ext_ids="115201" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG4A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg4A</sd-tag></span><sup>C77A</sup>‐<sd-tag id="sdTag235" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>‐<sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="protein" role="reporter" text="His6" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His6</sd-tag>. After 48 h interval, the cells were incubated for 2 h in <sd-tag id="sdTag229" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag>, and subjected to immunostaining with anti‐<sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag> and anti‐myc followed by <sd-tag id="sdTag232" source="sdapi" category="assay" entity_type="" role="" text="confocal microscopy" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">confocal microscopy</sd-tag> analysis. Quantification of cells containing <sd-tag id="sdTag233" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg16" ext_ids="Q676U5" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG16L1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">Atg16</sd-tag> structures larger than 2 μm from three independent experiments is presented at the right panel. Scale bar: 20 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=5032"/></sd-panel><sd-panel panel_id="5033"><b>(B)</b> <sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were transfected with <sd-tag id="sdTag261" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Hs" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Hs</sd-tag><span><sd-tag id="sdTag263" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg4A" ext_ids="115201" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG4A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg4A</sd-tag></span><sup>C77A</sup>‐<sd-tag id="sdTag241" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag>‐<sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="protein" role="reporter" text="His6" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His6</sd-tag> or empty vector (mock). After a 48 h interval, the cells were incubated for 2 h in <sd-tag id="sdTag245" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag>, fixed, and their ultrathin sections were analysed by <sd-tag id="sdTag246" source="sdapi" category="assay" entity_type="" role="" text="TEM" ext_ids="BAO_0000455" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="transmission electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">TEM</sd-tag> as described in 'Materials and methods'. <sup>*</sup><i>P</i>0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=5033"/></sd-panel></fig></article>

token_classification/10-1038_emboj-2011-1.xml

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+<article doi="10.1038/emboj.2011.1" abstract="Large alterations in transcription accompany neurodegeneration in polyglutamine (polyQ) diseases. These pathologies manifest both general polyQ toxicity and mutant protein-specific effects. In this study, we report that the fat tumour suppressor gene mediates neurodegeneration induced by the polyQ protein Atrophin. We have monitored early transcriptional alterations in a Drosophila model of Dentatorubral-pallidoluysian Atrophy and found that polyQ Atrophins downregulate fat. Fat protects from neurodegeneration and Atrophin toxicity through the Hippo kinase cascade. Fat/Hippo signalling does not provoke neurodegeneration by stimulating overgrowth; rather, it alters the autophagic flux in photoreceptor neurons, thereby affecting cell homeostasis. Our data thus provide a crucial insight into the specific mechanism of a polyQ disease and reveal an unexpected neuroprotective role of the Fat/Hippo pathway."><fig id="1955"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1955"/><sd-panel panel_id="5126"><b>(A)</b> <span>Illustration of the crossing and ageing scheme used to obtain total RNA extracts from</span> <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="organism" role="assayed" text="fly" ext_ids="7227" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Drosophila melanogaster" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">fly</sd-tag> <span>heads for the transcriptional profiling and all successive</span> <sd-tag id="sdTag2" source="sdapi" category="assay" entity_type="" role="" text="qPCR" ext_ids="BAO_0002084" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="real-time PCR " ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">qPCR</sd-tag> <span>assays. Expression of different</span> <sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atrophin" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atrophin</sd-tag> <span>forms with the</span> <i><sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="gene" role="component" text="GMR" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GMR</sd-tag></i> <span>driver was induced, owing to a temperature‐sensitive mutant</span> <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="gene" role="component" text="Gal80" ext_ids="854954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL80" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Gal80</sd-tag> <span>repressor. F1 flies were allowed to develop at 18°C; at this temperature the <sd-tag id="sdTag380" source="sdapi" category="entity" entity_type="gene" role="component" text="Gal80" ext_ids="854954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL80" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Gal80</sd-tag> repressor keeps transgenes silent. Newly eclosed flies (</span><sd-tag id="sdTag6" source="sdapi" category="time" entity_type="" role="" text="0-48 h" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">0-48 h</sd-tag><span>) were collected and killed immediately (0d) or aged for</span> <sd-tag id="sdTag7" source="sdapi" category="time" entity_type="" role="" text="2 or 14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">2 or <sd-pretag id="sdPretag14309060407540" parent-tag-id="207" class="time">14</sd-pretag> days</sd-tag> <span>at 29°C. This inactivates <sd-tag id="sdTag381" source="sdapi" category="entity" entity_type="gene" role="component" text="Gal80" ext_ids="854954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL80" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Gal80</sd-tag> and transgenes are switched on by</span> <i><sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="gene" role="component" text="GMR" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GMR</sd-tag>‐<sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="gene" role="component" text="Gal4" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Gal4</sd-tag></i><span>. This protocol allows comparing siblings that differ exclusively in their age and transgenes expression. Control flies crossed to</span> <i><sd-tag id="sdTag383" source="sdapi" category="entity" entity_type="gene" role="component" text="GMR" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GMR</sd-tag>‐<sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="gene" role="component" text="Gal4" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Gal4</sd-tag>;</i> <i>Ubi<sd-tag id="sdTag376" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Gal80" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Gal80</sd-tag></i><sup><i>ts</i></sup> <span>in all experiments are from the</span> <i>w</i><sup><i>1118</i></sup> <span>stock in which all</span> <sd-tag id="sdTag333" source="sdapi" category="entity" entity_type="gene" role="component" text="UAS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UAS</sd-tag> <span>transgenes have been generated.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=5126"/></sd-panel><sd-panel panel_id="5127"><b>(B)</b> Tangential <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> sections of flies representative of all the different populations used in the microarray analysis at all different time points. Weak degeneration is only visible after <sd-tag id="sdTag17" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">14 days</sd-tag> with polyQ <sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag>; in particular with <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag>75QN there is an initial loss of <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="photoreceptors" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptors</sd-tag> (<sd-tag id="sdTag336" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag>, arrow), 30.7% of the <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="tissue" role="component" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag> has lost at least 1 <sd-tag id="sdTag337" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag>, that is only 5.1% of all <sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neuronal" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neuronal</sd-tag> <sd-tag id="sdTag401" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag> have been lost at this stage (<i>N</i>=333).<graphic href="https://api.sourcedata.io/file.php?panel_id=5127"/></sd-panel></fig><fig id="1956"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1956"/><sd-panel panel_id="5128"><b>(A)</b> Heat maps for three subsets of the pattern clustering analysis generated using the Euclidean Distance metric. Upregulated genes are in red and downregulated genes are in green. The downregulating transcriptional activity increases with time. The main branch in clustering of the different <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag> mutants is along time points. See also Supplementary Figure 4.<graphic href="https://api.sourcedata.io/file.php?panel_id=5128"/></sd-panel></fig><fig id="1957"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1957"/><sd-panel panel_id="5130"><b>(A)</b> <sd-tag id="sdTag33" source="sdapi" category="assay" entity_type="" role="" text="qPCR" ext_ids="BAO_0002084" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="real-time PCR " ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">qPCR</sd-tag> analysis of the fold changes±s.<sd-pretag id="sdPretag14309063625720" parent-tag-id="235">d</sd-pretag>. of <i><sd-pretag id="sdPretag14309032074940" parent-tag-id="38">ft</sd-pretag></i> transcription. Downregulation starts at 2 days and progresses at <sd-tag id="sdTag34" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14309060673080" parent-tag-id="207">14</sd-pretag> days</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=5130"/></sd-panel><sd-panel panel_id="5131"><b>(B)</b> <sd-tag id="sdTag42" source="sdapi" category="assay" entity_type="" role="" text="qPCR" ext_ids="BAO_0002084" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="real-time PCR " ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">qPCR</sd-tag> analysis of the enrichment±s.<sd-pretag id="sdPretag14309063581940" parent-tag-id="235">d</sd-pretag>. of different regions of the <i><sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="gene" role="assayed" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i> regulatory elements in <sd-tag id="sdTag39" source="sdapi" category="assay" entity_type="" role="" text="ChIP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">ChIP</sd-tag> for <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag> from <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="organism" role="component" text="BG3" ext_ids="7227" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Drosophila melanogaster" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">BG3</sd-tag><sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neuronal" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neuronal</sd-tag> cell extracts. Enrichment is calculated as the percentage of <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="DNA" ext_ids="CHEBI:16991" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="deoxyribonucleic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DNA</sd-tag><sd-tag id="sdTag41" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> from extracts of cells in which <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag> expression has been induced, with respect to the amount <sd-tag id="sdTag46" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> from uninduced cell extracts according to the (<sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag>-No Ab)<sub>induced</sub>/(<sd-tag id="sdTag384" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag>−No Ab)<sub>uninduced</sub> formula. The <sd-tag id="sdTag385" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="DNA" ext_ids="CHEBI:16991" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="deoxyribonucleic acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">DNA</sd-tag> region from <sd-tag id="sdTag54" source="sdapi" category="entity" entity_type="subcellular" role="normalizing" text="IV chromosome" ext_ids="GO:0005694" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="chromosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">IV chromosome</sd-tag> has been previously shown not to be <sd-tag id="sdTag49" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> in <sd-tag id="sdTag50" source="sdapi" category="assay" entity_type="" role="" text="ChIP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">ChIP</sd-tag> for <sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag> ( Haecker <i>et al</i>, 2007) and has been used as a negative control.<graphic href="https://api.sourcedata.io/file.php?panel_id=5131"/></sd-panel><sd-panel panel_id="5132"><b>(C)</b> Histograms showing the number of <sd-tag id="sdTag62" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag> with a full complement (7) of <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag> in flies expressing <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="gene" role="component" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag>75QN with the <i><sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="gene" role="component" text="Rhodopsin1" ext_ids="42367" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ninaE" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Rhodopsin1</sd-tag></i> driver in either a control (<i>w</i><sup><i>1118</i></sup>) or different mutant backgrounds and aged at 29°C for <sd-tag id="sdTag57" source="sdapi" category="time" entity_type="" role="" text="28 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">28 days</sd-tag>. Heterozygosis for two independent <i><sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i> alleles and a <i><sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sav" ext_ids="252554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="sav" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sav</sd-tag></i> allele significantly enhances the loss of <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag>. Mild overexpression of <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Wts" ext_ids="43651" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="wts" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Wts</sd-tag> via a <i><sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="gene" role="component" text="GMR" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GMR</sd-tag>-<sd-tag id="sdTag339" source="sdapi" category="entity" entity_type="gene" role="intervention" text="wts" ext_ids="43651" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="wts" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">wts</sd-tag></i> transgene, which does not display any strong phenotype <i>per se</i>, significantly suppresses the loss of <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag>. No interaction was detected in this assay with <i><sd-tag id="sdTag402" source="sdapi" category="entity" entity_type="gene" role="intervention" text="wts" ext_ids="43651" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="wts" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">wts</sd-tag></i><sup><i>x1</i></sup> and <i><sd-tag id="sdTag61" source="sdapi" category="entity" entity_type="gene" role="intervention" text="yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">yki</sd-tag></i><sup><i>B5</i></sup> alleles in heterozygosity. <i>N</i>=430-963 from at least four <sd-tag id="sdTag340" source="sdapi" category="entity" entity_type="tissue" role="component" text="eyes" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eyes</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=5132"/></sd-panel><sd-panel panel_id="5133"><b>(D)</b> Tangential <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> sections and histograms showing the degeneration of <i><sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="gene" role="component" text="GMR" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GMR</sd-tag></i>&gt;<i><sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag>75QN, Ubi-<sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="gene" role="component" text="Gal80" ext_ids="854954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL80" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Gal80</sd-tag></i><sup><i>ts</i></sup> flies in combination with different <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="gene" role="component" text="UAS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UAS</sd-tag> transgenes and aged <sd-tag id="sdTag71" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14309060752250" parent-tag-id="207" class="time">14</sd-pretag> days</sd-tag> as in Figure 1A. <i><sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="gene" role="component" text="UAS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UAS</sd-tag>-<sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="EGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EGFP</sd-tag></i> is used as a negative control. Either <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Ft</sd-tag> or <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Wts" ext_ids="43651" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="wts" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Wts</sd-tag> overexpression strongly suppresses loss of <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag> caused by <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag>75QN. Lower panels are provided as examples of quantification. A more modest but still significant rescue is observed by overexpressing a <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Yki</sd-tag> RNAi contruct or <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Hpo" ext_ids="37247" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="hpo" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Hpo</sd-tag>; however, in this case it is to be considered that the overexpression of <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Hpo" ext_ids="37247" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="hpo" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Hpo</sd-tag><i>per se</i> brings about the loss of at least one <sd-tag id="sdTag386" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag> in ∼5% of <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag> (data not shown). No effect is detected with overexpression of <sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Sav" ext_ids="252554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="sav" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Sav</sd-tag>. Two‐tailed <i>t</i>‐test: <sup>*</sup><i>P</i>0.05; <sup>**</sup><i>P</i>0.01. The <i><sd-tag id="sdTag92" source="sdapi" category="entity" entity_type="gene" role="intervention" text="wts" ext_ids="43651" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="wts" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">wts</sd-tag></i><sup><i>EPG4808</i></sup> is a previously uncharacterised EP element insertion at the 5′ of the <i><sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="gene" role="intervention" text="wts" ext_ids="43651" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="wts" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">wts</sd-tag></i> gene. Rare homozygous escapers display larger <sd-pretag id="sdPretag14309060522520" parent-tag-id="206" class="component tissue">eyes</sd-pretag>, whereas in combination with <i><sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="gene" role="component" text="GMR" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GMR</sd-tag>-GMR</i> this line gives rise to smaller rough <sd-pretag id="sdPretag14309060366160" parent-tag-id="206" class="component tissue">eyes</sd-pretag>, and, finally, GMR analysis of <i><sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="gene" role="component" text="GMR" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GMR</sd-tag></i>&gt;<i><sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="gene" role="intervention" text="wts" ext_ids="43651" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="wts" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">wts</sd-tag></i><sup><i>EPG4808</i></sup> indicates a 10‐fold increase in the head content of <i><sd-tag id="sdTag387" source="sdapi" category="entity" entity_type="gene" role="intervention" text="wts" ext_ids="43651" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="wts" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">wts</sd-tag></i> mRNA (data not shown).<graphic href="https://api.sourcedata.io/file.php?panel_id=5133"/></sd-panel></fig><fig id="1958"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1958"/><sd-panel panel_id="5134"><b>(A)</b> Tangential <sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> sections through <i><sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup> clones aged 1, 7 and <sd-tag id="sdTag98" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14309060922680" parent-tag-id="207" class="time">14</sd-pretag> days</sd-tag>, of <i><sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup>,<i><sd-pretag id="sdPretag14309064061650" parent-tag-id="235" class="component gene">d</sd-pretag></i><sup><i>DGC13</i></sup> double mutant clones and of <i><sd-tag id="sdTag388" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup> clones in a <i><sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="gene" role="intervention" text="yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">yki</sd-tag></i><sup><i>B5</i></sup> heterozygous background aged <sd-tag id="sdTag102" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14309060439570" parent-tag-id="207" class="time">14</sd-pretag> days</sd-tag>. Clones are marked by the absence of yellow pigment. Arrows point at degenerating <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="photoreceptors" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptors</sd-tag>, arrowheads point at intact wt <sd-tag id="sdTag389" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="photoreceptors" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptors</sd-tag> in mosaic <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag>. The circled <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidium" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidium</sd-tag> is genetically <i>wt</i> but non‐autonomously flipped in its polarity and has not degenerated. Lower panels are masks that show clonal borders and quantification of <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag> number per <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag>. After <sd-tag id="sdTag108" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14309060039830" parent-tag-id="207" class="time">14</sd-pretag> days</sd-tag>, almost all <i><sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup> cells have degenerated, whereas almost all <i><sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup>,<i><sd-pretag id="sdPretag14309064187860" parent-tag-id="235" class="component gene">d</sd-pretag></i><sup><i>DGC13</i></sup> and some <i><sd-tag id="sdTag390" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup>,<i><sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="gene" role="intervention" text="yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">yki</sd-tag></i><sup><i>B5</i>/+</sup> <sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="cell_type" role="component" text="neuronal" ext_ids="CL:0000540" norm_text="" ext_dbs="CL" in_caption="True" ext_names="neuron" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">neuronal</sd-tag><sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="photoreceptors" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptors</sd-tag> have not.<graphic href="https://api.sourcedata.io/file.php?panel_id=5134"/></sd-panel><sd-panel panel_id="5135"><b>(B)</b> Histograms showing the quantification of degeneration in <i><sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup>, <i><sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup><i><sd-tag id="sdTag330" source="sdapi" category="entity" entity_type="gene" role="intervention" text="d" ext_ids="33245" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ds" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">d</sd-tag></i><sup><i>DGC13</i></sup> and <i><sd-tag id="sdTag391" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup><i><sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="gene" role="intervention" text="yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">yki</sd-tag></i><sup><i>B5</i>/+</sup> clones. Loss of <i><sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i> leads to statistically significant loss of neurons and this is suppressed at <sd-tag id="sdTag123" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">14 days</sd-tag> by <i><sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="gene" role="intervention" text="yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">yki</sd-tag></i><sup><i>B5</i></sup>and much more dramatically by <i><sd-tag id="sdTag332" source="sdapi" category="entity" entity_type="gene" role="intervention" text="d" ext_ids="33245" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ds" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">d</sd-tag></i><sup><i>DGC13</i></sup>. <sup>***</sup><i>P</i>0.001, <sup>**</sup><i>P</i>0.01; <sup>*</sup><i>P</i>0.05 in two‐tailed <i>t</i>‐test.<graphic href="https://api.sourcedata.io/file.php?panel_id=5135"/></sd-panel><sd-panel panel_id="5136"><b>(C)</b> Degeneration in mosaic <sd-tag id="sdTag132" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag> in <i><sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup> clones. At this stage of degeneration approximately half of the non‐pigmented (genotypically mutant) <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag> cells display a degenerative phenotype, whereas virtually all pigmented (genotypically <i>wt</i>) <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag> cells are normal. <i>χ</i><sup>2</sup>‐test: 82.38; <i>P</i>0.001. Total <sd-tag id="sdTag392" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag> <i>N</i>=310 (pigmented) and 327 (not pigmented).<graphic href="https://api.sourcedata.io/file.php?panel_id=5136"/></sd-panel><sd-panel panel_id="5137"><b>(D)</b> Tangential <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> sections through <sd-tag id="sdTag139" source="sdapi" category="assay" entity_type="" role="" text="MARCM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MARCM</sd-tag> clone mutants for <i><sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup> that express either no transgene or an RNAi construct against <i><sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="gene" role="intervention" text="yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">yki</sd-tag></i> (<i><sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="gene" role="component" text="UAS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UAS</sd-tag>-<sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="gene" role="intervention" text="yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">yki</sd-tag></i><sup><i>IR</i></sup>) with <i><sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="gene" role="component" text="Tub" ext_ids="40554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="tub" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Tub</sd-tag>-<sd-tag id="sdTag147" source="sdapi" category="entity" entity_type="gene" role="component" text="Gal4" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Gal4</sd-tag></i> and aged <sd-tag id="sdTag148" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14309060255250" parent-tag-id="207" class="time">14</sd-pretag> days</sd-tag> at 29°C. Because the transgene <i><sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="gene" role="component" text="UAS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UAS</sd-tag>-<sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="gene" role="intervention" text="yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">yki</sd-tag></i><sup><i>IR</i></sup> is on <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="subcellular" role="component" text="chromosomal arm 2 L" ext_ids="GO:0044427" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="chromosomal part" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">chromosomal arm 2 L</sd-tag>, the same as <i><sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i>, clones generated with this system carry two copies of <i><sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="gene" role="component" text="UAS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UAS</sd-tag>-<sd-tag id="sdTag154" source="sdapi" category="entity" entity_type="gene" role="intervention" text="yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">yki</sd-tag></i><sup><i>IR</i></sup> and therefore downregulate <i><sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="gene" role="intervention" text="yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">yki</sd-tag></i> very effectively. No other cell outside the clones expresses the construct and is therefore wt for <i><sd-tag id="sdTag393" source="sdapi" category="entity" entity_type="gene" role="intervention" text="yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">yki</sd-tag></i>. Mask panel is presented on the right of each section. A quantification of <sd-tag id="sdTag341" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="photoreceptor" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptor</sd-tag> numbers (far right) displays a very significant increase in the number of wt <sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag> (<i>N</i>=210 and 219 from four <sd-pretag id="sdPretag14309060310440" parent-tag-id="206" class="component tissue">eyes</sd-pretag>). <sup>***</sup><i>P</i>0.001 in two‐tailed <i>t</i>‐test. If all classes of <sd-tag id="sdTag394" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag> are considered, <i>χ</i><sup>2</sup>‐test=232.30; <i>P</i>0.001 for 3 degrees of freedom.<graphic href="https://api.sourcedata.io/file.php?panel_id=5137"/></sd-panel></fig><fig id="1959"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1959"/><sd-panel panel_id="5138"><b>(A)</b> Tangential <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> sections through <i><sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="gene" role="component" text="wts" ext_ids="43651" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="wts" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">wts</sd-tag></i><sup><i>X1</i></sup> mutant <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="organism" role="component" text="fly" ext_ids="7227" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Drosophila melanogaster" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">fly</sd-tag> <sd-tag id="sdTag342" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eyes" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eyes</sd-tag>. In clones for the null <i><sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="gene" role="component" text="wts" ext_ids="43651" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="wts" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">wts</sd-tag></i><sup><i>X1</i></sup> allele, degeneration inside the clones is at severe stages at <sd-tag id="sdTag165" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14309060300930" parent-tag-id="207" class="time">14</sd-pretag> days</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=5138"/></sd-panel><sd-panel panel_id="5139"><b>(B)</b> Tangential <sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> sections through <i><sd-tag id="sdTag172" source="sdapi" category="entity" entity_type="gene" role="component" text="sav" ext_ids="252554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="sav" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sav</sd-tag></i><sup><i>3</i></sup> clones. In <i><sd-tag id="sdTag395" source="sdapi" category="entity" entity_type="gene" role="component" text="sav" ext_ids="252554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="sav" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sav</sd-tag></i><sup><i>3</i></sup> after enclosure many <sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="photoreceptors" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptors</sd-tag> are intact but after <sd-tag id="sdTag174" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14309060877440" parent-tag-id="207">14</sd-pretag> days</sd-tag> at 29°C most <i><sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="gene" role="component" text="sav" ext_ids="252554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="sav" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sav</sd-tag></i> mutant <sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="photoreceptors" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptors</sd-tag> have degenerated.<graphic href="https://api.sourcedata.io/file.php?panel_id=5139"/></sd-panel><sd-panel panel_id="5140"><b>(C)</b> Histograms showing the quantification of <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag> with the full complement of <sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="photoreceptors" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptors</sd-tag> in <i><sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="gene" role="intervention" text="hpo" ext_ids="37247" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="hpo" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">hpo</sd-tag></i>, <i><sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="gene" role="intervention" text="wts" ext_ids="43651" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="wts" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">wts</sd-tag></i> and <i><sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="gene" role="intervention" text="sav" ext_ids="252554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="sav" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sav</sd-tag></i> mutant clones. The progression of loss of <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="photoreceptors" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptors</sd-tag> is evident and statistically significant in all cases. Mutants for <i><sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="gene" role="intervention" text="hpo" ext_ids="37247" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="hpo" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">hpo</sd-tag></i><sup><i>BF33</i></sup> do not survive for <sd-tag id="sdTag189" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14309060321470" parent-tag-id="207">14</sd-pretag> days</sd-tag> at 29<sup>o</sup>C and corresponding sections are shown in Supplementary Figure 12. <i>N</i>=195-268. <sup>***</sup><i>P</i>0.001, <sup>**</sup><i>P</i>0.01; <sup>*</sup><i>P</i>0.05 in two‐tailed <i>t</i>‐test.<graphic href="https://api.sourcedata.io/file.php?panel_id=5140"/></sd-panel></fig><fig id="1960"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1960"/><sd-panel panel_id="5141"><b>(A)</b> <sd-tag id="sdTag204" source="sdapi" category="assay" entity_type="" role="" text="Regression analysis" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Regression analysis</sd-tag> of the overgrowth versus the neurodegeneration observed in loss of function mutants (left) and overexpression of transgenes (right). Overgrowth quantification is shown in Supplementary Figure <sd-pretag id="sdPretag14309060079620" parent-tag-id="207">14</sd-pretag>. For loss of function mutant, the neurodegeneration was quantified at <sd-tag id="sdTag194" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14309060063480" parent-tag-id="207">14</sd-pretag> days</sd-tag> in clones (as shown in Figures 4 and 5). For <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="gene" role="component" text="UAS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UAS</sd-tag>‐overexpression transgenes neurodegeneration was quantified at <sd-tag id="sdTag196" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls=""><sd-pretag id="sdPretag14309060924230" parent-tag-id="207">14</sd-pretag> days</sd-tag> when expressed with <i>GMRGal4; UbiGal80</i><sup><i>ts</i></sup>. For CycD+Cdk4, these specific data are missing and have not been plotted; however, Supplementary Figure 13 shows that these mutants do not cause neurodegeneration in a different setup in which they are expressed during both development and adult life. In both cases the regression coefficient <i>r</i><sup>2</sup> is extremely low (0.21 and 0.03), indicating an absence of correlation between the two processes.<graphic href="https://api.sourcedata.io/file.php?panel_id=5141"/></sd-panel><sd-panel panel_id="5142"><b>(B)</b> Tangential <sd-tag id="sdTag208" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> sections through the <sd-tag id="sdTag209" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eyes" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eyes</sd-tag> of flies expressing with <i><sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="gene" role="component" text="GMR" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GMR</sd-tag>-<sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="gene" role="component" text="Gal4" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Gal4</sd-tag>, Ubi-<sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="gene" role="component" text="Gal80" ext_ids="854954" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL80" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Gal80</sd-tag></i><sup><i>ts</i></sup> either <i><sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="gene" role="component" text="UAS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UAS</sd-tag>-</i><sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="EGFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EGFP</sd-tag> or <sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="gene" role="component" text="UAS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UAS</sd-tag><i>-<sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Yki</sd-tag></i> or <i><sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="gene" role="component" text="UAS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UAS</sd-tag>-<sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Yki</sd-tag></i><sup><i>S111A,S168A,S250A</i></sup> and aged 1 or <sd-tag id="sdTag219" source="sdapi" category="time" entity_type="" role="" text="28 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">28 days</sd-tag>. Arrows point at missing or degenerated <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="photoreceptors" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptors</sd-tag>. The <i><sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="gene" role="component" text="UAS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">UAS</sd-tag>-<sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Yki</sd-tag></i><sup><i>S111A,S168A,S250A</i></sup> is so effective that even the very low expression leaking out with this system is enough to affect development and generate mild <sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> roughness and overproliferation of lattice cells. Histograms showing the quantification of cell loss in <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eyes" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eyes</sd-tag> shown in A and also <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eyes" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eyes</sd-tag> from flies aged at the intermediate <sd-tag id="sdTag207">14‐day</sd-tag> stage. Mild but significant degeneration is observed for both <sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Yki</sd-tag> forms, with respect to the negative control; however, no statistical difference is observed between the two <sd-tag id="sdTag396" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Yki" ext_ids="37851" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="yki" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Yki</sd-tag> proteins that have dramatically different effects on overgrowth. <sup>***</sup><i>P</i>0.001, <sup>**</sup><i>P</i>0.01; <sup>*</sup><i>P</i>0.05 in two‐tailed <i>t</i>‐test.<graphic href="https://api.sourcedata.io/file.php?panel_id=5142"/></sd-panel></fig><fig id="1961"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1961"/><sd-panel panel_id="8223">Neurodegeneration by polyQ <sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag> partially requires <em><sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="gene" role="intervention" text="dachs" ext_ids="33245" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ds" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">dachs</sd-tag></em>. Tangential <sd-tag id="sdTag237" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eye" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eye</sd-tag> sections through <em><sd-tag id="sdTag238" source="sdapi" category="entity" entity_type="gene" role="intervention" text="d" ext_ids="33245" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ds" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">d</sd-tag></em><sup><em>GC13</em></sup> clones (marked by the absence of yellow pigment) either in control flies or those expressing <sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atro" ext_ids="46156" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Gug" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atro</sd-tag>75QN with the <em><sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="gene" role="component" text="Rhodopsin1" ext_ids="42367" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ninaE" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Rhodopsin1</sd-tag></em> driver and aged <sd-tag id="sdTag240" source="sdapi" category="time" entity_type="" role="" text="28 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">28 days</sd-tag>. Mask panels below each section exemplify clonal boundaries and <sd-tag id="sdTag241" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="PR" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">PR</sd-tag> no. for the <sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag>. Early signs of degeneration indicated by reduced complement of <sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="photoreceptors" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptors</sd-tag> are detected specifically in the pigmented area (arrowhead). At this stage, inside <em><sd-tag id="sdTag235" source="sdapi" category="entity" entity_type="gene" role="intervention" text="d" ext_ids="33245" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ds" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">d</sd-tag></em> mutant clones all <sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag> are unaffected and display a <em>wt</em> arrangement (arrows). (<strong>B</strong>) Histograms showing the quantification of cell loss in <sd-tag id="sdTag245" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="eyes" ext_ids="UBERON:0000970" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="eye" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">eyes</sd-tag> shown in (<strong>A</strong>). A statistically significant rescue is obtained both for the number of wt <sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag> (<sup>*</sup><em>P</em>0.05 in two‐tailed <em>t</em>‐test) and for all other categories of <sd-tag id="sdTag397" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidia" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidia</sd-tag> (<em>χ</em><sup>2</sup>=44.76; <em>P</em>0.001 for 2 degrees of freedom).<graphic href="https://api.sourcedata.io/file.php?panel_id=8223"/></sd-panel></fig><fig id="1962"><title></title><label>Figure 8</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1962"/><sd-panel panel_id="5143"><b>(A)</b> <sd-tag id="sdTag252" source="sdapi" category="assay" entity_type="" role="" text="EM" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">EM</sd-tag> scan of a <i>wt</i> (left) and <i><sd-tag id="sdTag258" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup> mutant <sd-tag id="sdTag382" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidium" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidium</sd-tag> (right) of a <i><sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup> clone after <sd-tag id="sdTag253" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">14 days</sd-tag>. Scale bar: 1 μm. High‐magnification panels (far right, top to bottom) display <sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0032009" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="early phagosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> with undigested debris, damaged <sd-tag id="sdTag255" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> and forming <sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="phagophores" ext_ids="GO:0032009" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="early phagosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">phagophores</sd-tag> (arrowheads), found in <i><sd-tag id="sdTag398" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup> mutant cells. Scale bar: 0.2 μm for zoom‐in panels.<graphic href="https://api.sourcedata.io/file.php?panel_id=5143"/></sd-panel><sd-panel panel_id="5144"><b>(B)</b> Graphs of the quantification of autophagic <sd-tag id="sdTag261" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> (<sd-tag id="sdTag266" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="AV" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AV</sd-tag>) per <sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="tissue" role="component" text="photoreceptor" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptor</sd-tag> found in <sd-tag id="sdTag267" source="sdapi" category="assay" entity_type="" role="" text="EM" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">EM</sd-tag> sections of <sd-tag id="sdTag263" source="sdapi" category="time" entity_type="" role="" text="7‐day" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">7‐day</sd-tag> (left)‐ and <sd-tag id="sdTag264" source="sdapi" category="time" entity_type="" role="" text="14‐day" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">14‐day</sd-tag> (right)‐old <i><sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup> clones. Significant accumulation of <sd-tag id="sdTag399" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="AV" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AV</sd-tag> is found in mutant cells (not pigmented) with respect to genotypically wt (pigmented) cells. <sup>**</sup><i>P</i>0.01 and <sup>***</sup><i>P</i>0.001 in one‐tailed <i>t</i>‐test. <i>N</i>=12 pigmented cells versus 20 non‐pigmented cells for the <sd-tag id="sdTag269" source="sdapi" category="time" entity_type="" role="" text="7‐day" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">7‐day</sd-tag> graph and 13 pigmented cells versus 21 non‐pigmented cells for the 14‐day graph.<graphic href="https://api.sourcedata.io/file.php?panel_id=5144"/></sd-panel><sd-panel panel_id="5145"><b>(C)</b> <sd-tag id="sdTag272" source="sdapi" category="assay" entity_type="" role="" text="Confocal" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Confocal</sd-tag> pictures of whole‐mount <sd-tag id="sdTag273" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="retinae" ext_ids="UBERON:0000966" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="retina" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">retinae</sd-tag> of a <i><sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="gene" role="component" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup> clone aged <sd-tag id="sdTag274" source="sdapi" category="time" entity_type="" role="" text="7 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">7 days</sd-tag> and expressing <sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>∷<sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="gene" role="component" text="Atg8a" ext_ids="32001" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg8a" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg8a</sd-tag> ubiquitously with <i><sd-tag id="sdTag282" source="sdapi" category="entity" entity_type="gene" role="component" text="Tub" ext_ids="40554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="tub" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Tub</sd-tag>-<sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="gene" role="component" text="Gal4" ext_ids="855828" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAL4" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Gal4</sd-tag></i>. Red is <sd-tag id="sdTag276" source="sdapi" category="assay" entity_type="" role="" text="phalloidin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">phalloidin</sd-tag> marking <sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="rhabdomeres" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">rhabdomeres</sd-tag>, green is <sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> and the clone is marked by the absence of <sd-tag id="sdTag279" source="sdapi" category="assay" entity_type="" role="" text="β‐gal staining" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">β‐gal staining</sd-tag> (blue). Small <sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>∷<sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="gene" role="component" text="Atg8a" ext_ids="32001" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg8a" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg8a</sd-tag> dots accumulate specifically inside <i><sd-tag id="sdTag286" source="sdapi" category="entity" entity_type="gene" role="component" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i> mutant cells (arrow).<graphic href="https://api.sourcedata.io/file.php?panel_id=5145"/></sd-panel><sd-panel panel_id="5146"><b>(D)</b> <sd-tag id="sdTag288" source="sdapi" category="assay" entity_type="" role="" text="Confocal" ext_ids="BAO_0000453" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="confocal microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Confocal</sd-tag> pictures of whole‐mount <sd-tag id="sdTag289" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="retinae" ext_ids="UBERON:0000966" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="retina" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">retinae</sd-tag> of a <i><sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="gene" role="component" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i><sup><i>fd</i></sup> clone aged <sd-tag id="sdTag291" source="sdapi" category="time" entity_type="" role="" text="7 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">7 days</sd-tag> (left) and <sd-tag id="sdTag292" source="sdapi" category="time" entity_type="" role="" text="14 days" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">14 days</sd-tag> (right). Red is <sd-tag id="sdTag294" source="sdapi" category="assay" entity_type="" role="" text="phalloidin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">phalloidin</sd-tag> marking <sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="rhabdomeres" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">rhabdomeres</sd-tag>, blue is <sd-tag id="sdTag287" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="P19109" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rm62" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> and the clone is marked by the absence of <sd-tag id="sdTag296" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> staining (green). <sd-tag id="sdTag297" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p62" ext_ids="P19109" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rm62" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="https://www.uniprot.org/uniprot/">p62</sd-tag> starts to gather in small dots specifically inside <i><sd-tag id="sdTag299" source="sdapi" category="entity" entity_type="gene" role="component" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i> mutant cells (arrow) and then accumulates massively (arrow) in the <i><sd-tag id="sdTag400" source="sdapi" category="entity" entity_type="gene" role="component" text="ft" ext_ids="33627" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ft" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ft</sd-tag></i> mutant clones as many cells degenerate.<graphic href="https://api.sourcedata.io/file.php?panel_id=5146"/></sd-panel></fig><fig id="1963"><title></title><label>Figure 9</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1963"/><sd-panel panel_id="5147"><b>(A)</b> <sd-tag id="sdTag302" source="sdapi" category="assay" entity_type="" role="" text="EM" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">EM</sd-tag> scan of a <sd-tag id="sdTag303" source="sdapi" category="time" entity_type="" role="" text="7‐day" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">7‐day</sd-tag>‐old <i><sd-tag id="sdTag304" source="sdapi" category="entity" entity_type="gene" role="component" text="sav" ext_ids="252554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="sav" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sav</sd-tag></i><sup><i>3</i></sup> mutant <sd-tag id="sdTag305" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="ommatidium" ext_ids="UBERON:0000971" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="ommatidium" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">ommatidium</sd-tag> and zoom‐in on <sd-tag id="sdTag306" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autophagosomes" ext_ids="GO:0032009" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="early phagosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autophagosomes</sd-tag> containing undigested debris (arrowhead). Scale bar: 1 μm for panel on the left and 0.2 μm for zoom‐in panel on the right.<graphic href="https://api.sourcedata.io/file.php?panel_id=5147"/></sd-panel><sd-panel panel_id="5148"><b>(B)</b> Graph of the quantification of autophagic <sd-tag id="sdTag309" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="vesicles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">vesicles</sd-tag> (<sd-tag id="sdTag310" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="AV" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AV</sd-tag>) per <sd-tag id="sdTag311" source="sdapi" category="entity" entity_type="tissue" role="assayed" text="photoreceptor" ext_ids="UBERON:0005388" norm_text="" ext_dbs="Uberon" in_caption="True" ext_names="photoreceptor array" ext_tax_ids="" ext_tax_names="" ext_urls="https://www.ebi.ac.uk/ols/ontologies/uberon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_">photoreceptor</sd-tag> found in <sd-tag id="sdTag312" source="sdapi" category="assay" entity_type="" role="" text="EM" ext_ids="BAO_0000449" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="electron microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">EM</sd-tag> sections of <sd-tag id="sdTag308" source="sdapi" category="time" entity_type="" role="" text="1‐week" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">1‐week</sd-tag>‐old <i><sd-tag id="sdTag313" source="sdapi" category="entity" entity_type="gene" role="component" text="sav" ext_ids="252554" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="sav" ext_tax_ids="7227" ext_tax_names="Drosophila melanogaster" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">sav</sd-tag></i><sup><i>3</i></sup> clones. Significant accumulation of <sd-tag id="sdTag314" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="AV" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">AV</sd-tag> is found in mutant cells. <sup>***</sup><i>P</i>0.001 in one‐tailed <i>t</i>‐test. <i>N</i>=45 pigmented cells versus 42 non‐pigmented cells.<graphic href="https://api.sourcedata.io/file.php?panel_id=5148"/></sd-panel></fig></article>

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+<article doi="10.1038/emboj.2011.104" abstract="Autophagy is a conserved degradative process that is crucial for cellular homeostasis and cellular quality control via the selective removal of subcellular structures such as mitochondria. We demonstrate that a regulatory link exists between mitochondrial function and autophagy in Saccharomyces cerevisiae. During amino-acid starvation, the autophagic response consists of two independent regulatory arms-autophagy gene induction and autophagic flux-and our analysis indicates that mitochondrial respiratory deficiency severely compromises both. We show that the evolutionarily conserved protein kinases Atg1, target of rapamycin kinase complex I, and protein kinase A (PKA) regulate autophagic flux, whereas autophagy gene induction depends solely on PKA. Within this regulatory network, mitochondrial respiratory deficiency suppresses autophagic flux, autophagy gene induction, and recruitment of the Atg1-Atg13 kinase complex to the pre-autophagosomal structure by stimulating PKA activity. Our findings indicate an interrelation of two common risk factors-mitochondrial dysfunction and autophagy inhibition-for ageing, cancerogenesis, and neurodegeneration."><fig id="2563"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2563"/><sd-panel panel_id="7314"><div><b>(A)</b> Wild‐type and <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup> cells harbouring pr<sup><i><sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i></sup><i>‐<sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i> (upper panels) or pr<sup><i><sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i></sup><i>‐<sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag></i> (lower panels) were exposed to <sd-tag id="sdTag4" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> or <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nitrogen" ext_ids="CHEBI:25555" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nitrogen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nitrogen</sd-tag> starvation (‐N) medium supplemented with indicated carbon sources. Cells were analysed at indicated time points by whole cell extraction and <sd-tag id="sdTag9" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> analysis using α‐<sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> and α‐<sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Cdc11" ext_ids="P32458" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CDC11" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Cdc11</sd-tag> antibodies. Quantification of <i><sd-tag id="sdTag17" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i> induction is shown in the lower left panel. Total <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> signals (<sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg8" ext_ids="P38182///A6ZKM4" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ATG8///ATG8" ext_tax_ids="307796///559292" ext_tax_names="Saccharomyces cerevisiae YJM789///Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Atg8</sd-tag> and free <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>) were quantified and normalized to <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Cdc11" ext_ids="P32458" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CDC11" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Cdc11</sd-tag> signals. Normalized values at 0 h were set as one and relative changes are shown after 6 h starvation. Quantification of autophagic flux is shown in the lower right panel as ratio of free <sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> to total <sd-tag id="sdTag23" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> signals (<sd-tag id="sdTag24" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag25" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg8" ext_ids="P38182///A6ZKM4" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ATG8///ATG8" ext_tax_ids="307796///559292" ext_tax_names="Saccharomyces cerevisiae YJM789///Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Atg8</sd-tag> and free <sd-tag id="sdTag26" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>) after 6 h starvation. The means and s.d. of four (<i>n</i>=4) independent experiments are indicated.</div><graphic href="https://api.sourcedata.io/file.php?panel_id=7314"/></sd-panel><sd-panel panel_id="7315"><b>(B)</b> Fluorescence microscopical analysis. Wild‐type, <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup>, and Δ<i><sd-tag id="sdTag271" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg7</sd-tag></i> cells expressing pr<sup><i><sd-tag id="sdTag35" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i></sup><i>‐<sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i> were grown as described in (<b>A</b>) and exposed to <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> (left panel, <sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="galactose" ext_ids="CHEBI:28260" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="galactose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">galactose</sd-tag><span>) or <sd-tag id="sdTag272" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nitrogen" ext_ids="CHEBI:25555" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nitrogen atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nitrogen</sd-tag> starvation (right panel,</span> <sd-tag id="sdTag45" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="glucose" ext_ids="CHEBI:17234" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="glucose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">glucose</sd-tag> (‐N)) for 6 h<span>. <sd-tag id="sdTag273" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Vacuoles" ext_ids="GO:0005773" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Vacuoles</sd-tag> were visualized by over night</span> <sd-tag id="sdTag47" source="sdapi" category="assay" entity_type="" role="" text="FM4‐64" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">FM4‐64</sd-tag> (1 μM) staining (red). Arrowhead indicates a punctate <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag42" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg8" ext_ids="P38182///A6ZKM4" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ATG8///ATG8" ext_tax_ids="307796///559292" ext_tax_names="Saccharomyces cerevisiae YJM789///Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Atg8</sd-tag> structure. Transmission and <sd-tag id="sdTag262" source="sdapi" category="assay" entity_type="" role="" text="fluorescence light microscopy" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">fluorescence light microscopy</sd-tag> images were superimposed to visualize cellular boundaries. Cellular localization of <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> signal was analysed in at least 150 cells (<i>n</i>⩾150) for each strain and condition. Scale bars represent 1.5 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7315"/></sd-panel></fig><fig id="2564"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2564"/><sd-panel panel_id="7327"><p>Autophagic response in cells with compromised <sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="subcellular" role="intervention" text="respiratory chain complex III" ext_ids="GO:0045275" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="respiratory chain complex III" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">respiratory chain complex III</sd-tag>, IV, or V activity during <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation. Wild‐type, <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup>, <em><sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg7</sd-tag></em> cells and mutants that are selectively inhibited in the biogenesis of <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="subcellular" role="intervention" text="respiratory chain complex III" ext_ids="GO:0045275" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="respiratory chain complex III" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">respiratory chain complex III</sd-tag> (CIII: <em><sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="gene" role="intervention" text="cbs1" ext_ids="851491" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CBS1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">cbs1</sd-tag></em>), complex IV (CIV: <em><sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="gene" role="intervention" text="mss51" ext_ids="850900" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MSS51" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">mss51</sd-tag></em>, <sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="gene" role="intervention" text="pet111" ext_ids="855299" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PET111" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/"><em>pet111</em></sd-tag>, <em><sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="gene" role="intervention" text="pet122" ext_ids="856897" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PET122" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">pet122</sd-tag></em>), or the <span><sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="subcellular" role="intervention" text="F1Fo‐ATP synthase" ext_ids="GO:0045259" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="proton-transporting ATP synthase complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">F1Fo‐ATP synthase</sd-tag></span> (complex V; CV: <em><sd-tag id="sdTag276" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atp10" ext_ids="851109" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATP10" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atp10</sd-tag></em>) were exposed to <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag></p><p>starvation medium supplemented with <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="acetate" ext_ids="CHEBI:30089" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="acetate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">acetate</sd-tag> (<strong>A</strong>) or <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="galactose" ext_ids="CHEBI:28260" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="galactose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">galactose</sd-tag> (<strong>B</strong>). When indicated, wild‐type cells were exposed to <sd-tag id="sdTag59" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="antimycin A" ext_ids="CHEBI:22584" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="antimycin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">antimycin A</sd-tag> (AA) or <sd-tag id="sdTag60" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="oligomycin" ext_ids="CHEBI:25675" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oligomycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">oligomycin</sd-tag> (O) during the <sd-tag id="sdTag69" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation period. All strains expressed pr<sup><em><sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></em></sup><em>‐<sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></em> (upper panels) or pr<sup><em><sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></em></sup><em>‐<sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag></em> (lower panels). Samples were analysed as described in Figure 1A. The means and s.d. of five (<em>n</em>=5) independent experiments are indicated.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=7327"/></sd-panel></fig><fig id="2565"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2565"/><sd-panel panel_id="7316"><b>(A, B)</b> Wild‐type, <sd-tag id="sdTag83" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup>, and Δ<i><sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg7</sd-tag></i> cells were exposed to <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation medium supplemented with <sd-tag id="sdTag81" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="acetate" ext_ids="CHEBI:30089" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="acetate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">acetate</sd-tag> (<b>A</b>) or <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="galactose" ext_ids="CHEBI:28260" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="galactose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">galactose</sd-tag> (<b>B</b>). When indicated, wild‐type cells were exposed to <sd-tag id="sdTag85" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="antimycin A" ext_ids="CHEBI:22584" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="antimycin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">antimycin A</sd-tag> (AA) or <sd-tag id="sdTag86" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="oligomycin" ext_ids="CHEBI:25675" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oligomycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">oligomycin</sd-tag> (O) during the <sd-tag id="sdTag87" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation period. <sd-tag id="sdTag88" source="sdapi" category="entity" entity_type="molecule" role="assayed" text="ATP" ext_ids="CHEBI:15422" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="ATP" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ATP</sd-tag> and protein from total cells (upper panels) or isolated <sd-tag id="sdTag89" source="sdapi" category="entity" entity_type="subcellular" role="experiment" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> (lower panels) were determined at indicated time points.<graphic href="https://api.sourcedata.io/file.php?panel_id=7316"/></sd-panel><sd-panel panel_id="7317"><b>(C)</b> Wild‐type and Δ<i><sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg7</sd-tag></i> cells were exposed to <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation medium supplemented with <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="acetate" ext_ids="CHEBI:30089" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="acetate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">acetate</sd-tag> or <sd-tag id="sdTag95" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="galactose" ext_ids="CHEBI:28260" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="galactose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">galactose</sd-tag> for 3 h. Wild‐type cells were exposed to <sd-tag id="sdTag96" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="antimycin A" ext_ids="CHEBI:22584" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="antimycin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">antimycin A</sd-tag> (AA), <sd-tag id="sdTag97" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="oligomycin" ext_ids="CHEBI:25675" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oligomycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">oligomycin</sd-tag> (O), or <sd-tag id="sdTag104" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="CCCP" ext_ids="CHEBI:3259" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="CCCP" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">CCCP</sd-tag> (50 μM) during the <sd-tag id="sdTag98" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation period when indicated. Cells were treated with the mitochondrial membrane potential‐dependent dye <sd-tag id="sdTag266" source="sdapi" category="assay" entity_type="" role="" text="DiOC6(3)" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DiOC<sub>6</sub>(3)</sd-tag> and examined by <sd-tag id="sdTag105" source="sdapi" category="assay" entity_type="" role="" text="fluorescence microscopy" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">fluorescence microscopy</sd-tag>. Average pixel intensities for at least 10 <sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondrial tubules" ext_ids="GO:0005874///GO:0097427" norm_text="" ext_dbs="Gene Ontology///Gene Ontology" in_caption="True" ext_names="microtubule///microtubule bundle" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term////http://amigo.geneontology.org/amigo/term/">mitochondrial tubules</sd-tag> (<i>n</i>=10) in 5 representative cells were determined for each condition. Values for wild‐type <sd-tag id="sdTag99" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="mitochondria" ext_ids="GO:0005739" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="mitochondrion" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">mitochondria</sd-tag> in the presence of <sd-tag id="sdTag100" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="acetate" ext_ids="CHEBI:30089" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="acetate" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">acetate</sd-tag> were defined as 100% and relative values were calculated accordingly. The means and s.d. are shown.<graphic href="https://api.sourcedata.io/file.php?panel_id=7317"/></sd-panel></fig><fig id="2566"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2566"/><sd-panel panel_id="7318"><b>(A)</b> Wild‐type, <sd-tag id="sdTag109" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup>, Δ<i><sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="gene" role="intervention" text="npr2" ext_ids="856647" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="NPR2" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">npr2</sd-tag></i>, and Δ<i><sd-tag id="sdTag286" source="sdapi" category="entity" entity_type="gene" role="intervention" text="npr2" ext_ids="856647" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="NPR2" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">npr2</sd-tag></i> <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup> cells expressing pr<sup><i><sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i></sup><i>‐<sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i> (upper panel) or pr<sup><i><sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG8" ext_ids="P38182///A6ZKM4" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ATG8///ATG8" ext_tax_ids="307796///559292" ext_tax_names="Saccharomyces cerevisiae YJM789///Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ATG8</sd-tag></i></sup><i>‐<sd-tag id="sdTag115" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag></i> (lower panel) were exposed to <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation medium supplemented with <sd-tag id="sdTag117" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="galactose" ext_ids="CHEBI:28260" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="galactose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">galactose</sd-tag> in the absence or presence of <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag>. Samples were analysed as described in Figure 1A. The means and s.d. of four (<i>n</i>=4) independent experiments are indicated.<graphic href="https://api.sourcedata.io/file.php?panel_id=7318"/></sd-panel><sd-panel panel_id="7319"><b>(B)</b> Wild‐type, <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup>, Δ<i><sd-tag id="sdTag287" source="sdapi" category="entity" entity_type="gene" role="intervention" text="npr2" ext_ids="856647" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="NPR2" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">npr2</sd-tag></i>, and Δ<i><sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg7</sd-tag></i> cells expressing pr<sup><i><sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="gene" role="component" text="NPR1" ext_ids="855538" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="NPR1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NPR1</sd-tag></i></sup>‐<sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="gene" role="component" text="NPR1" ext_ids="855538" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="NPR1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NPR1</sd-tag>‐<sd-tag id="sdTag129" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> were exposed to <sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation medium supplemented with <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="galactose" ext_ids="CHEBI:28260" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="galactose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">galactose</sd-tag> in the absence (upper panels) or presence (lower panels) of <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag>. The hyperphosphorylated (<sd-tag id="sdTag289" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Npr1" ext_ids="P22211" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NPR1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Npr1</sd-tag>‐P) and dephosphorylated (<sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Npr1" ext_ids="P22211" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NPR1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Npr1</sd-tag>) forms of <sd-tag id="sdTag134" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Npr1" ext_ids="P22211" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NPR1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Npr1</sd-tag> are indicated. Cells were analysed at indicated time points by whole cell extraction and <sd-tag id="sdTag126" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> analysis using α‐<sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> and α‐<sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Cdc11" ext_ids="P32458" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CDC11" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Cdc11</sd-tag> antibodies.<graphic href="https://api.sourcedata.io/file.php?panel_id=7319"/></sd-panel><sd-panel panel_id="7320"><b>(C)</b> Wild‐type, <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup>, Δ<i><sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="gene" role="intervention" text="npr2" ext_ids="856647" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="NPR2" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">npr2</sd-tag></i>, and Δ<i><sd-tag id="sdTag291" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg7</sd-tag></i> cells were exposed to <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation medium supplemented with <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="galactose" ext_ids="CHEBI:28260" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="galactose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">galactose</sd-tag>. Additionally, wild‐type cells were treated with <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="rapamycin" ext_ids="CHEBI:9168" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="sirolimus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">rapamycin</sd-tag> during starvation (left panel). Phosphorylated (<sd-tag id="sdTag292" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg13" ext_ids="A6ZX59" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG13" ext_tax_ids="307796" ext_tax_names="Saccharomyces cerevisiae YJM789" ext_urls="https://www.uniprot.org/uniprot/">Atg13</sd-tag>‐P) and dephosphorylated (<sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg13" ext_ids="A6ZX59" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG13" ext_tax_ids="307796" ext_tax_names="Saccharomyces cerevisiae YJM789" ext_urls="https://www.uniprot.org/uniprot/">Atg13</sd-tag>) <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg13" ext_ids="A6ZX59" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG13" ext_tax_ids="307796" ext_tax_names="Saccharomyces cerevisiae YJM789" ext_urls="https://www.uniprot.org/uniprot/">Atg13</sd-tag> was monitored at indicated time points by whole cell extraction and <sd-tag id="sdTag143" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> analysis using α‐<sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg13" ext_ids="A6ZX59" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG13" ext_tax_ids="307796" ext_tax_names="Saccharomyces cerevisiae YJM789" ext_urls="https://www.uniprot.org/uniprot/">Atg13</sd-tag> and α‐<sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Cdc11" ext_ids="P32458" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CDC11" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Cdc11</sd-tag> antibodies.<graphic href="https://api.sourcedata.io/file.php?panel_id=7320"/></sd-panel></fig><fig id="2567"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2567"/><sd-panel panel_id="7321"><b>(A)</b> PKA‐dependent regulation of the autophagic response under <sd-tag id="sdTag158" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation. Wild‐type, <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup>, <i><sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="gene" role="intervention" text="pka" ext_ids="855898///853275" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="TPK2///TPK1" ext_tax_ids="559292///559292" ext_tax_names="Saccharomyces cerevisiae S288C///Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">pka</sd-tag></i>, and <i><sd-tag id="sdTag293" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ras2" ext_ids="855625" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RAS2" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ras2</sd-tag></i><sup><i>G19V</i></sup>‐expressing cells harbouring pr<sup><i><sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i></sup><i>‐<sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i> (upper panels) or pr<sup><i><sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG8" ext_ids="P38182///A6ZKM4" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ATG8///ATG8" ext_tax_ids="307796///559292" ext_tax_names="Saccharomyces cerevisiae YJM789///Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ATG8</sd-tag></i></sup><i>‐<sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag></i> (lower panels) were exposed to <sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation medium supplemented with <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="galactose" ext_ids="CHEBI:28260" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="galactose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">galactose</sd-tag>. PKA activity in <i>pka</i> was inhibited by addition of <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="1NM‐PP1" ext_ids="CHEBI:52310" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="1-NA-PP1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">1NM‐PP1</sd-tag> (<sd-tag id="sdTag157" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="PP1" ext_ids="CHEBI:52310" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="1-NA-PP1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">PP1</sd-tag>; 1 μg/ml). Samples were analysed as described in Figure 1A; autophagic flux was determined after 3 and 6 h.<graphic href="https://api.sourcedata.io/file.php?panel_id=7321"/></sd-panel><sd-panel panel_id="7322"><b>(B)</b><i>In vivo</i> activity of PKA. Wild‐type, <sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup>, <i><sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="gene" role="component" text="pka" ext_ids="855898///853275" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="TPK2///TPK1" ext_tax_ids="559292///559292" ext_tax_names="Saccharomyces cerevisiae S288C///Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">pka</sd-tag></i>, and <i><sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ras2" ext_ids="855625" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="RAS2" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ras2</sd-tag></i><sup><i>G19V</i></sup>‐expressing cells harbouring <i>6x<sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="protein" role="reporter" text="MYC" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">MYC</sd-tag>‐</i><i>cki1</i><sup><i>2</i>−<i>200(S125/130A)</i></sup> (<sd-tag id="sdTag186" source="sdapi" category="entity" entity_type="gene" role="component" text="Cki1" ext_ids="850824" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CKI1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Cki1</sd-tag>) were grown in <sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="molecule" role="component" text="galactose" ext_ids="CHEBI:28260" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="galactose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">galactose</sd-tag> medium. When indicated, wild‐type cells were grown in <sd-tag id="sdTag177" source="sdapi" category="entity" entity_type="molecule" role="component" text="galactose" ext_ids="CHEBI:28260" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="galactose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">galactose</sd-tag> medium in the presence of <sd-tag id="sdTag178" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="antimycin A" ext_ids="CHEBI:22584" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="antimycin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">antimycin A</sd-tag> (AA) or <sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="oligomycin" ext_ids="CHEBI:25675" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oligomycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">oligomycin</sd-tag> (O) for 6 h. PKA‐dependent phosphorylation of <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Cki1" ext_ids="P20485" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CKI1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Cki1</sd-tag> was analysed by whole cell extraction and <sd-tag id="sdTag181" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> analysis using a α‐<sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Myc" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Myc</sd-tag> antibody (upper panels). Ratio of phosphorylated (<sd-tag id="sdTag295" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Cki1" ext_ids="P20485" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CKI1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Cki1</sd-tag>‐P) and non‐phosphorylated (<sd-tag id="sdTag190" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Cki1" ext_ids="P20485" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CKI1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Cki1</sd-tag>) forms of <sd-tag id="sdTag191" source="sdapi" category="entity" entity_type="gene" role="component" text="Cki1" ext_ids="850824" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="CKI1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Cki1</sd-tag> relative to wild‐type cells (wt=1) (lower panels).<graphic href="https://api.sourcedata.io/file.php?panel_id=7322"/></sd-panel><sd-panel panel_id="7323"><b>(C)</b> PKA inhibition restores autophagic flux, but not <i><sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i> induction in the presence of mitochondrial dysfunction. Wild‐type, <sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup>, <i><sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="gene" role="intervention" text="pka" ext_ids="855898///853275" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="TPK2///TPK1" ext_tax_ids="559292///559292" ext_tax_names="Saccharomyces cerevisiae S288C///Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">pka</sd-tag></i>, and <i><sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="gene" role="intervention" text="pka" ext_ids="855898///853275" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="TPK2///TPK1" ext_tax_ids="559292///559292" ext_tax_names="Saccharomyces cerevisiae S288C///Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">pka</sd-tag></i> <sd-tag id="sdTag199" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup> cells expressing pr<sup><i><sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG8" ext_ids="P38182///A6ZKM4" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ATG8///ATG8" ext_tax_ids="307796///559292" ext_tax_names="Saccharomyces cerevisiae YJM789///Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ATG8</sd-tag></i></sup><i>‐<sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i> were treated as described in (<b>A</b>). Samples were analysed as described in Figure 1A. The means and s.d. of four (<i>n</i>=4) independent experiments are indicated in (<b>A</b>-<b>C</b>).<graphic href="https://api.sourcedata.io/file.php?panel_id=7323"/></sd-panel></fig><fig id="2568"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2568"/><sd-panel panel_id="7324"><b>(A)</b><i><sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG8" ext_ids="P38182///A6ZKM4" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ATG8///ATG8" ext_tax_ids="307796///559292" ext_tax_names="Saccharomyces cerevisiae YJM789///Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">ATG8</sd-tag></i> induction is independent of the <sd-tag id="sdTag298" source="sdapi" category="entity" entity_type="protein" role="component" text="Atg1" ext_ids="P53104" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Atg1</sd-tag>-<sd-tag id="sdTag299" source="sdapi" category="entity" entity_type="protein" role="component" text="Atg13" ext_ids="A6ZX59" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG13" ext_tax_ids="307796" ext_tax_names="Saccharomyces cerevisiae YJM789" ext_urls="https://www.uniprot.org/uniprot/">Atg13</sd-tag> complex and autophagic flux. Wild‐type, <sd-tag id="sdTag300" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup>, Δ<i><sd-tag id="sdTag301" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg1" ext_ids="852695" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg1</sd-tag></i>, Δ<i><sd-tag id="sdTag304" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg7</sd-tag></i>, Δ<i><sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg9" ext_ids="851406" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG9" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg9</sd-tag></i>, and Δ<i><sd-tag id="sdTag303" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg11" ext_ids="856162" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG11" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg11</sd-tag></i> cells harbouring pr<sup><i><sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i></sup><i>‐<sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i> were analysed as described in Figure 1A. The means and s.d. of four (<i>n</i>=4) independent experiments are indicated.<graphic href="https://api.sourcedata.io/file.php?panel_id=7324"/></sd-panel><sd-panel panel_id="7325"><b>(B)</b> <sd-tag id="sdTag306" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg1" ext_ids="P53104" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Atg1</sd-tag> and <sd-tag id="sdTag307" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg13" ext_ids="A6ZX59" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG13" ext_tax_ids="307796" ext_tax_names="Saccharomyces cerevisiae YJM789" ext_urls="https://www.uniprot.org/uniprot/">Atg13</sd-tag> recruitment to the <sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="subcellular" role="component" text="PAS" ext_ids="GO:0000407" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="pre-autophagosomal structure" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">PAS</sd-tag> depends on mitochondrial function. Wild‐type and <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup> cells harbouring pr<sup><i><sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i></sup><i>‐<sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG8" ext_ids="852200" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG8" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG8</sd-tag></i> and pr<sup><i><sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG1" ext_ids="P53104" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">ATG1</sd-tag></i></sup>‐<i><sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG1" ext_ids="852695" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG1</sd-tag></i>‐<sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag> (upper panels) or pr<sup><i><sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="protein" role="assayed" text="ATG13" ext_ids="A6ZX59" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG13" ext_tax_ids="307796" ext_tax_names="Saccharomyces cerevisiae YJM789" ext_urls="https://www.uniprot.org/uniprot/">ATG13</sd-tag></i></sup>‐<i><sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG13" ext_ids="856315" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG13" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG13</sd-tag></i>‐<sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag> (lower panels) were exposed to <sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="molecule" role="component" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation medium supplemented with <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="molecule" role="component" text="galactose" ext_ids="CHEBI:28260" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="galactose" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">galactose</sd-tag> for 3 h. Wild‐type cells were treated with <sd-tag id="sdTag230" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="antimycin A" ext_ids="CHEBI:22584" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="antimycin A" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">antimycin A</sd-tag> (AA 30′) after 2.5 h of starvation for 30 min or with <sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="oligomycin" ext_ids="CHEBI:25675" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="oligomycin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">oligomycin</sd-tag> (O) for 3 h of starvation. Arrowheads indicate the position of <sd-tag id="sdTag233" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐<sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg8" ext_ids="P38182///A6ZKM4" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="ATG8///ATG8" ext_tax_ids="307796///559292" ext_tax_names="Saccharomyces cerevisiae YJM789///Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">Atg8</sd-tag> puncta. Transmission and <sd-tag id="sdTag239" source="sdapi" category="assay" entity_type="" role="" text="fluorescence light microscopy" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">fluorescence light microscopy</sd-tag> images were superimposed to visualize cellular boundaries. Scale bar represents 1.5 μm.<graphic href="https://api.sourcedata.io/file.php?panel_id=7325"/></sd-panel><sd-panel panel_id="7326"><b>(C)</b> Steady‐state levels of <sd-tag id="sdTag242" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg1" ext_ids="P53104" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Atg1</sd-tag>‐ and <sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Atg13" ext_ids="A6ZX59" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="ATG13" ext_tax_ids="307796" ext_tax_names="Saccharomyces cerevisiae YJM789" ext_urls="https://www.uniprot.org/uniprot/">Atg13</sd-tag>‐<sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag> during <sd-tag id="sdTag245" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="amino‐acid" ext_ids="CHEBI:33709" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="amino acid" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">amino‐acid</sd-tag> starvation. Wild‐type, <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="gene" role="intervention" text="rho" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">rho</sd-tag><sup>0</sup>, and Δ<i><sd-tag id="sdTag308" source="sdapi" category="entity" entity_type="gene" role="intervention" text="atg7" ext_ids="856576" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG7" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">atg7</sd-tag></i> cells expressing pr<sup><i><sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG1" ext_ids="852695" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG1</sd-tag></i></sup>‐<i><sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG1" ext_ids="852695" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG1" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG1</sd-tag></i>‐<sd-tag id="sdTag249" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag> (upper panels) or pr<sup><i><sd-tag id="sdTag250" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG13" ext_ids="856315" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG13" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG13</sd-tag></i></sup>‐<i><sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="gene" role="component" text="ATG13" ext_ids="856315" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="ATG13" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ATG13</sd-tag></i>‐<sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="protein" role="reporter" text="mCherry" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">mCherry</sd-tag> (lower panels) were exposed and treated as described in (<b>B</b>) and analysed by whole cell extraction and <sd-tag id="sdTag253" source="sdapi" category="assay" entity_type="" role="" text="western blot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blot</sd-tag> analysis using α‐<sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="protein" role="reporter" text="dsRed" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">dsRed</sd-tag> and α‐<sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Cdc11" ext_ids="P32458" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CDC11" ext_tax_ids="559292" ext_tax_names="Saccharomyces cerevisiae S288C" ext_urls="https://www.uniprot.org/uniprot/">Cdc11</sd-tag> antibodies.<graphic href="https://api.sourcedata.io/file.php?panel_id=7326"/></sd-panel></fig><fig id="2569"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2569"/></fig></article>

token_classification/10-1038_emboj-2011-33.xml

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+<article doi="10.1038/emboj.2011.33" abstract="Ribosome biogenesis is a tightly controlled pathway that requires an intricate spatial and temporal interplay of protein networks. Most structural rRNA components are generated in the nucleolus and assembled into pre-ribosomal particles, which are transferred for further maturation to the nucleoplasm and cytoplasm. In metazoa, few regulatory components for these processes have been characterized. Previous work revealed a critical role for the SUMO-specific protease SENP3 in the nucleolar steps of ribosome biogenesis. We biochemically purified a SENP3-associated complex comprising PELP1, TEX10 and WDR18, and demonstrate that this complex is involved in maturation and nucleolar release of the large ribosomal subunit. We identified PELP1 and the PELP1-associated factor LAS1L as SENP3-sensitive targets of SUMO, and provide evidence that balanced SUMO conjugation/deconjugation determines the nucleolar partitioning of this complex. This defines the PELP1-TEX10-WDR18 complex as a regulator of ribosome biogenesis and suggests that its SUMO-controlled distribution coordinates the rate of ribosome formation. These findings contribute to the basic understanding of mammalian ribosome biogenesis and shed new light on the role of SUMO in this process."><fig id="1971"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1971"/><sd-panel panel_id="5180"><b>(A, B)</b> <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag><span>‐<sd-tag id="sdTag301" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP3" ext_ids="Q9H4L4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP3</sd-tag> or</span> <sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag><span>‐</span><sd-tag id="sdTag8" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> <span>was expressed in</span> <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> <span>cells as indicated. Proteins were captured on</span> <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag><span>‐ or</span> <sd-tag id="sdTag10" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag><span>‐beads and</span> <sd-tag id="sdTag4" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> <span>using antibodies directed against endogenous</span> <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> <span>or <sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP3" ext_ids="Q9H4L4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP3</sd-tag> as indicated.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=5180"/></sd-panel><sd-panel panel_id="5181"><b>(C)</b> <span>Endogenous</span> <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> <span>was</span> <sd-tag id="sdTag23" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> <span>from</span> <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> <span>cells with a rabbit polyclonal antibody and immunocomplexes were probed for the presence of <sd-tag id="sdTag303" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP3" ext_ids="Q9H4L4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP3</sd-tag> by</span> <sd-tag id="sdTag11" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag> <span>with an anti‐<sd-tag id="sdTag304" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP3" ext_ids="Q9H4L4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP3</sd-tag> antibody.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=5181"/></sd-panel><sd-panel panel_id="5182"><b>(D-F)</b> <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐ or <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐tagged proteins were expressed in <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells, captured on <sd-tag id="sdTag21" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐ or <sd-tag id="sdTag22" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐beads and subjected to <sd-tag id="sdTag17" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> as indicated. In all experiments, the inputs represent 2.5% of the total cell lysate.<graphic href="https://api.sourcedata.io/file.php?panel_id=5182"/></sd-panel></fig><fig id="1972"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1972"/><sd-panel panel_id="5183"><b>(A, B)</b> <sd-tag id="sdTag28" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag29" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> and <sd-tag id="sdTag30" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag27" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WDR18" ext_ids="Q9BV38" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDR18" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WDR18</sd-tag> were expressed in <sd-tag id="sdTag31" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells as indicated. <sd-tag id="sdTag32" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WDR18" ext_ids="Q9BV38" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDR18" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WDR18</sd-tag> was captured on <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐beads and the bound material was probed by <sd-tag id="sdTag35" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> for the presence of ectopically expressed <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐tagged <sd-tag id="sdTag38" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> or endogenous <sd-tag id="sdTag306" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> as indicated.<graphic href="https://api.sourcedata.io/file.php?panel_id=5183"/></sd-panel><sd-panel panel_id="5184"><b>(C)</b> Endogenous <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> was <sd-tag id="sdTag42" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> from <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells with a rabbit polyclonal antibody and immunocomplexes were probed for the presence of endogenous <sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WDR18" ext_ids="Q9BV38" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDR18" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WDR18</sd-tag> by <sd-tag id="sdTag45" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag> with an anti‐<sd-tag id="sdTag46" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WDR18" ext_ids="Q9BV38" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDR18" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WDR18</sd-tag> antibody.<graphic href="https://api.sourcedata.io/file.php?panel_id=5184"/></sd-panel><sd-panel panel_id="5185"><b>(D)</b> <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="gene" role="component" text="TEX10" ext_ids="54881" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TEX10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TEX10</sd-tag> was expressed with <sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag51" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> in <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells, captured on <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐beads and proteins were <sd-tag id="sdTag305" source="sdapi" category="assay" entity_type="" role="" text="immunoblotted" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotted</sd-tag> as indicated.<graphic href="https://api.sourcedata.io/file.php?panel_id=5185"/></sd-panel><sd-panel panel_id="5186"><b>(E)</b> <sd-tag id="sdTag55" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag56" source="sdapi" category="entity" entity_type="gene" role="assayed" text="TEX10" ext_ids="54881" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TEX10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TEX10</sd-tag> was expressed, captured on <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐beads and associated proteins were probed for the presence of endogenous <sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="protein" role="assayed" text="WDR18" ext_ids="Q9BV38" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="WDR18" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">WDR18</sd-tag> using <sd-tag id="sdTag59" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. The inputs represent 2.5% of the total cell lysate.<graphic href="https://api.sourcedata.io/file.php?panel_id=5186"/></sd-panel></fig><fig id="1973"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1973"/><sd-panel panel_id="5188"><b>(A-C)</b> <sd-tag id="sdTag65" source="sdapi" category="assay" entity_type="" role="" text="Immunofluorescence" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunofluorescence</sd-tag> staining of endogenous <sd-tag id="sdTag70" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag>, <sd-tag id="sdTag71" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP3" ext_ids="Q9H4L4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP3</sd-tag>, <sd-tag id="sdTag66" source="sdapi" category="entity" entity_type="protein" role="assayed" text="UBF1" ext_ids="P17480" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="UBTF" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">UBF1</sd-tag> and <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="protein" role="assayed" text="NPM1" ext_ids="P06748" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="NPM1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">NPM1</sd-tag> in <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells. <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Nuclei</sd-tag> were visualized using <sd-tag id="sdTag69" source="sdapi" category="assay" entity_type="" role="" text="DAPI" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAPI</sd-tag> staining.<graphic href="https://api.sourcedata.io/file.php?panel_id=5188"/></sd-panel></fig><fig id="1974"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1974"/><sd-panel panel_id="5190"><b>(B)</b> <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were transfected with siRNA duplexes targeting <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PELP1" ext_ids="27043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PELP1</sd-tag>, <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TEX10" ext_ids="54881" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TEX10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TEX10</sd-tag>, <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WDR18" ext_ids="57418" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WDR18" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WDR18</sd-tag>, <sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="gene" role="intervention" text="MDN1" ext_ids="23195" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MDN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">MDN1</sd-tag> or a control siRNA as indicated. Downregulation of the respective proteins was analysed by <sd-tag id="sdTag85" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag> as indicated (WB, three lower panels). At 72 h after transfection, cells were pulse labelled with <sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="32P" ext_ids="CHEBI:37972" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="phosphorus-32 atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId="><sup>32</sup>P</sd-tag>‐orthophosphate for 1 h and chased for 2.5 h. RNA was separated on a denaturing agarose gel and detected by <sd-tag id="sdTag82" source="sdapi" category="assay" entity_type="" role="" text="ethidium bromide" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">ethidium bromide</sd-tag> (<sd-tag id="sdTag81" source="sdapi" category="assay" entity_type="" role="" text="EtBr) staining" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EtBr) staining</sd-tag> and <sd-tag id="sdTag83" source="sdapi" category="assay" entity_type="" role="" text="autoradiography" ext_ids="BAO_0002527" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="autoradiography" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">autoradiography</sd-tag> after drying of the gel.<graphic href="https://api.sourcedata.io/file.php?panel_id=5190"/></sd-panel><sd-panel panel_id="5191"><b>(C)</b> The signal intensities of the <span><sd-tag id="sdTag311" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="28S" ext_ids="GO:1902377" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nuclear rDNA heterochromatin" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">28S</sd-tag></span> and <span><sd-tag id="sdTag292" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="32S" ext_ids="GO:0030684" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="preribosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">32S</sd-tag></span> rRNA forms were quantified by <sd-tag id="sdTag92">phosphoimager analysis</sd-tag> <span>and the ratio of <sd-tag id="sdTag290" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="28S" ext_ids="GO:1902377" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nuclear rDNA heterochromatin" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">28S</sd-tag>:</span><span><sd-tag id="sdTag310" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="32S" ext_ids="GO:0030684" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="preribosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">32S</sd-tag></span> rRNA was calculated. Values represent the average of four (two for si<sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="gene" role="intervention" text="MDN1" ext_ids="23195" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MDN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">MDN1</sd-tag>) independent experiments. Error bars indicate s.d.<graphic href="https://api.sourcedata.io/file.php?panel_id=5191"/></sd-panel><sd-panel panel_id="5192"><b>(D)</b> <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> is associated with <sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="ITS2" ext_ids="GO:0005567" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="cytosolic ribosomal RNA" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ITS2</sd-tag>‐containing RNA species. Endogenous <sd-tag id="sdTag307" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> was <sd-tag id="sdTag106" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> from <sd-tag id="sdTag107" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells. In total, 10% of the <sd-tag id="sdTag108" source="sdapi" category="assay" entity_type="" role="" text="immunoprecipitated" ext_ids="BAO_0002508" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="immunoprecipitation" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoprecipitated</sd-tag> material was analysed by <sd-tag id="sdTag109" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag> (lower panel). The remaining material was used for RNA isolation and cDNA synthesis. The cDNA was used as template for <sd-tag id="sdTag102" source="sdapi" category="assay" entity_type="" role="" text="PCR amplification" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">PCR amplification</sd-tag> using primers within the <sd-tag id="sdTag110" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="ITS2" ext_ids="GO:0005567" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="cytosolic ribosomal RNA" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">ITS2</sd-tag><span>/<sd-tag id="sdTag296" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="28S" ext_ids="GO:1902377" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nuclear rDNA heterochromatin" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">28S</sd-tag> region or</span> <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="gene" role="normalizing" text="GAPDH" ext_ids="2597" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="GAPDH" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GAPDH</sd-tag> as a control. Input corresponds to 10% of the cell lysate. Vertical line in the upper panel indicates removal of irrelevant adjacent lanes.<graphic href="https://api.sourcedata.io/file.php?panel_id=5192"/></sd-panel><sd-panel panel_id="5193"><b>(E)</b> <sd-tag id="sdTag118" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="Pre‐ribosomal particles" ext_ids="GO:0030684" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="preribosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Pre‐ribosomal particles</sd-tag> were separated by <sd-tag id="sdTag114" source="sdapi" category="assay" entity_type="" role="" text="sucrose gradient centrifugation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">sucrose gradient centrifugation</sd-tag> of nuclear extracts. Proteins were recovered from the fractions by <sd-tag id="sdTag115" source="sdapi" category="assay" entity_type="" role="" text="TCA precipitation" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">TCA precipitation</sd-tag> and further analysed by <sd-tag id="sdTag116" source="sdapi" category="assay" entity_type="" role="" text="SDS–PAGE" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SDS-PAGE</sd-tag> and <sd-tag id="sdTag117" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag> using antibodies as indicated. Vertical lines solely indicate loading onto two separate gels.<graphic href="https://api.sourcedata.io/file.php?panel_id=5193"/></sd-panel><sd-panel panel_id="5194"><b>(F)</b> Nucleolar export of <sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="pre‐60S" ext_ids="GO:0030684" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="preribosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">pre‐60S</sd-tag> particles is strongly compromised in cells depleted of <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="gene" role="intervention" text="PELP1" ext_ids="27043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PELP1</sd-tag>, <sd-tag id="sdTag131" source="sdapi" category="entity" entity_type="gene" role="intervention" text="TEX10" ext_ids="54881" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="TEX10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">TEX10</sd-tag>, <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="gene" role="intervention" text="WDR18" ext_ids="57418" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="WDR18" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">WDR18</sd-tag>, <sd-tag id="sdTag133" source="sdapi" category="entity" entity_type="gene" role="intervention" text="MDN1" ext_ids="23195" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="MDN1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">MDN1</sd-tag> or <sd-tag id="sdTag143" source="sdapi" category="entity" entity_type="gene" role="intervention" text="SENP3" ext_ids="26168" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="SENP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">SENP3</sd-tag>. <sd-tag id="sdTag135" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells expressing <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>‐<sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="protein" role="assayed" text="RpL27" ext_ids="P61353" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="RPL27" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">RpL27</sd-tag> from a <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="molecule" role="component" text="tetracycline" ext_ids="CHEBI:27902" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="tetracycline" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">tetracycline</sd-tag>‐inducible promoter were transfected with the indicated siRNAs. After 24 h, expression of <sd-tag id="sdTag136" source="sdapi" category="entity" entity_type="protein" role="reporter" text="YFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">YFP</sd-tag>‐<sd-tag id="sdTag137" source="sdapi" category="entity" entity_type="protein" role="assayed" text="RpL27" ext_ids="P61353" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="RPL27" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">RpL27</sd-tag> was induced and 72 h later the localization of <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="protein" role="assayed" text="RpL27" ext_ids="P61353" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="RPL27" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">RpL27</sd-tag> was monitored. Pictures were taken using identical exposure times.<graphic href="https://api.sourcedata.io/file.php?panel_id=5194"/></sd-panel></fig><fig id="1975"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1975"/><sd-panel panel_id="5195"><b>(A)</b> <sd-tag id="sdTag148" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> was expressed alone or in combination with <sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO1</sd-tag> or <sd-tag id="sdTag146" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO2</sd-tag> in the presence or absence of <sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="protein" role="reporter" text="SV5" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">SV5</sd-tag>‐tagged <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP3" ext_ids="Q9H4L4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP3</sd-tag> in <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells. Expression of the respective proteins was verified by <sd-tag id="sdTag152" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag>. Detection of <sd-tag id="sdTag147" source="sdapi" category="entity" entity_type="subcellular" role="normalizing" text="β‐tubulin" ext_ids="GO:0045298" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="tubulin complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">β‐tubulin</sd-tag> served as loading control.<graphic href="https://api.sourcedata.io/file.php?panel_id=5195"/></sd-panel><sd-panel panel_id="5196"><b>(B)</b> <sd-pretag id="sdPretag14309820658730" parent-tag-id="174">SUMO</sd-pretag> modification of endogenous <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> was monitored by anti‐<sd-tag id="sdTag308" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> <sd-tag id="sdTag160" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> in <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells transfected with siRNAs as indicated. Depletion of the respective proteins was verified by <sd-tag id="sdTag162" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=5196"/></sd-panel><sd-panel panel_id="5197"><b>(C)</b> <sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were transfected with siRNAs and plasmids as indicated. <sd-tag id="sdTag171" source="sdapi" category="entity" entity_type="protein" role="reporter" text="His" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His</sd-tag>‐<sd-tag id="sdTag174" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO</sd-tag> conjugates were recovered on <sd-tag id="sdTag175" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="Ni" ext_ids="CHEBI:28112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nickel atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Ni</sd-tag>‐<sd-tag id="sdTag176" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="NTA" ext_ids="CHEBI:39054" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="NTA" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">NTA</sd-tag> beads and subjected to <sd-tag id="sdTag172" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag> using anti‐<sd-tag id="sdTag173" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> antibodies.<graphic href="https://api.sourcedata.io/file.php?panel_id=5197"/></sd-panel><sd-panel panel_id="5198"><b>(D)</b> <sd-tag id="sdTag179" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> or <sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag182" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag><sup>K826R</sup> was expressed in the presence of <sd-tag id="sdTag183" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO1</sd-tag> or <sd-tag id="sdTag184" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO2</sd-tag> in <sd-tag id="sdTag185" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells. Expression of the respective proteins was analysed by <sd-tag id="sdTag186" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag>. Detection of <sd-tag id="sdTag187" source="sdapi" category="entity" entity_type="subcellular" role="normalizing" text="β‐tubulin" ext_ids="GO:0045298" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="tubulin complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">β‐tubulin</sd-tag> served as loading control.<graphic href="https://api.sourcedata.io/file.php?panel_id=5198"/></sd-panel><sd-panel panel_id="5199"><b>(E, F)</b> <sd-tag id="sdTag192" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag191" source="sdapi" category="entity" entity_type="protein" role="assayed" text="p14" ext_ids="Q8N726" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="CDKN2A" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">p14</sd-tag><sup>ARF</sup> and <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO</sd-tag> were expressed in <sd-tag id="sdTag194" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells and <sd-tag id="sdTag195" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO</sd-tag> modification of ectopically expressed <sd-tag id="sdTag196" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐<sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> or endogenous <sd-tag id="sdTag309" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> was monitored by <sd-tag id="sdTag199" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> with anti‐<sd-tag id="sdTag200" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag> or anti‐<sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> antibodies as indicated. Arrowheads indicate <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO</sd-tag>-<sd-tag id="sdTag203" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> conjugates.<graphic href="https://api.sourcedata.io/file.php?panel_id=5199"/></sd-panel></fig><fig id="1976"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1976"/><sd-panel panel_id="5200"><b>(A)</b> <sd-tag id="sdTag210" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag211" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO2</sd-tag> was expressed in <sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells by transient transfection. <sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO2</sd-tag>‐expressing cells were visualized by <sd-tag id="sdTag209" source="sdapi" category="assay" entity_type="" role="" text="indirect immunofluorescence" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">indirect immunofluorescence</sd-tag>. The localization of endogenous <sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> was monitored in <sd-tag id="sdTag216" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag217" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO2</sd-tag>‐positive cells (green arrowheads) or untransfected cells (white arrowheads) using anti‐<sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> antibody.<graphic href="https://api.sourcedata.io/file.php?panel_id=5200"/></sd-panel><sd-panel panel_id="5201"><b>(B-D)</b> <sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were transfected with siRNAs as indicated. After fixation and permeabilization, the localization of <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag>, <sd-tag id="sdTag221" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAS1L" ext_ids="Q9Y4W2" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAS1L" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAS1L</sd-tag>, <sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="protein" role="assayed" text="TEX10" ext_ids="Q9NXF1" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="TEX10" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">TEX10</sd-tag> or <sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PES1" ext_ids="O00541" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PES1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PES1</sd-tag> was monitored by <sd-tag id="sdTag226" source="sdapi" category="assay" entity_type="" role="" text="indirect immunofluorescence" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">indirect immunofluorescence</sd-tag> using the corresponding antibodies.<graphic href="https://api.sourcedata.io/file.php?panel_id=5201"/></sd-panel><sd-panel panel_id="5202"><b>(E)</b> <sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were depleted of endogenous <sd-tag id="sdTag241" source="sdapi" category="entity" entity_type="gene" role="component" text="PELP1" ext_ids="27043" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">PELP1</sd-tag> and reconstituted with siRNA resistant constructs expressing either wild‐type <sd-tag id="sdTag233" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐tagged <sd-tag id="sdTag234" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag> or a <sd-tag id="sdTag235" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐tagged <sd-tag id="sdTag236" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag>-<sd-tag id="sdTag237" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO2</sd-tag> fusion protein. The localization of the respective proteins was monitored by <sd-tag id="sdTag238" source="sdapi" category="assay" entity_type="" role="" text="indirect immunofluorescence" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">indirect immunofluorescence</sd-tag> using either anti‐<sd-tag id="sdTag239" source="sdapi" category="entity" entity_type="protein" role="reporter" text="HA" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">HA</sd-tag>‐ or anti‐<sd-tag id="sdTag240" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐antibodies.<graphic href="https://api.sourcedata.io/file.php?panel_id=5202"/></sd-panel><sd-panel panel_id="5203"><b>(F)</b> The localization of <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAS1L" ext_ids="Q9Y4W2" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAS1L" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAS1L</sd-tag> or <sd-tag id="sdTag247" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP3" ext_ids="Q9H4L4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP3</sd-tag> was analysed in cells expressing <sd-tag id="sdTag248" source="sdapi" category="entity" entity_type="protein" role="reporter" text="Flag" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Flag</sd-tag>‐<sd-tag id="sdTag249" source="sdapi" category="entity" entity_type="protein" role="assayed" text="PELP1" ext_ids="Q8IZL8" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="PELP1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">PELP1</sd-tag>-<sd-tag id="sdTag250" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO2</sd-tag>. <sd-tag id="sdTag245" source="sdapi" category="assay" entity_type="" role="" text="Indirect immunofluorescence" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Indirect immunofluorescence</sd-tag> was done using anti‐<sd-tag id="sdTag251" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAS1L" ext_ids="Q9Y4W2" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAS1L" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAS1L</sd-tag> or anti‐<sd-tag id="sdTag252" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SENP3" ext_ids="Q9H4L4" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SENP3" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SENP3</sd-tag> antibodies. <sd-tag id="sdTag253" source="sdapi" category="entity" entity_type="subcellular" role="component" text="Nuclei" ext_ids="GO:0005634" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="nucleus" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">Nuclei</sd-tag> were counterstained with <sd-tag id="sdTag254" source="sdapi" category="assay" entity_type="" role="" text="DAPI" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">DAPI</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=5203"/></sd-panel></fig><fig id="1977"><title></title><label>Figure 7</label><graphic href="https://api.sourcedata.io/file.php?figure_id=1977"/><sd-panel panel_id="5204"><b>(A)</b> <sd-tag id="sdTag260" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAS1L" ext_ids="Q9Y4W2" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAS1L" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAS1L</sd-tag> was generated by <sd-tag id="sdTag258"><i>in vitro</i> transcription/translation</sd-tag> and incubated with recombinant <sd-tag id="sdTag264" source="sdapi" category="entity" entity_type="protein" role="component" text="E1" ext_ids="Q9UBE0///Q9UBT2" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="SAE1///UBA2" ext_tax_ids="9606///9606" ext_tax_names="Homo sapiens///Homo sapiens" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">E1</sd-tag> and <sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="protein" role="component" text="E2" ext_ids="P63279" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="UBE2I" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">E2</sd-tag> enzymes and <sd-tag id="sdTag261" source="sdapi" category="entity" entity_type="protein" role="intervention" text="SUMO1" ext_ids="P63165" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO1" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO1</sd-tag> or <sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="protein" role="intervention" text="SUMO2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO2</sd-tag>, respectively, in the presence of <sd-tag id="sdTag259" source="sdapi" category="entity" entity_type="molecule" role="component" text="ATP" ext_ids="CHEBI:15422" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="ATP" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">ATP</sd-tag>. In the control reaction (lane 1) <sd-tag id="sdTag263" source="sdapi" category="entity" entity_type="protein" role="intervention" text="SUMO" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO</sd-tag> was not added.<graphic href="https://api.sourcedata.io/file.php?panel_id=5204"/></sd-panel><sd-panel panel_id="5205"><b>(B)</b> <sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were transfected with siRNAs and plasmids as indicated. Expression of the respective proteins was verified by <sd-tag id="sdTag269" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag>. Detection of <sd-tag id="sdTag270" source="sdapi" category="entity" entity_type="subcellular" role="normalizing" text="β‐tubulin" ext_ids="GO:0045298" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="tubulin complex" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">β‐tubulin</sd-tag> served as loading control.<graphic href="https://api.sourcedata.io/file.php?panel_id=5205"/></sd-panel><sd-panel panel_id="5206"><b>(C)</b> <sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="cell_line" role="component" text="HeLa" ext_ids="CVCL_0030" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="HeLa" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://identifiers.org/cellosaurus:">HeLa</sd-tag> cells were transfected with siRNAs and plasmids as indicated. <sd-tag id="sdTag276" source="sdapi" category="entity" entity_type="protein" role="reporter" text="His" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">His</sd-tag>‐<sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="protein" role="assayed" text="SUMO2" ext_ids="P61956" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="SUMO2" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">SUMO2</sd-tag> conjugates were captured on magnetic <sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="Ni" ext_ids="CHEBI:28112" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nickel atom" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Ni</sd-tag>‐<sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="molecule" role="reporter" text="NTA" ext_ids="CHEBI:39054" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="NTA" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">NTA</sd-tag> beads and subjected to <sd-tag id="sdTag280" source="sdapi" category="assay" entity_type="" role="" text="western blotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">western blotting</sd-tag> using anti‐<sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LAS1L" ext_ids="Q9Y4W2" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="LAS1L" ext_tax_ids="9606" ext_tax_names="Homo sapiens" ext_urls="https://www.uniprot.org/uniprot/">LAS1L</sd-tag> antibodies. Vertical lines indicate removal of irrelevant neighbouring lanes from the initial gel (see Supplementary Figure 14).<graphic href="https://api.sourcedata.io/file.php?panel_id=5206"/></sd-panel></fig></article>

token_classification/10-1038_emboj-2011-398.xml

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+<article doi="10.1038/emboj.2011.398" abstract="Autophagy controls the quality and quantity of the eukaryotic cytoplasm while performing two evolutionarily highly conserved functions: cell-autonomous provision of energy and nutrients by cytosol autodigestion during starvation, and removal of defunct organelles and large aggregates exceeding the capacity of other cellular degradative systems. In contrast to these autodigestive processes, autophagy in yeast has additional, biogenesis functions. However, no equivalent biosynthetic roles have been described for autophagy in mammals. Here, we show that in mammalian cells, autophagy has a hitherto unappreciated positive contribution to the biogenesis and secretion of the proinflammatory cytokine IL-1β via an export pathway that depends on Atg5, inflammasome, at least one of the two mammalian Golgi reassembly stacking protein (GRASP) paralogues, GRASP55 (GORASP2) and Rab8a. This process, which is a type of unconventional secretion, expands the functional manifestations of autophagy beyond autodigestive and quality control roles in mammals. It enables a subset of cytosolic proteins devoid of signal peptide sequences, and thus unable to access the conventional pathway through the ER, to enter an autophagy-based secretory pathway facilitating their exit from the cytoplasm."><fig id="2356"><title></title><label>Figure 1</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2356"/><sd-panel panel_id="6511"><b>(A)</b> <sd-tag id="sdTag9" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag><sup>fl/fl</sup> <span><sd-tag id="sdTag359" source="sdapi" category="entity" entity_type="gene" role="component" text="Cre" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cre</sd-tag></span><sup>−</sup> and <sd-tag id="sdTag11" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag><sup>fl/fl</sup> Cre<sup>+</sup> <sd-tag id="sdTag1" source="sdapi" category="entity" entity_type="cell_type" role="component" text="bone marrow‐derived macrophages" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">bone marrow‐derived macrophages</sd-tag> (<sd-tag id="sdTag2" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag>), pretreated overnight with 100 ng/ml <sd-tag id="sdTag3" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag>, were stimulated for 1 h with the inflammasome agonist <sd-tag id="sdTag5" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nigericin" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nigericin</sd-tag> (20 μM) with (Starvation; <sd-tag id="sdTag6" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag>) or without (Full; full medium) autophagic induction. Cell culture supernatants were assayed for murine <sd-tag id="sdTag7" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> by <sd-tag id="sdTag8" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag>. Data represent mean values±s.d. (<i>n</i>≥3); <sup>*</sup><i>P</i>0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=6511"/></sd-panel><sd-panel panel_id="6512"><b>(B)</b> <sd-tag id="sdTag12" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag>‐pretreated <sd-tag id="sdTag13" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag><sup>fl/fl</sup> <sd-tag id="sdTag362" source="sdapi" category="entity" entity_type="gene" role="component" text="Cre" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cre</sd-tag><sup>−</sup> and <sd-tag id="sdTag14" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag><sup>fl/fl</sup> <sd-tag id="sdTag363" source="sdapi" category="entity" entity_type="gene" role="component" text="Cre" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cre</sd-tag><sup>+</sup> <sd-tag id="sdTag15" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were stimulated with 20 μM <sd-tag id="sdTag16" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nigericin" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nigericin</sd-tag> for 1 h in <sd-tag id="sdTag20" source="sdapi" category="entity" entity_type="undefined" role="component" text="OptiMEM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">OptiMEM</sd-tag> and the release of active <sd-tag id="sdTag19" source="sdapi" category="entity" entity_type="protein" role="assayed" text="caspase‐1" ext_ids="P29452" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Casp1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">caspase‐1</sd-tag> and <sd-tag id="sdTag18" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> was determined by <sd-tag id="sdTag21" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=6512"/></sd-panel><sd-panel panel_id="6513"><b>(C)</b> As in (<b>A</b><span>), assayed for <sd-tag id="sdTag365" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐18" ext_ids="P70380" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il18" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐18</sd-tag>. Data represent mean values±s.d. (</span><i>n</i>≥3); <sup>*</sup><i>P</i>0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=6513"/></sd-panel><sd-panel panel_id="6514"><b>(D)</b> <sd-tag id="sdTag33" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag>‐pretreated <sd-tag id="sdTag34" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were exposed to <sd-tag id="sdTag37" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="alum" ext_ids="CHEBI:74768" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="aluminium sulfate (anhydrous)" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">alum</sd-tag> (250 μg/ml) for 1 h with or without autophagic induction by starvation. Secreted <sd-tag id="sdTag36" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> was measured as in (<b>A</b>). Data represent mean values±s.d. (<i>n</i>⩾3); <sup>*</sup><i>P</i>0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=6514"/></sd-panel><sd-panel panel_id="6515"><b>(E)</b> <sd-tag id="sdTag40" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag>‐pretreated <sd-tag id="sdTag41" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were exposed to <sd-tag id="sdTag44" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="silica" ext_ids="CHEBI:30563" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="silicon dioxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">silica</sd-tag> (250 μg/ml) for 1 h with or without autophagic induction by starvation. Secreted <sd-tag id="sdTag43" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> was measured as in (<b>A</b>). Data represent mean values±s.d. (<i>n</i>⩾3); <sup>*</sup><i>P</i>0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=6515"/></sd-panel><sd-panel panel_id="6516"><b>(F)</b> <sd-tag id="sdTag48" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were transfected with scramble (Scr) control siRNA or siRNAs against <sd-tag id="sdTag52" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ASC" ext_ids="66824" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Pycard" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ASC</sd-tag> and <sd-tag id="sdTag53" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NLRP3" ext_ids="216799" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Nlrp3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NLRP3</sd-tag>. After 48 h following transfection, cells were treated overnight with <sd-tag id="sdTag49" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> and subjected to <sd-tag id="sdTag50" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nigericin" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nigericin</sd-tag> (20 μM) and starvation for 1 h. Data represent mean values±s.d. (<i>n</i>⩾3); <sup>*</sup><i>P</i>0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=6516"/></sd-panel><sd-panel panel_id="6517"><b>(G)</b> <sd-tag id="sdTag59" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag> analysis of <sd-tag id="sdTag57" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ASC" ext_ids="66824" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Pycard" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ASC</sd-tag> and <sd-tag id="sdTag58" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NLRP3" ext_ids="216799" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Nlrp3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NLRP3</sd-tag> knockdowns.<graphic href="https://api.sourcedata.io/file.php?panel_id=6517"/></sd-panel><sd-panel panel_id="6518"><b>(H)</b> <sd-tag id="sdTag63" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were transfected with scramble (Scr) control siRNA or siRNAs against <sd-tag id="sdTag64" source="sdapi" category="entity" entity_type="gene" role="intervention" text="ASC" ext_ids="66824" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Pycard" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">ASC</sd-tag> and <sd-tag id="sdTag65" source="sdapi" category="entity" entity_type="gene" role="intervention" text="NLRP3" ext_ids="216799" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Nlrp3" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">NLRP3</sd-tag>. After 48 h following transfection, cells were treated overnight with <sd-tag id="sdTag67" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> and subjected to <sd-tag id="sdTag68" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="silica" ext_ids="CHEBI:30563" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="silicon dioxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">silica</sd-tag> (250 μg/ml) and starvation for 1 h. Data represent mean values±s.d. (<i>n</i>⩾3); <sup>*</sup><i>P</i>0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=6518"/></sd-panel><sd-panel panel_id="6519"><b>(I)</b> Colocalization of <sd-tag id="sdTag72" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> with the basal autophagic machinery factor <sd-tag id="sdTag77" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>. Fluorescence: <sd-tag id="sdTag78" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (green, <sd-tag id="sdTag313" source="sdapi" category="assay" entity_type="" role="" text="Alexa488" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Alexa488</sd-tag>); <sd-tag id="sdTag73" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> (red, <sd-tag id="sdTag314" source="sdapi" category="assay" entity_type="" role="" text="Alexa568" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Alexa568</sd-tag>). <sd-tag id="sdTag74" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were from <sd-tag id="sdTag82" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag79" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="67443///66734" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> knock‐in <sd-tag id="sdTag84" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag>, treated with <sd-tag id="sdTag75" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> then prepared for <sd-tag id="sdTag83" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence microscopy" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunofluorescence microscopy</sd-tag> using fluorescently labelled antibodies against <sd-tag id="sdTag80" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> and <sd-tag id="sdTag76" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=6519"/></sd-panel><sd-panel panel_id="6520"><b>(J, K)</b> A line fluorescence tracing from images in (<b>I</b>).<graphic href="https://api.sourcedata.io/file.php?panel_id=6520"/></sd-panel><sd-panel panel_id="6521"><b>(L)</b> Pearson's colocalization coefficient for <sd-tag id="sdTag93" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> and <sd-tag id="sdTag94" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>. Pearson's coefficient was derived from three independent experiments with five fields per experiment, for a total of 15 fields contributing to the cumulative result. Figure source data can be found in Supplementary data.<graphic href="https://api.sourcedata.io/file.php?panel_id=6521"/></sd-panel></fig><fig id="2357"><title></title><label>Figure 2</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2357"/><sd-panel panel_id="6522"><b>(A, B)</b> <sd-tag id="sdTag101" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag>‐pretreated <sd-tag id="sdTag102" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were treated with 20 μM <sd-tag id="sdTag103" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nigericin" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nigericin</sd-tag> (<sd-tag id="sdTag321" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Nig" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Nig</sd-tag>) and 100 nM <sd-tag id="sdTag106" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (Baf) with (Starvation) or without (Full) autophagic induction for 1 h and secreted <sd-tag id="sdTag105" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> (<b>A</b>) and <sd-tag id="sdTag368" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐18" ext_ids="P70380" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il18" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐18</sd-tag> (<b>B</b>) were measured. Data represent mean values±s.d. (<i>n</i>⩾3); <sup>*</sup><i>P</i>0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=6522"/></sd-panel><sd-panel panel_id="6523"><b>(C)</b> <sd-tag id="sdTag111" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag>‐pretreated <sd-tag id="sdTag112" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were treated with 250 μg/ml of <sd-tag id="sdTag113" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="silica" ext_ids="CHEBI:30563" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="silicon dioxide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">silica</sd-tag> and 100 nM <sd-tag id="sdTag114" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">bafilomycin A1</sd-tag> (Baf) with (Starvation) or without (Full) autophagic induction for 1 h and secreted <sd-tag id="sdTag116" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> were measured. Data represent mean values±s.d. (<i>n</i>⩾3); <sup>*</sup><i>P</i>0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=6523"/></sd-panel><sd-panel panel_id="6524"><b>(D)</b> Colocalization of <sd-tag id="sdTag128" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cathepsin B" ext_ids="P10605" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ctsb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cathepsin B</sd-tag> with the basal autophagic machinery factor <sd-tag id="sdTag119" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and <sd-tag id="sdTag120" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag>. Fluorescence; <sd-tag id="sdTag121" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (green, <sd-tag id="sdTag324" source="sdapi" category="assay" entity_type="" role="" text="Alexa488" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Alexa488</sd-tag>), <sd-tag id="sdTag122" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> (red, <sd-tag id="sdTag322" source="sdapi" category="assay" entity_type="" role="" text="Alexa568" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Alexa568</sd-tag>), and <sd-tag id="sdTag130" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cathepsin B" ext_ids="P10605" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ctsb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cathepsin B</sd-tag> (blue, <sd-tag id="sdTag323" source="sdapi" category="assay" entity_type="" role="" text="Alexa633" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Alexa633</sd-tag>). <sd-tag id="sdTag123" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> from <sd-tag id="sdTag124" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag125" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="67443///66734" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> knock‐in <sd-tag id="sdTag126" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> were treated with <sd-tag id="sdTag127" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> and then analysed for <sd-tag id="sdTag129" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunofluorescence</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=6524"/></sd-panel><sd-panel panel_id="6525"><b>(E)</b> Colocalization line tracing analysis from images in (<b>D</b>).<graphic href="https://api.sourcedata.io/file.php?panel_id=6525"/></sd-panel><sd-panel panel_id="6526"><b>(F)</b> <sd-tag id="sdTag139" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag>‐pretreated <sd-tag id="sdTag140" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were treated with 20 μM <sd-tag id="sdTag141" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nigericin" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nigericin</sd-tag> and <sd-tag id="sdTag142" source="sdapi" category="entity" entity_type="protein" role="component" text="cathepsin B" ext_ids="P10605" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ctsb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cathepsin B</sd-tag> inhibitor <sd-tag id="sdTag145" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="CA‐074 Me" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">CA‐074 Me</sd-tag> (10 μM), with (Starvation) or without (Full) autophagic induction, for 1 h and secreted <sd-tag id="sdTag144" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> was measured. Data represent mean values±s.d. (<i>n</i>⩾3); <sup>*</sup><i>P</i>0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=6526"/></sd-panel><sd-panel panel_id="6527"><b>(G)</b> <sd-tag id="sdTag149" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag>‐pretreated <sd-tag id="sdTag150" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag><sup>fl/fl</sup> <sd-tag id="sdTag373" source="sdapi" category="entity" entity_type="gene" role="component" text="Cre" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cre</sd-tag><sup>−</sup> and <sd-tag id="sdTag151" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag><sup>fl/fl</sup> <sd-tag id="sdTag374" source="sdapi" category="entity" entity_type="gene" role="component" text="Cre" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cre</sd-tag><sup>+</sup> <sd-tag id="sdTag152" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were stimulated with 20 μM <sd-tag id="sdTag153" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nigericin" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nigericin</sd-tag> for 1 h in <sd-tag id="sdTag155" source="sdapi" category="entity" entity_type="undefined" role="component" text="OptiMEM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">OptiMEM</sd-tag> and release of <sd-tag id="sdTag156" source="sdapi" category="entity" entity_type="protein" role="assayed" text="cathepsin B" ext_ids="P10605" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Ctsb" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">cathepsin B</sd-tag> was determined by <sd-tag id="sdTag157" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. Figure source data can be found in Supplementary data.<graphic href="https://api.sourcedata.io/file.php?panel_id=6527"/></sd-panel></fig><fig id="2358"><title></title><label>Figure 3</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2358"/><sd-panel panel_id="6528"><b>(A)</b> Colocalization of <sd-tag id="sdTag170" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Rab8a" ext_ids="P55258" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rab8a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Rab8a</sd-tag> with the basal autophagic machinery factor <sd-tag id="sdTag159" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and <sd-tag id="sdTag160" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag>. Fluorescence; <sd-tag id="sdTag161" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (green, <sd-tag id="sdTag329" source="sdapi" category="assay" entity_type="" role="" text="Alexa488" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Alexa488</sd-tag>), <sd-tag id="sdTag162" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> (red, <sd-tag id="sdTag330" source="sdapi" category="assay" entity_type="" role="" text="Alexa568" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Alexa568</sd-tag>), <sd-tag id="sdTag171" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Rab8a" ext_ids="P55258" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rab8a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Rab8a</sd-tag> (blue, <sd-tag id="sdTag331" source="sdapi" category="assay" entity_type="" role="" text="Alexa633" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Alexa633</sd-tag>). <sd-tag id="sdTag163" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> from <sd-tag id="sdTag164" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag165" source="sdapi" category="entity" entity_type="gene" role="component" text="LC3" ext_ids="67443///66734" norm_text="" ext_dbs="NCBI gene///NCBI gene" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene////http://www.ncbi.nlm.nih.gov/gene/">LC3</sd-tag> knock‐in <sd-tag id="sdTag166" source="sdapi" category="entity" entity_type="organism" role="component" text="mice" ext_ids="10090" norm_text="" ext_dbs="NCBI taxon" in_caption="True" ext_names="Mus musculus" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ncbi.nlm.nih.gov/taxonomy/">mice</sd-tag> were pretreated with <sd-tag id="sdTag167" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> <span>and analysed by <sd-tag id="sdTag376" source="sdapi" category="assay" entity_type="" role="" text="immunofluorescence microscopy" ext_ids="BAO_0000450" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="fluorescence microscopy" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunofluorescence microscopy</sd-tag>. Arrows indicate triple colocalization.</span><graphic href="https://api.sourcedata.io/file.php?panel_id=6528"/></sd-panel><sd-panel panel_id="6529"><b>(B)</b> Line tracing analysis of fluorescence signal intensity.<graphic href="https://api.sourcedata.io/file.php?panel_id=6529"/></sd-panel><sd-panel panel_id="6530"><b>(C)</b> Pearson's colocalization coefficient for <sd-tag id="sdTag180" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> and <sd-tag id="sdTag181" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Rab8a" ext_ids="P55258" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rab8a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Rab8a</sd-tag>. Pearson's coefficients were derived from three completely independent experiments with &gt;5 fields per experiment, for a total of ⩾15 fields contributing to the cumulative result.<graphic href="https://api.sourcedata.io/file.php?panel_id=6530"/></sd-panel><sd-panel panel_id="6531"><b>(D)</b> <sd-tag id="sdTag188" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were transfected with siRNAs against <sd-tag id="sdTag189" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Rab8a" ext_ids="17274" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Rab8a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Rab8a</sd-tag> or scramble (Scr) control. At 24 h after the first transfection, cells were transfected again with siRNA, treated with <sd-tag id="sdTag190" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> and the day after subjected to <sd-tag id="sdTag191" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nigericin" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nigericin</sd-tag> in full medium for 1 h, and <sd-tag id="sdTag193" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> secretion measured.<graphic href="https://api.sourcedata.io/file.php?panel_id=6531"/></sd-panel><sd-panel panel_id="6532"><b>(E)</b> <sd-tag id="sdTag196" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag> analysis of <sd-tag id="sdTag197" source="sdapi" category="entity" entity_type="protein" role="assayed" text="Rab8a" ext_ids="P55258" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Rab8a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">Rab8a</sd-tag> knockdown in <sd-tag id="sdTag198" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag>.<graphic href="https://api.sourcedata.io/file.php?panel_id=6532"/></sd-panel><sd-panel panel_id="6533"><b>(F)</b> <span><sd-tag id="sdTag388" source="sdapi" category="entity" entity_type="cell_line" role="component" text="RAW 264.7" ext_ids="CVCL_0493" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="RAW 264.7" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">RAW 264.7</sd-tag> macrophages</span> were transfected with <sd-tag id="sdTag201" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>‐tagged <sd-tag id="sdTag202" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Rab8a" ext_ids="17274" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Rab8a" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Rab8a</sd-tag> constructs (WT, wild type; S22N, dominant‐negative mutant), treated overnight with <sd-tag id="sdTag203" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> and stimulated for 1 h with 20 μM <sd-tag id="sdTag205" source="sdapi" category="entity" entity_type="molecule" role="component" text="nigericin" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nigericin</sd-tag> along with induction of autophagy by starvation. <sd-tag id="sdTag206" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> secretion was measured by <sd-tag id="sdTag207" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag>. Data represent mean values±s.d. (<i>n</i>≥3); <sup>*</sup><i>P</i>0.05. Figure source data can be found in Supplementary data.<graphic href="https://api.sourcedata.io/file.php?panel_id=6533"/></sd-panel></fig><fig id="2359"><title></title><label>Figure 4</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2359"/><sd-panel panel_id="6534"><b>(A)</b> <sd-tag id="sdTag220" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMM" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMM</sd-tag> cells were transfected with scramble (Scr) control siRNA or siRNA against <sd-tag id="sdTag219" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GRASP55" ext_ids="Q99JX3" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Gorasp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">GRASP55</sd-tag>. After 48 h of transfection, cells were treated with <sd-tag id="sdTag212" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> and the day after subjected to 20 μM <sd-tag id="sdTag213" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nigericin" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nigericin</sd-tag> in <sd-tag id="sdTag214" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag>, and secreted <sd-tag id="sdTag215" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> was measured by <sd-tag id="sdTag216" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag>. Data represent mean values±s.d. (<i>n</i>⩾3); <sup>*</sup><i>P</i>0.05. Inset: <sd-tag id="sdTag217" source="sdapi" category="assay" entity_type="" role="" text="Immunoblot" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">Immunoblot</sd-tag> analysis of <sd-tag id="sdTag218" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GRASP55" ext_ids="71680" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="0610011A07Rik" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GRASP55</sd-tag> knockdown.<graphic href="https://api.sourcedata.io/file.php?panel_id=6534"/></sd-panel><sd-panel panel_id="6535"><b>(B)</b> <sd-tag id="sdTag233" source="sdapi" category="assay" entity_type="" role="" text="Immunofluorescence confocal microscopy" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Immunofluorescence confocal microscopy</sd-tag> analysis of <sd-tag id="sdTag222" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and <sd-tag id="sdTag223" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GRASP55" ext_ids="Q99JX3" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Gorasp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">GRASP55</sd-tag> distribution. <sd-tag id="sdTag224" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> (green, <sd-tag id="sdTag347" source="sdapi" category="assay" entity_type="" role="" text="Alexa488" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Alexa488</sd-tag>), <sd-tag id="sdTag225" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GRASP55" ext_ids="Q99JX3" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Gorasp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">GRASP55</sd-tag> (red, <sd-tag id="sdTag348" source="sdapi" category="assay" entity_type="" role="" text="Alexa568" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Alexa568</sd-tag>). <sd-tag id="sdTag226" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were pretreated overnight with 100 ng/ml <sd-tag id="sdTag227" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag> and either not stimulated (Ctrl) or stimulated (<sd-tag id="sdTag231" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Nig" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Nig</sd-tag>) for 30 min with the inflammasome agonist <sd-tag id="sdTag228" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nigericin" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nigericin</sd-tag> (20 μM) in full medium.<graphic href="https://api.sourcedata.io/file.php?panel_id=6535"/></sd-panel><sd-panel panel_id="6536"><b>(C)</b> Line tracings, analysis of fluorescence signal intensity from images in (<b>B</b>).<graphic href="https://api.sourcedata.io/file.php?panel_id=6536"/></sd-panel><sd-panel panel_id="6537"><b>(D)</b> Pearson's coefficients for <sd-tag id="sdTag243" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> and <sd-tag id="sdTag244" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GRASP55" ext_ids="Q99JX3" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Gorasp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">GRASP55</sd-tag> were quantified using SlideBook morphometric analysis software as a measure of adjacency between <sd-tag id="sdTag245" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GRASP55" ext_ids="Q99JX3" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Gorasp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">GRASP55</sd-tag> and <sd-tag id="sdTag246" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> profiles. Pearson's coefficients were derived from three independent experiments with five fields per experiment, for a total of 15 fields contributing to the cumulative result. Figure source data can be found in Supplementary data.<graphic href="https://api.sourcedata.io/file.php?panel_id=6537"/></sd-panel></fig><fig id="2360"><title></title><label>Figure 5</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2360"/><sd-panel panel_id="6538"><b>(A, B)</b> Effect of <sd-tag id="sdTag254" source="sdapi" category="entity" entity_type="protein" role="assayed" text="GRASP55" ext_ids="Q99JX3" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Gorasp2" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">GRASP55</sd-tag> on autophagy induction by measuring <sd-tag id="sdTag379" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐II. <sd-tag id="sdTag256" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMM" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMM</sd-tag> cells were transfected with <sd-tag id="sdTag257" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GRASP55" ext_ids="71680" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="0610011A07Rik" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GRASP55</sd-tag> siRNAs or scramble (Scr) control. At 72 h post transfection, cells were induced for autophagy, treated or not with <sd-tag id="sdTag262" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="Bafilomycin A1" ext_ids="CHEBI:22689" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="bafilomycin A1" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">Bafilomycin A1</sd-tag> (Baf) to inhibit autophagic degradation and <sd-tag id="sdTag380" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q91VR7///Q9CQV6" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3a///Map1lc3b" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag>‐II/<sd-tag id="sdTag260" source="sdapi" category="entity" entity_type="protein" role="normalizing" text="actin" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">actin</sd-tag> ratios determined by <sd-tag id="sdTag259" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag> (<b>A</b>) followed by densitometry (<b>B</b>). Data represent mean values±s.d. (<i>n</i>⩾3); <sup>*</sup><i>P</i>0.05.<graphic href="https://api.sourcedata.io/file.php?panel_id=6538"/></sd-panel><sd-panel panel_id="6539"><b>(C, D)</b> <sd-tag id="sdTag284" source="sdapi" category="entity" entity_type="cell_line" role="assayed" text="RAW 264.7" ext_ids="CVCL_0493" norm_text="" ext_dbs="CVCL" in_caption="True" ext_names="RAW 264.7" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://identifiers.org/cellosaurus:">RAW 264.7</sd-tag> was transfected with <sd-tag id="sdTag265" source="sdapi" category="entity" entity_type="gene" role="intervention" text="GRASP55" ext_ids="71680" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="0610011A07Rik" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">GRASP55</sd-tag> siRNAs or scramble (Scr) siRNA control. Following 48 h of siRNA treatment, cells were transfected with <sd-tag id="sdTag277" source="sdapi" category="entity" entity_type="protein" role="reporter" text="RFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RFP</sd-tag>-<sd-tag id="sdTag267" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag>-<sd-tag id="sdTag268" source="sdapi" category="entity" entity_type="protein" role="assayed" text="LC3" ext_ids="Q9CQV6///Q91VR7" norm_text="" ext_dbs="Uniprot///Uniprot" in_caption="True" ext_names="Map1lc3b///Map1lc3a" ext_tax_ids="10090///10090" ext_tax_names="Mus musculus///Mus musculus" ext_urls="https://www.uniprot.org/uniprot////https://www.uniprot.org/uniprot/">LC3</sd-tag> plasmid (<sd-tag id="sdTag269" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag> is sensitive to acidification, whereas <sd-tag id="sdTag278" source="sdapi" category="entity" entity_type="protein" role="reporter" text="RFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RFP</sd-tag> is not), after 24 h induced for autophagy in <sd-tag id="sdTag271" source="sdapi" category="entity" entity_type="undefined" role="component" text="EBSS" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">EBSS</sd-tag> for 1 h and autophagic induction and flux quantified (graph in <b>D</b>) by determining the number of <sd-tag id="sdTag355" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="early autophagic organelles" ext_ids="GO:0005776" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autophagic vacuole" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">early autophagic organelles</sd-tag> (<sd-tag id="sdTag273" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag><sup>+</sup><sd-tag id="sdTag279" source="sdapi" category="entity" entity_type="protein" role="reporter" text="RFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RFP</sd-tag><sup>+</sup> puncta) and <sd-tag id="sdTag283" source="sdapi" category="entity" entity_type="subcellular" role="assayed" text="autolysosomal organelles" ext_ids="GO:0044754" norm_text="" ext_dbs="Gene Ontology" in_caption="True" ext_names="autolysosome" ext_tax_ids="" ext_tax_names="" ext_urls="http://amigo.geneontology.org/amigo/term/">autolysosomal organelles</sd-tag> (<sd-tag id="sdTag274" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag><sup>−</sup><sd-tag id="sdTag280" source="sdapi" category="entity" entity_type="protein" role="reporter" text="RFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RFP</sd-tag><sup>+</sup> puncta) per cell as illustrated in fluorescent images (yellow arrows, <sd-tag id="sdTag275" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag><sup>+</sup><sd-tag id="sdTag281" source="sdapi" category="entity" entity_type="protein" role="reporter" text="RFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RFP</sd-tag><sup>+</sup>; red arrows, <sd-tag id="sdTag276" source="sdapi" category="entity" entity_type="protein" role="reporter" text="GFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">GFP</sd-tag><sup>−</sup><sd-tag id="sdTag282" source="sdapi" category="entity" entity_type="protein" role="reporter" text="RFP" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">RFP</sd-tag><sup>+</sup>). Total, yellow+red puncta per cell. Data represent mean values±s.d. (<i>n</i>⩾3); <sup>*</sup><i>P</i>0.05. Figure source data can be found in Supplementary data.<graphic href="https://api.sourcedata.io/file.php?panel_id=6539"/></sd-panel></fig><fig id="2361"><title></title><label>Figure 6</label><graphic href="https://api.sourcedata.io/file.php?figure_id=2361"/><sd-panel panel_id="6540"><p><strong>(A)</strong> <sd-tag id="sdTag285" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag><sup>fl/fl</sup> <sd-tag id="sdTag381" source="sdapi" category="entity" entity_type="gene" role="component" text="Cre" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cre</sd-tag><sup>−</sup> and <sd-tag id="sdTag286" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag><sup>fl/fl</sup> <sd-tag id="sdTag382" source="sdapi" category="entity" entity_type="gene" role="component" text="Cre" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cre</sd-tag><sup>+</sup> <sd-tag id="sdTag287" source="sdapi" category="entity" entity_type="cell_type" role="component" text="bone marrow‐derived macrophages" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">bone marrow‐derived macrophages</sd-tag> (<sd-tag id="sdTag288" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag>), pretreated overnight with 100 ng/ml <sd-tag id="sdTag289" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag>, were stimulated for 1 h with the inflammasome agonist <sd-tag id="sdTag291" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nigericin" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nigericin</sd-tag> (20 μM) with (Starvation; EBSS) or without (Full; full medium) autophagic induction. Cell culture supernatants were assayed for murine <sd-tag id="sdTag294" source="sdapi" category="entity" entity_type="protein" role="assayed" text="IL‐1β" ext_ids="P10749" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Il1b" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">IL‐1β</sd-tag> by <sd-tag id="sdTag295" source="sdapi" category="assay" entity_type="" role="" text="ELISA" ext_ids="BAO_0000134" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="ELISA" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">ELISA</sd-tag>. Data represent mean values±s.d. (<em>n</em>⩾3); <sup>*</sup><em>P</em>0.05.</p><graphic href="https://api.sourcedata.io/file.php?panel_id=6540"/></sd-panel><sd-panel panel_id="6541"><b>(B)</b> <sd-tag id="sdTag296" source="sdapi" category="entity" entity_type="molecule" role="component" text="LPS" ext_ids="CHEBI:6494" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="lipopolysaccharide" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">LPS</sd-tag>‐pretreated <sd-tag id="sdTag297" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag><sup>fl/fl</sup> <sd-tag id="sdTag385" source="sdapi" category="entity" entity_type="gene" role="component" text="Cre" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cre</sd-tag><sup>−</sup> and <sd-tag id="sdTag298" source="sdapi" category="entity" entity_type="gene" role="intervention" text="Atg5" ext_ids="11793" norm_text="" ext_dbs="NCBI gene" in_caption="True" ext_names="Atg5" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="http://www.ncbi.nlm.nih.gov/gene/">Atg5</sd-tag><sup>fl/fl</sup> <sd-tag id="sdTag386" source="sdapi" category="entity" entity_type="gene" role="component" text="Cre" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">Cre</sd-tag><sup>+</sup> <sd-tag id="sdTag299" source="sdapi" category="entity" entity_type="cell_type" role="component" text="BMMs" ext_ids="CL:0002476" norm_text="" ext_dbs="CL" in_caption="True" ext_names="bone marrow macrophage" ext_tax_ids="" ext_tax_names="" ext_urls=" https://identifiers.org/">BMMs</sd-tag> were stimulated with 20 μM <sd-tag id="sdTag300" source="sdapi" category="entity" entity_type="molecule" role="intervention" text="nigericin" ext_ids="CHEBI:7569" norm_text="" ext_dbs="ChEBI" in_caption="True" ext_names="nigericin" ext_tax_ids="" ext_tax_names="" ext_urls="http://www.ebi.ac.uk/chebi/searchId.do?chebiId=">nigericin</sd-tag> for 1 h in <sd-tag id="sdTag302" source="sdapi" category="entity" entity_type="undefined" role="component" text="OptiMEM" ext_ids="" norm_text="" ext_dbs="" in_caption="True" ext_names="" ext_tax_ids="" ext_tax_names="" ext_urls="">OptiMEM</sd-tag> and the release of <sd-tag id="sdTag304" source="sdapi" category="entity" entity_type="protein" role="assayed" text="HMGB1" ext_ids="P63158" norm_text="" ext_dbs="Uniprot" in_caption="True" ext_names="Hmgb1" ext_tax_ids="10090" ext_tax_names="Mus musculus" ext_urls="https://www.uniprot.org/uniprot/">HMGB1</sd-tag> was determined by <sd-tag id="sdTag303" source="sdapi" category="assay" entity_type="" role="" text="immunoblotting" ext_ids="BAO_0002424" norm_text="" ext_dbs="BAO" in_caption="True" ext_names="western blot" ext_tax_ids="" ext_tax_names="" ext_urls="https://bioportal.bioontology.org/ontologies/BAO/?p=classes&amp;conceptid=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23">immunoblotting</sd-tag>. Figure source data can be found in Supplementary data.<graphic href="https://api.sourcedata.io/file.php?panel_id=6541"/></sd-panel></fig></article>