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http://www.ncbi.nlm.nih.gov/pubmed/16919755,http://www.ncbi.nlm.nih.gov/pubmed/22512712,http://www.ncbi.nlm.nih.gov/pubmed/23458658,http://www.ncbi.nlm.nih.gov/pubmed/25793307

Which test is used to diagnose colour synesthesia?

A standardized test battery for the study of synesthesia. We used synesthetic versions of the Stroop test with colored letters and numbers presented either in the right or the left visual field of thirty-four synesthetes. Assessment of the hemispheric lateralization of grapheme-color synesthesia with Stroop-type tests. Stroop-type testsWeWe used synesthetic versions of the Stroop test with colored letters and numbers presented either in the right or the left visual field of thirty-four synesthetes

http://www.ncbi.nlm.nih.gov/pubmed/28846097

How does increased GDF15 affect body weight?

In humans, elevated GDF15 correlates with weight loss, and the administration of GDF15 to mice with obesity reduces body weight, at least in part, by decreasing food intake.

http://www.ncbi.nlm.nih.gov/pubmed/27739534,http://www.ncbi.nlm.nih.gov/pubmed/26657634,http://www.ncbi.nlm.nih.gov/pubmed/26873924,http://www.ncbi.nlm.nih.gov/pubmed/27167008,http://www.ncbi.nlm.nih.gov/pubmed/29165116,http://www.ncbi.nlm.nih.gov/pubmed/26556385,http://www.ncbi.nlm.nih.gov/pubmed/27493192

Which are the best methods for the prediction of circular RNA (circRNA)?

A circRNA prediction software for plants . Circular RNA profile in gliomas revealed by identification tool UROBORUS. Numerous algorithms that are used to detect genome-wide circRNA expression from RNA sequencing data have been developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. MiARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis. Here, we use common RNAseq datasets to scrutinize and compare the output from five different algorithms; circRNA_finder, find_circ, CIRCexplorer, CIRI, and MapSplice and evaluate the levels of bona fide and false positive circRNAs based on RNase R resistance. Numerous algorithms that are used to detect genome-wide circRNA expression from RNA sequencing (RNA-seq) data have been developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. We developed the software tandem, DCC and CircTest DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. A circRNA prediction software for plants (termed PcircRNA_finder) was developed that is more sensitive in detecting circRNAs than other frequently used programs (such as find_circ and CIRCexplorer)Numerous algorithms that are used to detect genome-wide circRNA expression from RNA sequencing (RNA-seq) data have been developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. We developed the software tandem, DCC and CircTest DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. Circular RNA profile in gliomas revealed by identification tool UROBORUS. Here, we use common RNAseq datasets to scrutinize and compare the output from five different algorithms; circRNA_finder, find_circ, CIRCexplorer, CIRI, and MapSplice and evaluate the levels of bona fide and false positive circRNAs based on RNase R resistance.PcircRNAfinder : a software for circRNA prediction in plants. A circRNA expression from RNA sequencing here, we use common RNAseq datasets to scrutinize and compare the output from five different algorithms; circRNAfinder, findcirc, CIRCexplorer, CIRI, and MapSplice and evaluate the levels of bona fide and false positive circRNAs based on RNase R resistance. Numerous algorithms that are used to detect genome-wide circRNA prediction software for plants was developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. We developed the software tandem, DCC and CircTest DCC uses output from the STAR read mapper to systematically detect circRNAs in total RNA-seq data. MiARma-Seq : a comprehensive tool for miRNA, mRNA and circRNA analysis. Circular RNA profile in gliomas revealed by identification tool UROBORUS. The best methods for the prediction of circular RNA are: circRNA_finder, find_circ, CIRCexplorer, CIRI, MapSplice, UROBORUS, Circ TEST DCC and miARma-Seq. Numerous algorithms that are used to detect genome-wide circRNA expression from RNA sequencing (RNA-seq) data have been developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. We developed the software tandem, DCC and CircTest DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. Circular RNA profile in gliomas revealed by identification tool UROBORUS.

http://www.ncbi.nlm.nih.gov/pubmed/27568322,http://www.ncbi.nlm.nih.gov/pubmed/28472537,http://www.ncbi.nlm.nih.gov/pubmed/28280216,http://www.ncbi.nlm.nih.gov/pubmed/27966237,http://www.ncbi.nlm.nih.gov/pubmed/28958504,http://www.ncbi.nlm.nih.gov/pubmed/28209746,http://www.ncbi.nlm.nih.gov/pubmed/25712685,http://www.ncbi.nlm.nih.gov/pubmed/24186235,http://www.ncbi.nlm.nih.gov/pubmed/23136195

What is inhibited by a drug rilotumumab?

Rilotumumab is a fully human monoclonal antibody that selectively targets the hepatocyte growth factor (HGF). It is used for treatment of cancer.

http://www.ncbi.nlm.nih.gov/pubmed/12692127,http://www.ncbi.nlm.nih.gov/pubmed/9869639,http://www.ncbi.nlm.nih.gov/pubmed/21450810,http://www.ncbi.nlm.nih.gov/pubmed/26929337,http://www.ncbi.nlm.nih.gov/pubmed/8636112,http://www.ncbi.nlm.nih.gov/pubmed/17535246,http://www.ncbi.nlm.nih.gov/pubmed/7678416,http://www.ncbi.nlm.nih.gov/pubmed/8599945,http://www.ncbi.nlm.nih.gov/pubmed/8876173,http://www.ncbi.nlm.nih.gov/pubmed/8090778,http://www.ncbi.nlm.nih.gov/pubmed/21454497,http://www.ncbi.nlm.nih.gov/pubmed/22396529

Which RNA polymerase II subunit carries RNA cleavage activity?

The eukaryotic transcription factor TFIIS enhances elongation and nascent transcript cleavage activities of RNA polymerase II in a stalled elongation complex.The eukaryotic transcription factor TFIIS enhances elongation and nascent transcript cleavage activities of RNA polymerase II in a stalled elongation complex. The transcription factor TFIIS zinc ribbon dipeptide Asp-Glu is critical for stimulation of elongation and RNA cleavage by RNA polymerase II.In contrast, Pol II is fully protected through association with the cleavage stimulatory factor TFIIS, which enables rapid recovery from any depth by RNA cleavage.In contrast, Pol II is fully protected through association with the cleavage stimulatory factor TFIIS, which enables rapid recovery from any depth by RNA cleavage. This mechanism is also used by transcription factor IIS, a factor that can bind Pol II and induce strong RNA cleavage.

http://www.ncbi.nlm.nih.gov/pubmed/28228471,http://www.ncbi.nlm.nih.gov/pubmed/14634212,http://www.ncbi.nlm.nih.gov/pubmed/17977614

Which is the transcriptome of RNA polymerase III?

RNA polymerase III (Pol III) transcribes a limited set of short genes in eukaryotes producing abundant small RNAs, mostly tRNA. The originally defined yeast Pol III transcriptome appears to be expanding owing to the application of new methods. Newly identified Pol III transcripts include small nucleolar RNAs, microRNAs, short interspersed nuclear element-encoded or tRNA-derived RNAs and novel classes of ncRNA that can display significant sequence complementarity to protein-coding genes and might thus regulate their expression.

http://www.ncbi.nlm.nih.gov/pubmed/23028697,http://www.ncbi.nlm.nih.gov/pubmed/15107834,http://www.ncbi.nlm.nih.gov/pubmed/25772236,http://www.ncbi.nlm.nih.gov/pubmed/21172801,http://www.ncbi.nlm.nih.gov/pubmed/24190887,http://www.ncbi.nlm.nih.gov/pubmed/9658103,http://www.ncbi.nlm.nih.gov/pubmed/22773875,http://www.ncbi.nlm.nih.gov/pubmed/23734343

How many PML isoforms exist in the human genome?

PML, the organizer of nuclear bodies (NBs), is expressed in several isoforms designated PMLI to VII which differ in their C-terminal region due to alternative splicing of a single gene.The PML isoforms that are most sensitive to virus infection correspond closely to those which have recently been identified as being covalently conjugated to PIC1. PML, the organizer of nuclear bodies (NBs), is expressed in several isoforms designated PMLI to VII which differ in their C-terminal region due to alternative splicing of a single gene.

http://www.ncbi.nlm.nih.gov/pubmed/25775132,http://www.ncbi.nlm.nih.gov/pubmed/28855414,http://www.ncbi.nlm.nih.gov/pubmed/29048557,http://www.ncbi.nlm.nih.gov/pubmed/26268193,http://www.ncbi.nlm.nih.gov/pubmed/28388405,http://www.ncbi.nlm.nih.gov/pubmed/24205087

Do cephalopods use RNA editing less frequently than other species?

Extensive messenger RNA editing generates transcript and protein diversity in genes involved in neural excitability, as previously described, as well as in genes participating in a broad range of other cellular functions. No. Extensive messenger RNA editing generates transcript and protein diversity in cephalopod genes involved in neural excitability, as previously described, as well as in genes participating in a broad range of other cellular functionsExtensive messenger RNA editing generates transcript and protein diversity in genes involved in neural excitability, as previously described, as well as in genes participating in a broad range of other cellular functions

http://www.ncbi.nlm.nih.gov/pubmed/28893208

Is there an RNAi drug being developed to treat amyloidosis?

Yes, patisiran is an investigational RNA interference (RNAi) therapeutic in development for the treatment of hereditary ATTR (hATTR) amyloidosis.

http://www.ncbi.nlm.nih.gov/pubmed/28846099

Which receptor does GDF15 bind?

GDF15 binds specifically to GDNF family receptor α-like (GFRAL)

http://www.ncbi.nlm.nih.gov/pubmed/7453210,http://www.ncbi.nlm.nih.gov/pubmed/11568027,http://www.ncbi.nlm.nih.gov/pubmed/22364692,http://www.ncbi.nlm.nih.gov/pubmed/8131775,http://www.ncbi.nlm.nih.gov/pubmed/26564596,http://www.ncbi.nlm.nih.gov/pubmed/7236050,http://www.ncbi.nlm.nih.gov/pubmed/261962

Is there an association between carcinoid syndrome and mitral valve disease?

Yes, mitral valve damage was reported in patients with carcinoid syndrome.

http://www.ncbi.nlm.nih.gov/pubmed/9658103,http://www.ncbi.nlm.nih.gov/pubmed/24190887

How many of the human PML isoforms are cytosolic?

Using a system in which only a single EYFP-linked PML isoform is expressed, we demonstrate that PMLI, PMLII and PMLVI accumulate in the cytoplasm following arsenic treatment, whereas PMLIII, PMLIV and PMLV do not the PML isoforms that are most sensitive to virus infection correspond closely to those which have recently been identified as being covalently conjugated to PIC1. Using a system in which only a single EYFP-linked PML isoform is expressed, we demonstrate that PMLI, PMLII and PMLVI accumulate in the cytoplasm following arsenic treatment, whereas PMLIII, PMLIV and PMLV do not The PML isoforms that are most sensitive to virus infection correspond closely to those which have recently been identified as being covalently conjugated to PIC1. Using a system in which only a single EYFP-linked PML isoform is expressed, PMLI, PMLII and PMLVI accumulate in the cytoplasm following arsenic treatment, whereas PMLIII, PMLIV and PMLV do notUsing a system in which only a single EYFP-linked PML isoform is expressed, we demonstrate that PMLI, PMLII and PMLVI accumulate in the cytoplasm following arsenic treatment, whereas PMLIII, PMLIV and PMLV do notUsing a system in which only a single EYFP-linked PML isoform is expressed, we demonstrate that PMLI, PMLII and PMLVI accumulate in the cytoplasm following arsenic treatment, whereas PMLIII, PMLIV and PMLV do notThe PML isoforms that are most sensitive to virus infection correspond closely to those which have recently been identified as being covalently conjugated to PIC1.The PML isoforms that are most sensitive to virus infection correspond closely to those which have recently been identified as being covalently conjugated to PIC1. Using a system in which only a single EYFP-linked PML isoform is expressed, we demonstrate that PMLI, PMLII and PMLVI accumulate in the cytoplasm following arsenic treatment, whereas PMLIII, PMLIV and PMLV do not. Using a system in which only a single EYFP-linked PML isoform is expressed, we demonstrate that PMLI, PMLII and PMLVI accumulate in the cytoplasm following arsenic treatment, whereas PMLIII, PMLIV and PMLV do not the PML isoforms that are most sensitive to virus infection correspond closely to those which have recently been identified as being covalently conjugated to PIC1.

http://www.ncbi.nlm.nih.gov/pubmed/28765477,http://www.ncbi.nlm.nih.gov/pubmed/3488531,http://www.ncbi.nlm.nih.gov/pubmed/26007263

Which tendons are affected in the Dequervain's tenosynovitis?

DeQuervain's tenosynovitis is a common cause of radial-sided wrist pain. Symptoms result from a narrow first dorsal compartment and associated tendinosis of the enclosed extensor pollicis brevis and/or abductor pollicis longus.

http://www.ncbi.nlm.nih.gov/pubmed/27009268

Are there RNAi approaches considered for the treatment of kidney injury?

Yes, RNAi approaches are being considered for the treatment of kidney injury.

http://www.ncbi.nlm.nih.gov/pubmed/24210139

What does davunetide do to microtubules?

Davunetide or NAP is a microtubule-stabilizer.

http://www.ncbi.nlm.nih.gov/pubmed/24505868,http://www.ncbi.nlm.nih.gov/pubmed/27813086,http://www.ncbi.nlm.nih.gov/pubmed/27473874,http://www.ncbi.nlm.nih.gov/pubmed/27756073,http://www.ncbi.nlm.nih.gov/pubmed/24557492,http://www.ncbi.nlm.nih.gov/pubmed/21385205,http://www.ncbi.nlm.nih.gov/pubmed/26400030,http://www.ncbi.nlm.nih.gov/pubmed/21853649,http://www.ncbi.nlm.nih.gov/pubmed/20071038,http://www.ncbi.nlm.nih.gov/pubmed/22299307,http://www.ncbi.nlm.nih.gov/pubmed/21115582,http://www.ncbi.nlm.nih.gov/pubmed/27737446,http://www.ncbi.nlm.nih.gov/pubmed/23812512,http://www.ncbi.nlm.nih.gov/pubmed/22503260,http://www.ncbi.nlm.nih.gov/pubmed/21837992,http://www.ncbi.nlm.nih.gov/pubmed/27068061,http://www.ncbi.nlm.nih.gov/pubmed/24346925,http://www.ncbi.nlm.nih.gov/pubmed/25511837

Is propranolol used for treatment of infantile hemangioma?

Yes, propranolol is becoming the treatment of choice for complicated infantile hemangioma.

http://www.ncbi.nlm.nih.gov/pubmed/28109959

Can the CEP290 gene mutations be targeted by AAV-mediated gene therapy?

The large size of the CEP290 gene prevents its use in adeno-associated virus (AAV)-mediated gene augmentation therapy.

http://www.ncbi.nlm.nih.gov/pubmed/8491706,http://www.ncbi.nlm.nih.gov/pubmed/10734216,http://www.ncbi.nlm.nih.gov/pubmed/16096648,http://www.ncbi.nlm.nih.gov/pubmed/9559263,http://www.ncbi.nlm.nih.gov/pubmed/1779707,http://www.ncbi.nlm.nih.gov/pubmed/18390649,http://www.ncbi.nlm.nih.gov/pubmed/12697649,http://www.ncbi.nlm.nih.gov/pubmed/23567752

Which proteins are controlling sterol metabolism in S. cerevisiae?

The yeast genome encodes seven oxysterol binding protein homologs, Osh1p-Osh7p, which have been implicated in regulating intracellular lipid and vesicular transport The yeast genome encodes seven oxysterol binding protein homologs, Osh1p-Osh7p, which have been implicated in regulating intracellular lipid and vesicular transport Upc2p, a transcription factor of the zinc cluster family, is an important regulator of sterol biosynthesis and azole drug resistance in Candida albicansUCP2 and its major targets ERG11, ERG2, NCP1 as well as Osh1p-Osh7pSterol metabolism and ERG2 gene regulation in the yeast Saccharomyces cerevisiae. Upc2p, a transcription factor of the zinc cluster family, is an important regulator of sterol biosynthesis and azole drug resistance in Candida albicans. The yeast genome encodes seven oxysterol binding protein homologs, Osh1p-Osh7p, which have been implicated in regulating intracellular lipid and vesicular transport. Northern blot analysis showed that increased binding correlates with increased expression for the analyzed Upc2p targets . Taken together, our results indicate that Upc2p is a key regulator of ergosterol metabolism. The yeast genome encodes seven oxysterol binding protein homologs, Osh1p-Osh7p, which have been implicated in regulating intracellular lipid and vesicular transport northern blot analysis showed that increased binding correlates with increased expression for the analyzed Upc2p included 12 genes involved in ergosterol biosynthesis to better understand Upc2p function in C. albicans, we used genomewide location profiling to identify the transcriptional targets of Upc2p in vivo. Upc2p, a transcription factor of the zinc cluster family, is an important regulator of sterol biosynthesis and azole drug resistance in Candida albicans sterol metabolism and ERG2 gene regulation in the yeast Saccharomyces cerevisiae. They also suggest that Upc2p may contribute to azole resistance by regulating the expression of drug efflux pump-encoding genes in addition to ergosterol metabolism. Overrepresented functional groups of genes whose promoters were bound by Upc2p is a key regulator of ergosterol metabolism. We have taken advantage of this property to study the regulation of the Delta8-Delta7-sterol isomerase-encoding ERG2 gene in an ergosterol auxotrophic mutant devoid of squalene-synthase activity. Ergosterol starvation leads to an 8-16-fold increase in ERG2 gene expression. Sterol metabolism and ERG2 gene regulation in the yeast Saccharomyces cerevisiae. Upc2p, a transcription factor of the zinc cluster family, is an important regulator of sterol biosynthesis and azole drug resistance in Candida albicans. The yeast genome encodes seven oxysterol binding protein homologs, Osh1p-Osh7p, which have been implicated in regulating intracellular lipid and vesicular transport. Northern blot analysis showed that increased binding correlates with increased expression for the analyzed Upc2p targets . Taken together, our results indicate that Upc2p is a key regulator of ergosterol metabolism. To better understand Upc2p function in C. albicans, we used genomewide location profiling to identify the transcriptional targets of Upc2p in vivo. Overrepresented functional groups of genes whose promoters were bound by Upc2p included 12 genes involved in ergosterol biosynthesis . They also suggest that Upc2p may contribute to azole resistance by regulating the expression of drug efflux pump-encoding genes in addition to ergosterol biosynthesis genes. We have taken advantage of this property to study the regulation of the Delta8-Delta7-sterol isomerase-encoding ERG2 gene in an ergosterol auxotrophic mutant devoid of squalene-synthase activity. The yeast genome encodes seven oxysterol binding protein homologs, Osh1p-Osh7p, which have been implicated in regulating intracellular lipid and vesicular transport northern blot analysis showed that increased binding correlates with increased expression for the analyzed Upc2p targets ( ERG11, MDR1, CDR1, YOR1, SUT1, SMF12, and CBP1 ).Taken together, our results indicate that upc2p is a key regulator of ergosterol metabolism.Overrepresented functional groups of genes whose promoters were bound by upc2p included 12 genes involved in ergosterol biosynthesis ( ncp1, erg11, erg2, and others ) to better understand upc2p function in c. albicans, we used genomewide location profiling to identify the transcriptional targets of upc2p in vivo.Upc2p, a transcription factor of the zinc cluster family, is an important regulator of sterol biosynthesis and azole drug resistance in candida albicans sterol metabolism and erg2 gene regulation in the yeast saccharomyces cerevisiae.We have taken advantage of this property to study the regulation of the delta8-delta7-sterol isomerase-encoding erg2 gene expression.Ergosterol starvation leads to an 8-16-fold increase in ERG2 gene expression.

http://www.ncbi.nlm.nih.gov/pubmed/25064607,http://www.ncbi.nlm.nih.gov/pubmed/19136460,http://www.ncbi.nlm.nih.gov/pubmed/20215442,http://www.ncbi.nlm.nih.gov/pubmed/17706299,http://www.ncbi.nlm.nih.gov/pubmed/24891501

Which enzymes are responsible for base J creation in Trypanosoma brucei?

The base is synthesized in a two-step pathway. Initially, a thymidine residue in DNA is hydroxylated by a thymidine hydroxylase (TH). This intermediate (HOMedU) is then glucosylated to form base J. Two proteins involved in J synthesis, JBP1 (J binding protein 1) and JBP2, contain a putative TH domain related to the family of Fe(2+)/2-oxoglutarate-dependent hydroxylases. JBP2 is a chromatin re-modeling protein that induces de novo J-synthesis, allowing JBP1, a J-DNA binding protein, to stimulate additional J-synthesis. A recent computational screen identified a possible candidate for the base J-associated glucosyltransferase (JGT) in trypanosomatid genomes.JBP2 and JBP1The deletion of both alleles of JGT from the genome of Trypanosoma brucei generates a cell line that completely lacks base J. We conclude that JBP2 and JBP1 are the TH enzymes involved in J biosynthesis. -d-glucopyranosyloxymethyluracil . The base is synthesized in a two-step pathway. Synthesis of the modified thymine base, beta-d-glucosyl-hydroxymethyluracil or J, within telomeric DNA of Trypanosoma brucei correlates with the bloodstream form specific epigenetic silencing of telomeric variant surface glycoprotein genes involved in antigenic variation. Two thymidine hydroxylases differentially regulate the formation of glucosylated DNA at regions flanking polymerase II polycistronic transcription units throughout the genome of Trypanosoma brucei. A recent computational screen identified a possible candidate for the base J-associated glucosyltransferase in trypanosomatid genomes. This intermediate is then glucosylated to form base J. Here we discuss the regulation of hmU and base J formation in the trypanosome genome by JGT and base J-binding protein. Chromosome-internal J deposition is primarily mediated by JBP1, whereas JBP2-stimulated J deposition at the telomeric regions. Two proteins involved in J synthesis, JBP1 /2-oxoglutarate-dependent hydroxylases. JBP2 and JBP1 are capable of stimulating de novo J-synthesis. We have previously characterized two thymidine-hydroxylases (TH), JBP1 and JBP2, which regulate J-biosynthesis.JBP2 is a chromatin re-modeling protein that induces de novo J-synthesis, allowing JBP1, a J-DNA binding protein, to stimulate additional J-synthesis.Chromosome-internal J deposition is primarily mediated by JBP1, whereas JBP2-stimulated J deposition at the telomeric regions.Here we show that mutation of key residues in the TH domain of JBP2 ablate its ability to induce de novo J synthesis.JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J biosynthesis in genomic DNA of African trypanosomes.Here we discuss the regulation of hmU and base J formation in the trypanosome genome by JGT and base J-binding protein.The deletion of both alleles of JGT from the genome of Trypanosoma brucei generates a cell line that completely lacks base JWe have recently proposed a model in which chromatin remodeling by a SWI2/SNF2-like protein (JBP2) regulates the developmental and de novo site-specific localization of J synthesis within bloodstream form trypanosome DNA.

http://www.ncbi.nlm.nih.gov/pubmed/18818371,http://www.ncbi.nlm.nih.gov/pubmed/26830453,http://www.ncbi.nlm.nih.gov/pubmed/27402900,http://www.ncbi.nlm.nih.gov/pubmed/24192834,http://www.ncbi.nlm.nih.gov/pubmed/25189781,http://www.ncbi.nlm.nih.gov/pubmed/23056304

Which method for subsampling of NGS reads requires only gene counts?

SamExploreR : exploring reproducibility and robustness of RNA-seq results based on SAM files.We introduce the subseq r package, which uses a novel efficient approach to perform this subsampling and to calculate informative metrics at each depth required to inform a broad range of functional and evolutionary studies.Our methods are broadly applicable for polymorphism discovery in moderate to large genomes even at highly diverged loci, and we established by subsampling the illumina sbs coverage depth related questions for the experimental design.SubSeq : determining appropriate sequencing depth through efficient read subsampling.Our methods are broadly applicable for polymorphism discovery in moderate to large genomes even at highly diverged loci, and we established by subsampling the Illumina SBS coverage depth required to inform a broad range of functional and evolutionary studies. We introduce the subSeq R package, which uses a novel efficient approach to perform this subsampling and to calculate informative metrics at each depthThe subSeq R package, which uses a novel efficient approach to perform this subsampling and to calculate informative metrics at each depthWe applied subsampling to ascertain the effect of training sample size and the number of RNA sequencing reads on classification accuracy of molecular subtype and routine biomarker prediction models . We introduce the subSeq R package, which uses a novel efficient approach to perform this subsampling and to calculate informative metrics at each depth. Interestingly, after subsampling to the same coverage for GSNAP and TopHat, we find that both mappers have similar performance, implying that the advantage of TopHat is mainly an artifact of the lower coverage.

http://www.ncbi.nlm.nih.gov/pubmed/16651657,http://www.ncbi.nlm.nih.gov/pubmed/23935120,http://www.ncbi.nlm.nih.gov/pubmed/7932731,http://www.ncbi.nlm.nih.gov/pubmed/2840207,http://www.ncbi.nlm.nih.gov/pubmed/1332607,http://www.ncbi.nlm.nih.gov/pubmed/18570880,http://www.ncbi.nlm.nih.gov/pubmed/6090122,http://www.ncbi.nlm.nih.gov/pubmed/2842762,http://www.ncbi.nlm.nih.gov/pubmed/21767457,http://www.ncbi.nlm.nih.gov/pubmed/6323017,http://www.ncbi.nlm.nih.gov/pubmed/12888496,http://www.ncbi.nlm.nih.gov/pubmed/1316274

Which topoisomerase is essential in yeast?

Eukaryotic DNA topoisomerase II is an abundant nuclear enzyme that is essential for cell proliferation. Yeast DNA topoisomerase II is encoded by a single-copy, essential gene.Yeast DNA topoisomerase II is encoded by a single-copy, essential gene. Disruption of one copy of the gene in a diploid yeast creates a recessive lethal mutation, indicating that the single DNA topoisomerase II gene of yeast has an essential function.Yeast DNA topoisomerase II is encoded by a single-copy, essential gene.

http://www.ncbi.nlm.nih.gov/pubmed/24123922,http://www.ncbi.nlm.nih.gov/pubmed/18798845,http://www.ncbi.nlm.nih.gov/pubmed/26338144,http://www.ncbi.nlm.nih.gov/pubmed/24039113,http://www.ncbi.nlm.nih.gov/pubmed/24715367,http://www.ncbi.nlm.nih.gov/pubmed/23395478

What is the genetic basis of Ohdo syndrome?

MED12 cause X-linked Ohdo syndromeInMutations in MED12 cause X-linked Ohdo syndromeMutations in MED12 cause X-linked Ohdo syndrome The occurrence of three different hemizygous missense mutations in three unrelated families affected by Ohdo syndrome MKB type shows that mutations in MED12 are the underlying cause of this X-linked form of Ohdo syndrome.Mutations in MED12 cause X-linked Ohdo syndrome In the two families, MED12 missense mutations (c.3443G>A [p.Arg1148His] or c.3493T>C [p.Ser1165Pro]) segregating with the phenotype were identified.FG syndrome, Lujan syndrome, and Ohdo syndrome, the Maat-Kievit-Brunner type, have been described as distinct syndromes with overlapping non-specific features and different missense mutations of the MED12 gene have been reported in all of them. Mutations in MED12 cause X-linked Ohdo syndromeThe occurrence of three different hemizygous missense mutations in three unrelated families affected by Ohdo syndrome MKB type shows that mutations in MED12 are the underlying cause of this X-linked form of Ohdo syndrome.Mutations in MED12 cause X-linked Ohdo syndrome FG syndrome, Lujan syndrome, and Ohdo syndrome, the Maat-Kievit-Brunner type, have been described as distinct syndromes with overlapping non-specific features and different missense mutations of the MED12 gene have been reported in all of them.MED12

http://www.ncbi.nlm.nih.gov/pubmed/27896938,http://www.ncbi.nlm.nih.gov/pubmed/25891173,http://www.ncbi.nlm.nih.gov/pubmed/28987768,http://www.ncbi.nlm.nih.gov/pubmed/28822576,http://www.ncbi.nlm.nih.gov/pubmed/26846323,http://www.ncbi.nlm.nih.gov/pubmed/28964438,http://www.ncbi.nlm.nih.gov/pubmed/28125365

Which drugs were tested in the KEYNOTE-006 study?

KEYNOTE-006 study compared pembrolizumab versus ipilimumab for advanced melanoma.

http://www.ncbi.nlm.nih.gov/pubmed/22630782,http://www.ncbi.nlm.nih.gov/pubmed/22492479,http://www.ncbi.nlm.nih.gov/pubmed/25771422,http://www.ncbi.nlm.nih.gov/pubmed/22489911,http://www.ncbi.nlm.nih.gov/pubmed/26474615,http://www.ncbi.nlm.nih.gov/pubmed/24369275,http://www.ncbi.nlm.nih.gov/pubmed/28004298,http://www.ncbi.nlm.nih.gov/pubmed/27647529,http://www.ncbi.nlm.nih.gov/pubmed/25186156,http://www.ncbi.nlm.nih.gov/pubmed/21899835,http://www.ncbi.nlm.nih.gov/pubmed/28660987,http://www.ncbi.nlm.nih.gov/pubmed/23203733,http://www.ncbi.nlm.nih.gov/pubmed/21198706,http://www.ncbi.nlm.nih.gov/pubmed/28429557

What is the purpose of the FRAX scale?

The FRAX score (The WHO Fracture Risk Assessment Tool), is a free web-based clinical scale assessing the 10-year probability of major osteoporotic fracture risk and need for lifestyle advice/reassurance, dual X-ray absorptiometry (DEXA) scanning or preventive treatment.

http://www.ncbi.nlm.nih.gov/pubmed/19475561,http://www.ncbi.nlm.nih.gov/pubmed/17581973

Are mutations in the nf1 gene associated with memory?

Yes, distinct functional domains of neurofibromatosis type 1 regulate immediate versus long-term memory formation.

http://www.ncbi.nlm.nih.gov/pubmed/26876963,http://www.ncbi.nlm.nih.gov/pubmed/26915297,http://www.ncbi.nlm.nih.gov/pubmed/27013738,http://www.ncbi.nlm.nih.gov/pubmed/25987504

Has Cas9 gene editing the potential to correct inhereted hearing loss?

CRISPR/Cas9-mediated genome editing can be efficiently performed in the mammalian inner ear in vivo. The genetic correction of induced pluripotent stem cells (iPSCs) induced from somatic cells of patients with sensorineural hearing loss (caused by hereditary factors) is a promising method for its treatment. The correction of gene mutations in iPSCs could restore the normal function of cells and provide a rich source of cells for transplantation.

http://www.ncbi.nlm.nih.gov/pubmed/21964334,http://www.ncbi.nlm.nih.gov/pubmed/24534946,http://www.ncbi.nlm.nih.gov/pubmed/26154016,http://www.ncbi.nlm.nih.gov/pubmed/22976956,http://www.ncbi.nlm.nih.gov/pubmed/24657531,http://www.ncbi.nlm.nih.gov/pubmed/26929370,http://www.ncbi.nlm.nih.gov/pubmed/27083996,http://www.ncbi.nlm.nih.gov/pubmed/25934638,http://www.ncbi.nlm.nih.gov/pubmed/25837375,http://www.ncbi.nlm.nih.gov/pubmed/26711177

How may CTCF mediate splicing?

Two different mechanisms convey DNA methylation information into the regulation of alternative splicing. The first involves modulation of the elongation rate of RNA polymerase II (Pol II) by CCCTC-binding factor (CTCF) and methyl-CpG binding protein 2 (MeCP2); the second involves the formation of a protein bridge by heterochromatin protein 1 (HP1) that recruits splicing factors onto transcribed alternative exons.CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Intragenic 5-methylcytosine and CTCF mediate opposing effects on pre-mRNA splicing: CTCF promotes inclusion of weak upstream exons through RNA polymerase II pausing, whereas 5-methylcytosine evicts CTCF, leading to exon exclusion.CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.Here we provide the first evidence that a DNA-binding protein, CCCTC-binding factor (CTCF), can promote inclusion of weak upstream exons by mediating local RNA polymerase II pausing both in a mammalian model system for alternative splicing, CD45, and genome-wideCTCF also functions in RNA polymerase II regulation and in doing so can influence co-transcriptional splicing events.CTCF is ubiquitously expressed and plays diverse roles in gene regulation, imprinting, insulation, intra/interchromosomal interactions, nuclear compartmentalisation, and alternative splicing.In particular, the CCCTC-binding factor (CTCF), the Argonaute protein AGO1, and members of the heterochromatin protein 1 (HP1) family have been implicated in the regulation of splicing associated with chromatin and the elongation of RNAPII.Furthermore, we found mutations in the splicing factor SFPQ and in the nonclassic regulators of mRNA processing CTCF and RAD21.However, there was no correlation between the KTS+/KTS- splicing variants of WT1 and the methylation status of the CpGs of the CTCF binding site.

http://www.ncbi.nlm.nih.gov/pubmed/27485083

Is ACI-35 a passive vaccine?

No, ACI-35 is an active vaccine.

http://www.ncbi.nlm.nih.gov/pubmed/27751937,http://www.ncbi.nlm.nih.gov/pubmed/28169013,http://www.ncbi.nlm.nih.gov/pubmed/26341328,http://www.ncbi.nlm.nih.gov/pubmed/27411304,http://www.ncbi.nlm.nih.gov/pubmed/28592343,http://www.ncbi.nlm.nih.gov/pubmed/28782647,http://www.ncbi.nlm.nih.gov/pubmed/28396132,http://www.ncbi.nlm.nih.gov/pubmed/28501926,http://www.ncbi.nlm.nih.gov/pubmed/27533048

Which main ribotype of Clostridium difficile is responsible of the recent outbreak?

The outbreak of the hypervirulent strain belonging to ribotype 027 has increased the incidence and severity of CDI in some countries.

http://www.ncbi.nlm.nih.gov/pubmed/22544605,http://www.ncbi.nlm.nih.gov/pubmed/18628399,http://www.ncbi.nlm.nih.gov/pubmed/16648643,http://www.ncbi.nlm.nih.gov/pubmed/15082542,http://www.ncbi.nlm.nih.gov/pubmed/21761155,http://www.ncbi.nlm.nih.gov/pubmed/17535246,http://www.ncbi.nlm.nih.gov/pubmed/15359273

What is the function of the TFIIS transcriptional factor (Dst1) in yeast?

TFIIS, an elongation factor encoded by DST1 in Saccharomyces cerevisiae, stimulates transcript cleavage in arrested RNA polymerase II.TFIIS, an elongation factor encoded by DST1 in Saccharomyces cerevisiae, stimulates transcript cleavage in arrested RNA polymerase II. Co-immunoprecipitation experiments showed that TFIIS can bind the Cdk8 module and SAGA in cell-free extracts Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS. It is proposed that TFIIS and the Spt8-containing form of SAGA co-operate to rescue RNA polymerase II from unproductive elongation complexes, and that the Cdk8 module temporarily blocks transcription during transcript cleavage.TFIIS, an elongation factor encoded by DST1 in Saccharomyces cerevisiae, stimulates transcript cleavage in arrested RNA polymerase II. Co-immunoprecipitation experiments showed that TFIIS can bind the Cdk8 module and SAGA in cell-free extracts Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS. It is proposed that TFIIS and the Spt8-containing form of SAGA co-operate to rescue RNA polymerase II from unproductive elongation complexes, and that the Cdk8 module temporarily blocks transcription during transcript cleavage. TFIIS promotes the intrinsic ability of RNA polymerase II to cleave the 3'-end of the newly synthesized RNA. TFIIS and Rpb9 are essential when the cells are challenged with microtubule-destabilizing drugs;Transcription factor IIS (TFIIS) stimulates RNA cleavage by RNA polymerase II by allowing backtracked enzymes to resume transcription elongation. TFIIS promotes the intrinsic ability of RNA polymerase II to cleave the 3'-end of the newly synthesized RNA. Recent studies revealed that TFIIS has also a role in Pol II transcription initiation. TFIIS is required under stress conditions and that TFIIS is important for the transition between initiation and elongation in vivo.TFIIS, an elongation factor encoded by DST1 in Saccharomyces cerevisiae, stimulates transcript cleavage in arrested RNA polymerase II. Co-immunoprecipitation experiments showed that TFIIS can bind the Cdk8 module and SAGA in cell-free extracts Members of the SAGA and Mediator complexes are partners of the transcription elongation factor TFIIS. TFIIS and Pol III occupancies correlated well genome-wide on this novel class of targets. These data provide strong in vivo and in vitro evidence in favor of a role of TFIIS as a general Pol III transcription factor. Transcription factor IIS (TFIIS) stimulates RNA cleavage by RNA polymerase II by allowing backtracked enzymes to resume transcription elongation.

http://www.ncbi.nlm.nih.gov/pubmed/26484155,http://www.ncbi.nlm.nih.gov/pubmed/20602769,http://www.ncbi.nlm.nih.gov/pubmed/22960375,http://www.ncbi.nlm.nih.gov/pubmed/21964334,http://www.ncbi.nlm.nih.gov/pubmed/26305225,http://www.ncbi.nlm.nih.gov/pubmed/24419148,http://www.ncbi.nlm.nih.gov/pubmed/23085715,http://www.ncbi.nlm.nih.gov/pubmed/24812327,http://www.ncbi.nlm.nih.gov/pubmed/23408854,http://www.ncbi.nlm.nih.gov/pubmed/24916973,http://www.ncbi.nlm.nih.gov/pubmed/21835883,http://www.ncbi.nlm.nih.gov/pubmed/23686312,http://www.ncbi.nlm.nih.gov/pubmed/23502848,http://www.ncbi.nlm.nih.gov/pubmed/28413449

Is DNA methylation correlated with nucleosome occupancy?

DNA methylation can determine nucleosome positioning. Using a novel bioinformatics pipeline, we show a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions that is not present at promoters. DNA methylation determines nucleosome occupancy in the 5'-CpG islands of tumor suppressor genes. In contrast, exons demonstrate a high degree of methylation and nucleosome occupancy. Although global DNA demethylation has been observed after treatment, it is unclear to what extent demethylation induces changes in nucleosome occupancy, a key determinant of gene expression. In order to systematically evaluate potential diversities among CGIs and ultimately to illuminate the link between diversity of CGIs and their epigenetic variation, we analyzed the nucleotide-resolution DNA methylation maps of multiple cellular origins. Using this global approach, we observe the dependency of nucleosome occupancy upon the DNA methylation status. Exonic DNA methylation seems to function together with exonic nucleosomes and H3K36me3 for the proper splicing of transcripts with different expression levels. Transcription, histone modifications, and DNA methylation alter this "ground state" by having distinct effects on both nucleosome positioning and occupancy. Human promoters containing a CpG island tend to remain nucleosome-free as well as methylation-free.Exonic dna methylation can determine nucleosome positioning.In contrast, exons demonstrate a high degree of methylation and nucleosome occupancy.Using this global approach, we observe the dependency of nucleosome occupancy upon the dna methylation seems to function together with exonic nucleosomes and h3k36me3 for the proper splicing of transcripts with different expression levels.In order to systematically evaluate potential diversities among cgis and ultimately to illuminate the link between diversity of cgis and their epigenetic variation, we analyzed the nucleotide-resolution dna methylation status.Transcription, histone modifications, and dna methylation determines nucleosome occupancy in the 5'-cpg islands of tumor suppressor genes.Although global DNA demethylation has been observed after treatment, it is unclear to what extent demethylation induces changes in nucleosome occupancy, a key determinant of gene expression.Using this global approach, we analyzed the nucleotide-resolution dna methylation maps ( methylomes ) of multiple cellular origins.Dna methylation alter this "ground state" by having distinct effects on both nucleosome positioning.In contrast, exons demonstrate a high degree of methylation and nucleosome occupancy.Nucleosome-free regions were observed only in promoters containing a CpG islandHere I show that CpG islands were associated not only with methylation-free promoters but also with nucleosome-free promoters.In contrast to the methylation-and nucleosome-free states of CpG-island promoters, exons were densely methylated at CpGs and packaged into nucleosomes.I also found that nucleosomes, DNA methylation, and H3K36me3 marked the exons of transcripts with low, medium, and high gene expression levels, respectively.DNA methylation determines nucleosome occupancy in the 5'-CpG islands of tumor suppressor genes.DNA methylation can determine nucleosome positioning.DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter.The mostly unmethylated CpG islands have reduced nucleosome occupancy and are enriched in cell type-independent binding sites for CTCF.Three positions at the splice sites show high CpG abundance and accompany elevated nucleosome occupancy in a leveled GC architecture.Here I show that CpG islands were associated not only with methylation-free promoters but also with nucleosome-free promoters. Nucleosome-free regions were observed only in promoters containing a CpG island In contrast to the methylation-and nucleosome-free states of CpG-island promoters, exons were densely methylated at CpGs and packaged into nucleosomes. In contrast, exons demonstrate a high degree of methylation and nucleosome occupancy.Using this global approach, we observe the dependency of nucleosome occupancy upon the DNA methylation seems to function together with exonic nucleosomes and H3K36me3 for the proper splicing of transcripts with different expression levels. Using a novel bioinformatics pipeline, we show a striking anti-correlation between nucleosome occupancy and DNA methylation maps of multiple cellular origins. Transcription, histone modifications, and DNA methylation determines nucleosome occupancy in the 5'-CpG islands of tumor suppressor genes. Exonic DNA methylation can determine nucleosome positioning. In order to systematically evaluate potential diversities among CGIs and ultimately to illuminate the link between diversity of CGIs and their epigenetic variation, we analyzed the nucleotide-resolution DNA methylation and nucleosome occupancy. Although global DNA demethylation has been observed after treatment, it is unclear to what extent demethylation induces changes in nucleosome occupancy, a key determinant of gene expression levels. Human promoters containing a CpG island tend to remain nucleosome-free as well as methylation-free. In contrast, exons demonstrate a high degree of methylation status. DNA methylation at CTCF regions that is not present at promoters. Recent reports have identified distinct histone methylation patterns, elevated nucleosome occupancy and enriched DNA methylation at exons relative to introns. DNA methylation directly silences genes with non-CpG island promoters and establishes a nucleosome occupied promoter. Using a novel bioinformatics pipeline a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions that is not present at promoters can be shown. The induction of DNA hypomethylation events by genetic (DNMT1/DNMT3B deficient cells) or drug (a DNA demethylating agent) approaches is associated with the eviction of nucleosomes from previously hypermethylated CpG islands of tumor suppressor genes.DNA methylation can determine nucleosome positioning. Using a novel bioinformatics pipeline, we show a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions that is not present at promoters. DNA methylation determines nucleosome occupancy in the 5'-CpG islands of tumor suppressor genes. In contrast, exons demonstrate a high degree of methylation and nucleosome occupancy. In contrast, exons demonstrate a high degree of methylation and nucleosome occupancy. Using a novel bioinformatics pipeline, we show a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions that is not present at promoters. yes

http://www.ncbi.nlm.nih.gov/pubmed/28961763

Which R/Bioconductor package has been developed for the analysis of psychiatric disease genes?

PsyGeNET is a knowledge resource on psychiatric diseases and their genes, developed by text mining and curated by domain experts. Psygenet2r is an R package that contains a variety of functions for leveraging PsyGeNET database and facilitating its analysis and interpretation. The package offers different types of queries to the database along with variety of analysis and visualization tools, including the study of the anatomical structures in which the genes are expressed and gaining insight of gene's molecular function. Psygenet2r is especially suited for network medicine analysis of psychiatric disorders.psygenet2r

http://www.ncbi.nlm.nih.gov/pubmed/25762693

Which Janus kinase does decernotinib target?

Decernotinib (VX-509) is a potent and selective inhibitor of janus kinase 3 (JAK3).

http://www.ncbi.nlm.nih.gov/pubmed/11306557,http://www.ncbi.nlm.nih.gov/pubmed/12841365,http://www.ncbi.nlm.nih.gov/pubmed/11763990,http://www.ncbi.nlm.nih.gov/pubmed/11186112,http://www.ncbi.nlm.nih.gov/pubmed/15700718,http://www.ncbi.nlm.nih.gov/pubmed/19708722,http://www.ncbi.nlm.nih.gov/pubmed/12736803,http://www.ncbi.nlm.nih.gov/pubmed/10498237

What is the genetic basis of the Delayed Sleep-Phase Syndrome (DSPS)?

Circadian gene mutations are also associated with circadian rhythm disorders such as familial advanced sleep phase syndrome, delayed sleep phase syndrome, and non-24-hour sleep-wake syndrome. Possible association of human leucocyte antigen DR1 with delayed sleep phase syndrome. The study investigated the human leucocyte antigen (HLA), types A, B and DR, of 42 patients with delayed sleep phase syndrome (DSPS) and compared the frequencies of the antigens with those in 117 healthy controls. The comparison revealed that the gene frequencies and positivities of HLA-A, -B and -DR, except for DR1, had no significant differences between the patients and controls. The frequency of HLA-DR1 was increased in the DSPS patients as compared with that in the healthy controls (P = 0.0069 in positivity). In human leukocyte antigen (HLA) typing, the incidence of DR1 positivity alone was significantly higher in DSPS patients than in healthy subjects. Circadian gene mutations are also associated with circadian rhythm disorders such as familial advanced sleep phase syndrome, delayed sleep phase syndrome, and non-24-hour sleep-wake syndrome. A possible association of human leucocyte antigen DR1 with delayed sleep phase syndrome has been reported. In human leukocyte antigen (HLA) typing, the incidence of DR1 positivity alone was significantly higher in DSPS patients than in healthy subjects. A length polymorphism in the circadian clock gene Per3 is linked to delayed sleep phase syndrome and extreme diurnal preference. The data suggest that AA-NAT could be a susceptibility gene for DSPS.We studied the association between the AA-NAT gene and delayed sleep phase syndrome . Association of the length polymorphism in the human Per3 gene with the delayed sleep-phase syndrome: does latitude have an influence upon it?. Recent progress in biological clock research has facilitated genetic analysis of circadian rhythm sleep disorders, such as delayed sleep phase syndrome . One of the haplotypes was significantly associated with DSPS in our study population. In human leukocyte antigen typing, the incidence of DR1 positivity alone was significantly higher in DSPS patients than in healthy subjects. Polymorphisms in the CLOCK, BMAL1, Per3 and TIMELESS genes have been associated with susceptibility to mood disorder, and single nucleotide polymorphisms and haplotypes in several circadian genes have been observed among those displaying certain circadian phenotypes, including worse mood in the evening, insomnia in mania and early, middle or late insomnia in depression. The Per3 polymorphism correlated significantly with extreme diurnal preference, the longer allele associating with morningness and the shorter allele with eveningness. The frequency of the 129 threonine allele is significantly higher in the patients than in the controls .

http://www.ncbi.nlm.nih.gov/pubmed/26994322,http://www.ncbi.nlm.nih.gov/pubmed/22819198

What are jakinibs?

Jakinibs are Janus kinase (JAK) inhibitors. They are considered a new class of kinase inhibitors in cancer and autoimmune disease. Jakinibs can differ substantially in their selectivity against JAKs.

http://www.ncbi.nlm.nih.gov/pubmed/28530548,http://www.ncbi.nlm.nih.gov/pubmed/29117565,http://www.ncbi.nlm.nih.gov/pubmed/28250012,http://www.ncbi.nlm.nih.gov/pubmed/29069650,http://www.ncbi.nlm.nih.gov/pubmed/28374903

What is the function of the gene MDA5?

Melanoma differentiation-associated gene 5 (MDA5) is a pattern recognition receptor that recognizes cytoplasmic viral double-stranded RNA (dsRNA) and initiates rapid innate antiviral responses. MDA5 forms a filament-like multimer along the dsRNA leading to oligomerization, which in turn activates the adaptor protein mitochondrial antiviral signaling protein (MAVS) to provide a signal platform for the induction of type I interferon (IFN) and proinflammatory cytokines. The conformational switch of MDA5 causes antiviral defense, but excessive activation of the MDA5-MAVS pathway may result in autoimmune diseases.

http://www.ncbi.nlm.nih.gov/pubmed/7731693

Which is the conserved motif of DEAD box proteins?

The conserved motif is: Asp(D)-Glu-(E)-Ala(A)-Asp(D)

http://www.ncbi.nlm.nih.gov/pubmed/26216344,http://www.ncbi.nlm.nih.gov/pubmed/19567577,http://www.ncbi.nlm.nih.gov/pubmed/19164560,http://www.ncbi.nlm.nih.gov/pubmed/26207384,http://www.ncbi.nlm.nih.gov/pubmed/21408168,http://www.ncbi.nlm.nih.gov/pubmed/25864056,http://www.ncbi.nlm.nih.gov/pubmed/23548695,http://www.ncbi.nlm.nih.gov/pubmed/27570628

Which individuals show preferential colonization of the Prevotellaceae bacteria in their guts?

Although the distinction of enterotypes as either discrete clusters or a continuum will require additional investigation, numerous studies have demonstrated the co-exclusion of the closely related Prevotellaceae and Bacteroides genera in the gut microbiota of healthy human subjects where Prevotella appears to be a discriminatory taxon for residence in more agrarian societies.

http://www.ncbi.nlm.nih.gov/pubmed/28007912

Describe GARLIC (GWAS-based Prediction Toolkit for Connecting Diseases and Cell Types)

GARLIC (GWAS-based Prediction Toolkit for Connecting Diseases and Cell Types) is a bioinformatic toolkit for aetiologically connecting diseases and cell type-specific regulatory maps. GARLIC can be used to retrieve potential disease-causative genetic variants overlapping regulatory sequences of interest. Overall, GARLIC can satisfy several important needs within the field of medical genetics, thus potentially assisting in the ultimate goal of uncovering the elusive and complex genetic basis of common human disorders.GARLIC is a bioinformatic toolkit for aetiologically connecting diseases and cell type-specific regulatory maps.

http://www.ncbi.nlm.nih.gov/pubmed/18628399,http://www.ncbi.nlm.nih.gov/pubmed/28521214,http://www.ncbi.nlm.nih.gov/pubmed/24780862,http://www.ncbi.nlm.nih.gov/pubmed/14690608,http://www.ncbi.nlm.nih.gov/pubmed/15082542,http://www.ncbi.nlm.nih.gov/pubmed/16492753,http://www.ncbi.nlm.nih.gov/pubmed/17535246,http://www.ncbi.nlm.nih.gov/pubmed/14704159,http://www.ncbi.nlm.nih.gov/pubmed/15359273

How does Dst1 knock-out affect transcription in yeast?

While TFIIS has a pronounced effect on transcription elongation in vitro, the deletion of DST1 has no major effect on cell viability. We showed that: dst1 and rpb9 mutants have a synthetic growth defective phenotype when combined with fyv4, gim5, htz1, yal011w, ybr231c, soh1, vps71, and vps72 mutants that is exacerbated during germination or at high salt concentrations. In vivo, some dst1 mutants were partly defective in tRNA synthesis and showed a reduced Pol III occupancy at the restrictive temperature.While TFIIS has a pronounced effect on transcription elongation in vitro, the deletion of DST1 has no major effect on cell viability.

http://www.ncbi.nlm.nih.gov/pubmed/25899749,http://www.ncbi.nlm.nih.gov/pubmed/28416406,http://www.ncbi.nlm.nih.gov/pubmed/27727040,http://www.ncbi.nlm.nih.gov/pubmed/27920714,http://www.ncbi.nlm.nih.gov/pubmed/27625113,http://www.ncbi.nlm.nih.gov/pubmed/26872887,http://www.ncbi.nlm.nih.gov/pubmed/28887767,http://www.ncbi.nlm.nih.gov/pubmed/27224445,http://www.ncbi.nlm.nih.gov/pubmed/28479184,http://www.ncbi.nlm.nih.gov/pubmed/26894245,http://www.ncbi.nlm.nih.gov/pubmed/27268941,http://www.ncbi.nlm.nih.gov/pubmed/27477871,http://www.ncbi.nlm.nih.gov/pubmed/27215215,http://www.ncbi.nlm.nih.gov/pubmed/27568285,http://www.ncbi.nlm.nih.gov/pubmed/26088268,http://www.ncbi.nlm.nih.gov/pubmed/25567155,http://www.ncbi.nlm.nih.gov/pubmed/27317414,http://www.ncbi.nlm.nih.gov/pubmed/25789661,http://www.ncbi.nlm.nih.gov/pubmed/27575900,http://www.ncbi.nlm.nih.gov/pubmed/26095746,http://www.ncbi.nlm.nih.gov/pubmed/27175894,http://www.ncbi.nlm.nih.gov/pubmed/27697436

Which drug can be reversed with idarucizumab?

Idarucizumab is an antibody fragment that specifically reverses dabigatran mediated anticoagulation.

http://www.ncbi.nlm.nih.gov/pubmed/29088312

What is the function of the TMEM132 genes?

The extra-cellular portions of TMEM132 proteins contain five conserved domains including three tandem immunoglobulin domains, and a cohesin domain homologue, the first such domain found in animals. These findings strongly predict a cellular adhesion function for TMEM132 family, connecting the extracellular medium with the intracellular actin cytoskeleton.

http://www.ncbi.nlm.nih.gov/pubmed/28596291

Does DDX54 play a role in DNA damage response?

Yes. DDX54, a candidate genotoxic stress responsive RNA helicase, regulates transcriptome dynamics during DNA damage response.

http://www.ncbi.nlm.nih.gov/pubmed/10378364,http://www.ncbi.nlm.nih.gov/pubmed/29157614,http://www.ncbi.nlm.nih.gov/pubmed/29157615,http://www.ncbi.nlm.nih.gov/pubmed/29157616,http://www.ncbi.nlm.nih.gov/pubmed/28856089,http://www.ncbi.nlm.nih.gov/pubmed/21035860,http://www.ncbi.nlm.nih.gov/pubmed/2029023,http://www.ncbi.nlm.nih.gov/pubmed/25984208,http://www.ncbi.nlm.nih.gov/pubmed/22724593,http://www.ncbi.nlm.nih.gov/pubmed/10978936,http://www.ncbi.nlm.nih.gov/pubmed/17895817,http://www.ncbi.nlm.nih.gov/pubmed/26130736,http://www.ncbi.nlm.nih.gov/pubmed/7699917,http://www.ncbi.nlm.nih.gov/pubmed/19863172,http://www.ncbi.nlm.nih.gov/pubmed/27338259,http://www.ncbi.nlm.nih.gov/pubmed/24268501,http://www.ncbi.nlm.nih.gov/pubmed/21221584,http://www.ncbi.nlm.nih.gov/pubmed/17940990,http://www.ncbi.nlm.nih.gov/pubmed/25341835,http://www.ncbi.nlm.nih.gov/pubmed/27208909,http://www.ncbi.nlm.nih.gov/pubmed/2227242,http://www.ncbi.nlm.nih.gov/pubmed/8699962,http://www.ncbi.nlm.nih.gov/pubmed/19546057

List main clinical features of the POEMS syndrome.

POEMS is an acronym for the main clinical features of the syndrome, namely, Polyneuropathy, Organomegaly, Endocrinopathy, M protein, and Skin abnormalities. Other features include papilledema, extravascular volume overload, sclerotic bone lesions, thrombocytosis, and Castleman disease. It is a multisystemc disorder with a good long-term prognosis.

http://www.ncbi.nlm.nih.gov/pubmed/28712537

Which retinal dystrophy related gene is targeted by the AAV2-hRPE65v2 drug?

AAV2-hRPE65v2, also called voretigene neparvovec, targets the RPE65 gene, whose mutations lead to retinal dystrophy.

http://www.ncbi.nlm.nih.gov/pubmed/27474163,http://www.ncbi.nlm.nih.gov/pubmed/19716786,http://www.ncbi.nlm.nih.gov/pubmed/22139922,http://www.ncbi.nlm.nih.gov/pubmed/21525956,http://www.ncbi.nlm.nih.gov/pubmed/22504286,http://www.ncbi.nlm.nih.gov/pubmed/28815538,http://www.ncbi.nlm.nih.gov/pubmed/29167439,http://www.ncbi.nlm.nih.gov/pubmed/22641694

What is the function of yeast TERRA RNAs?

The ends of linear eukaryotic chromosomes are transcribed into different species of non-coding transcripts (the telomeric transcriptome), including TERRA (telomeric repeat-containing RNA) molecules. TERRA are part of the DNA damage response triggered by dysfunctional telomeres. In addition to its role as a template-encoding telomeric DNA synthesis, telomerase RNA has been shown to function as a flexible scaffold for protein subunits of the RNP holoenzyme.We further show that TERRA (Telomeric Repeat-containing RNA) is increased in post-mitotic cells with short telomeres and correlates with telomere rearrangementsWe further show that TERRA (Telomeric Repeat-containing RNA) is increased in post-mitotic cells with short telomeres and correlates with telomere rearrangements Like human and budding yeast, fission yeast harbours a population of telomeric RNA molecules containing G-rich telomeric repeats transcribed from the subtelomere to the telomere. The ends of linear eukaryotic chromosomes are transcribed into different species of non-coding transcripts (the telomeric transcriptome), including TERRA (telomeric repeat-containing RNA) molecules TERRA is part of the DNA damage response triggered by dysfunctional telomeres Telomeric repeat-containing RNA (TERRA) has been implicated in the control of heterochromatin and telomerase. yeast TERRA is regulated by telomere-binding proteins in a chromosome-end-specific manner that is dependent on subtelomeric repetitive DNA elements

http://www.ncbi.nlm.nih.gov/pubmed/9120866,http://www.ncbi.nlm.nih.gov/pubmed/23931059,http://www.ncbi.nlm.nih.gov/pubmed/23583354,http://www.ncbi.nlm.nih.gov/pubmed/10867774,http://www.ncbi.nlm.nih.gov/pubmed/12799851,http://www.ncbi.nlm.nih.gov/pubmed/12776909,http://www.ncbi.nlm.nih.gov/pubmed/29135930,http://www.ncbi.nlm.nih.gov/pubmed/7734328,http://www.ncbi.nlm.nih.gov/pubmed/15041917,http://www.ncbi.nlm.nih.gov/pubmed/28282278,http://www.ncbi.nlm.nih.gov/pubmed/28002223

What are the 4 cardinal signs of inflammation according to Celsus?

redness or rubor , heat or calor, swelling or tumor, and pain or dolorTumor, calor, rubor, and dolor describe four cardinal signs of inflammation.

http://www.ncbi.nlm.nih.gov/pubmed/8007629,http://www.ncbi.nlm.nih.gov/pubmed/24786571

Do bacteria from the genus Morexella cause respiratory infections?

Bacteria from the genus Morexella can cause respiratory infections

http://www.ncbi.nlm.nih.gov/pubmed/25097590,http://www.ncbi.nlm.nih.gov/pubmed/26122142,http://www.ncbi.nlm.nih.gov/pubmed/25389115,http://www.ncbi.nlm.nih.gov/pubmed/26171675,http://www.ncbi.nlm.nih.gov/pubmed/17873119,http://www.ncbi.nlm.nih.gov/pubmed/27375208,http://www.ncbi.nlm.nih.gov/pubmed/25931195,http://www.ncbi.nlm.nih.gov/pubmed/25846706,http://www.ncbi.nlm.nih.gov/pubmed/28428902,http://www.ncbi.nlm.nih.gov/pubmed/25129392,http://www.ncbi.nlm.nih.gov/pubmed/21465659,http://www.ncbi.nlm.nih.gov/pubmed/22810475,http://www.ncbi.nlm.nih.gov/pubmed/26159157,http://www.ncbi.nlm.nih.gov/pubmed/22171123

Which two genes are implicated in Juvenile polyposis syndrome?

Juvenile polyposis syndrome (JPS) is a rare autosomal dominant disorder predisposing to gastrointestinal hamartomatous polyps and cancer with a pathogenic SMAD4 or BMPR1A germline mutation being identified in about 40-50% of patients.

http://www.ncbi.nlm.nih.gov/pubmed/23275551

Do chromatin features predict genes associated with eQTLs?

Yes, genomic proximity plus five TF and chromatin features are able to predict>90% of target genes within 1 megabase of eQTLs

http://www.ncbi.nlm.nih.gov/pubmed/18566967,http://www.ncbi.nlm.nih.gov/pubmed/21567934,http://www.ncbi.nlm.nih.gov/pubmed/27677223,http://www.ncbi.nlm.nih.gov/pubmed/21567925,http://www.ncbi.nlm.nih.gov/pubmed/28116328,http://www.ncbi.nlm.nih.gov/pubmed/17192541,http://www.ncbi.nlm.nih.gov/pubmed/23613367,http://www.ncbi.nlm.nih.gov/pubmed/21670757,http://www.ncbi.nlm.nih.gov/pubmed/25656619,http://www.ncbi.nlm.nih.gov/pubmed/19533842,http://www.ncbi.nlm.nih.gov/pubmed/19907330,http://www.ncbi.nlm.nih.gov/pubmed/27576954,http://www.ncbi.nlm.nih.gov/pubmed/25565926,http://www.ncbi.nlm.nih.gov/pubmed/23301918,http://www.ncbi.nlm.nih.gov/pubmed/25007323,http://www.ncbi.nlm.nih.gov/pubmed/23054245,http://www.ncbi.nlm.nih.gov/pubmed/27942778

List the 6 genes associated with the autosomal recessive form of Osteogenesis imperfecta

There are at least 6 genes associated with osteogenesis imperfecta, Sp7/Osx, FK506-binding protein, Hsp47/SERPINH1, WNT1, CRTAP, P3H1, and PPIB, LEPRE1,PLOD2, TMEM38B

http://www.ncbi.nlm.nih.gov/pubmed/25961655,http://www.ncbi.nlm.nih.gov/pubmed/25344204,http://www.ncbi.nlm.nih.gov/pubmed/24602916

What is masitinib an inhibitor of?

Masitinib is an inhibitor of mast cell-glia axis and a Fyn kinase blocker. It is an oral tyrosine kinase inhibitor with activity against c-Kit and platelet-derived growth factor receptors (PDGFR).

http://www.ncbi.nlm.nih.gov/pubmed/28893208

What is the name of the RNAi investigational drug being developed against hereditary amyloidosis?

Patisiran.The investigational RNAi drug in development for the treatment of hereditary amyloidosis is patisiran.

http://www.ncbi.nlm.nih.gov/pubmed/19546235,http://www.ncbi.nlm.nih.gov/pubmed/16815976,http://www.ncbi.nlm.nih.gov/pubmed/16575185,http://www.ncbi.nlm.nih.gov/pubmed/24990148,http://www.ncbi.nlm.nih.gov/pubmed/20047949,http://www.ncbi.nlm.nih.gov/pubmed/21282187,http://www.ncbi.nlm.nih.gov/pubmed/19293570,http://www.ncbi.nlm.nih.gov/pubmed/16378710,http://www.ncbi.nlm.nih.gov/pubmed/21600199,http://www.ncbi.nlm.nih.gov/pubmed/24023912,http://www.ncbi.nlm.nih.gov/pubmed/8842735,http://www.ncbi.nlm.nih.gov/pubmed/18719115,http://www.ncbi.nlm.nih.gov/pubmed/16006531,http://www.ncbi.nlm.nih.gov/pubmed/23585276,http://www.ncbi.nlm.nih.gov/pubmed/21991322,http://www.ncbi.nlm.nih.gov/pubmed/19584898,http://www.ncbi.nlm.nih.gov/pubmed/16107875,http://www.ncbi.nlm.nih.gov/pubmed/23230275

What is the function of the H19 (ICR) locus in the human genome?

We found that localized DNA demethylation at the H19 imprinting control region (ICR) induced by 5-AzaCdR, reduced IGF2, increased H19 expression, increased CTCF and cohesin recruitment and changed histone modifications.The H19 locus acts in vivo as a tumor suppressor. The H19 locus belongs to a cluster of imprinted genes that is linked to the human Beckwith-Wiedemann syndrome. The expression of H19 and its closely associated IGF2 gene is frequently deregulated in some human tumors, such as Wilms' tumors.

http://www.ncbi.nlm.nih.gov/pubmed/26768289,http://www.ncbi.nlm.nih.gov/pubmed/22403112,http://www.ncbi.nlm.nih.gov/pubmed/16463613,http://www.ncbi.nlm.nih.gov/pubmed/20205677,http://www.ncbi.nlm.nih.gov/pubmed/15940379,http://www.ncbi.nlm.nih.gov/pubmed/22370296,http://www.ncbi.nlm.nih.gov/pubmed/20872215,http://www.ncbi.nlm.nih.gov/pubmed/24625372,http://www.ncbi.nlm.nih.gov/pubmed/17538470,http://www.ncbi.nlm.nih.gov/pubmed/26104116,http://www.ncbi.nlm.nih.gov/pubmed/19604460

What is the mode of action of teriparatide?

Teripartide is is an effective anabolic (i.e., bone growing) agent used in the treatment of some forms of osteoporosis.

http://www.ncbi.nlm.nih.gov/pubmed/28522612,http://www.ncbi.nlm.nih.gov/pubmed/28954988,http://www.ncbi.nlm.nih.gov/pubmed/29020110,http://www.ncbi.nlm.nih.gov/pubmed/24678773,http://www.ncbi.nlm.nih.gov/pubmed/28177460,http://www.ncbi.nlm.nih.gov/pubmed/23842810,http://www.ncbi.nlm.nih.gov/pubmed/27002637,http://www.ncbi.nlm.nih.gov/pubmed/27874022,http://www.ncbi.nlm.nih.gov/pubmed/22581179

What is the Strelka workflow?

Whole genome and exome sequencing of matched tumor-normal sample pairs is becoming routine in cancer research. The consequent increased demand for somatic variant analysis of paired samples requires methods specialized to model this problem so as to sensitively call variants at any practical level of tumor impurity. Strelka is a method for somatic SNV and small indel detection from sequencing data of matched tumor-normal samples. The method uses a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, while leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. Strelka has superior accuracy and sensitivity on impure samples compared with approaches based on either diploid genotype likelihoods or general allele-frequency tests.

http://www.ncbi.nlm.nih.gov/pubmed/26647377

Describe the Manta algorithm for detection of structural variants

Manta is a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid germline and somatic analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of these variant types: for example NA12878 at 50× genomic coverage is analyzed in less than 20 min. Manta can discover and score variants based on supporting paired and split-read evidence, with scoring models optimized for germline analysis of diploid individuals and somatic analysis of tumor-normal sample pairs. Call quality is similar to or better than comparable methods, as determined by pedigree consistency of germline calls and comparison of somatic calls to COSMIC database variants. Manta consistently assembles a higher fraction of its calls to base-pair resolution, allowing for improved downstream annotation and analysis of clinical significance.

http://www.ncbi.nlm.nih.gov/pubmed/22220246,http://www.ncbi.nlm.nih.gov/pubmed/19534241,http://www.ncbi.nlm.nih.gov/pubmed/23814399,http://www.ncbi.nlm.nih.gov/pubmed/19124637,http://www.ncbi.nlm.nih.gov/pubmed/28913640,http://www.ncbi.nlm.nih.gov/pubmed/19321060,http://www.ncbi.nlm.nih.gov/pubmed/21811863,http://www.ncbi.nlm.nih.gov/pubmed/11915453,http://www.ncbi.nlm.nih.gov/pubmed/19949820,http://www.ncbi.nlm.nih.gov/pubmed/28160398

Is Kummell’s disease an avascular necrosis of the vertebral body?

Yes, Kummell’s disease is an avascular necrosis of the vertebral body.

http://www.ncbi.nlm.nih.gov/pubmed/15529083,http://www.ncbi.nlm.nih.gov/pubmed/11195858,http://www.ncbi.nlm.nih.gov/pubmed/18299911,http://www.ncbi.nlm.nih.gov/pubmed/23856549,http://www.ncbi.nlm.nih.gov/pubmed/19216010,http://www.ncbi.nlm.nih.gov/pubmed/17072191,http://www.ncbi.nlm.nih.gov/pubmed/27269656,http://www.ncbi.nlm.nih.gov/pubmed/16911735,http://www.ncbi.nlm.nih.gov/pubmed/24198977

What causes "Puffy hand syndrome"?

Puffy hand syndrome is a complication of intravenous drug abuse.

http://www.ncbi.nlm.nih.gov/pubmed/28398597,http://www.ncbi.nlm.nih.gov/pubmed/26990079,http://www.ncbi.nlm.nih.gov/pubmed/28147349,http://www.ncbi.nlm.nih.gov/pubmed/27144850,http://www.ncbi.nlm.nih.gov/pubmed/28812220,http://www.ncbi.nlm.nih.gov/pubmed/26702336,http://www.ncbi.nlm.nih.gov/pubmed/28765121,http://www.ncbi.nlm.nih.gov/pubmed/28279838,http://www.ncbi.nlm.nih.gov/pubmed/28783871,http://www.ncbi.nlm.nih.gov/pubmed/29125718,http://www.ncbi.nlm.nih.gov/pubmed/26239599,http://www.ncbi.nlm.nih.gov/pubmed/26398681,http://www.ncbi.nlm.nih.gov/pubmed/27049060

Describe mechanism of action of Ozanimod.

Ozanimod is a novel, selective, oral sphingosine-1-phosphate (1 and 5) receptor modulator in clinical development for the treatment of chronic immune-mediated, inflammatory diseases, such as multiple sclerosis and inflammatory bowel disease. Yet its exact mechanism of action is unknown.

http://www.ncbi.nlm.nih.gov/pubmed/28894943,http://www.ncbi.nlm.nih.gov/pubmed/23013418,http://www.ncbi.nlm.nih.gov/pubmed/28701501,http://www.ncbi.nlm.nih.gov/pubmed/24474263,http://www.ncbi.nlm.nih.gov/pubmed/23517301,http://www.ncbi.nlm.nih.gov/pubmed/18065505

Describe swirl sign in intracerebral hemorrhage.

Swirl sign is described as areas of low attenuation, radiolucency or irregular density. It was previously described in epidural hematomas. In intracerebral hemorrhage swirl sign is associated with greater hematoma volume, unfavorable outcomes and greater mortality risk.

http://www.ncbi.nlm.nih.gov/pubmed/21749875,http://www.ncbi.nlm.nih.gov/pubmed/27269255,http://www.ncbi.nlm.nih.gov/pubmed/16489838,http://www.ncbi.nlm.nih.gov/pubmed/28665169,http://www.ncbi.nlm.nih.gov/pubmed/21437061,http://www.ncbi.nlm.nih.gov/pubmed/27789971,http://www.ncbi.nlm.nih.gov/pubmed/25879673,http://www.ncbi.nlm.nih.gov/pubmed/21390982,http://www.ncbi.nlm.nih.gov/pubmed/29052453,http://www.ncbi.nlm.nih.gov/pubmed/28392653,http://www.ncbi.nlm.nih.gov/pubmed/28299553,http://www.ncbi.nlm.nih.gov/pubmed/21110523,http://www.ncbi.nlm.nih.gov/pubmed/23326202,http://www.ncbi.nlm.nih.gov/pubmed/25192328,http://www.ncbi.nlm.nih.gov/pubmed/24671866

What is Morgellons disease?

It is a skin condition in which individuals have skin lesions that contain some kind of fibers. Patients often complain of bugs crawling under their skin. The disease is of unknown origin and may be psychosomatic, however recent evidence indicates it could be transmitted by a tick.

http://www.ncbi.nlm.nih.gov/pubmed/22693220,http://www.ncbi.nlm.nih.gov/pubmed/28535294

What is Cellbase?

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.Cellbase is a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase.CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. CellBase provides a solution to the growing necessity of integration by easing the access to biological data.CellBase is a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.

http://www.ncbi.nlm.nih.gov/pubmed/10591352

What is the asosciation between the eustachian tube and the palatine muscle of the uvula?

Palatal musculature is known to be responsible for the active opening of the eustachian tube. The palatine musculature is involved in the opening of the eustachian tube.Palatal musculature is known to be responsible for the active opening of the eustachian (auditory) tube Palatal musculature is known to be responsible for the active opening of the eustachian (auditory) tubePalatal musculature is known to be responsible for the active opening of the eustachian tube. Palatal musculature is known to be responsible for the active opening of the eustachian (auditory) tube.

http://www.ncbi.nlm.nih.gov/pubmed/28417603,http://www.ncbi.nlm.nih.gov/pubmed/28637293

Are Conserved Nonexonic Elements (CNEEs) important in phylogenomics research?

Yes. Conserved Nonexonic Elements (CNEEs) appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis.

http://www.ncbi.nlm.nih.gov/pubmed/21914852,http://www.ncbi.nlm.nih.gov/pubmed/28158860,http://www.ncbi.nlm.nih.gov/pubmed/22889666,http://www.ncbi.nlm.nih.gov/pubmed/17158163,http://www.ncbi.nlm.nih.gov/pubmed/20371324,http://www.ncbi.nlm.nih.gov/pubmed/25215414,http://www.ncbi.nlm.nih.gov/pubmed/27262581,http://www.ncbi.nlm.nih.gov/pubmed/28448767,http://www.ncbi.nlm.nih.gov/pubmed/12200417,http://www.ncbi.nlm.nih.gov/pubmed/27540088,http://www.ncbi.nlm.nih.gov/pubmed/27601258,http://www.ncbi.nlm.nih.gov/pubmed/21081559

What is the definition of General Regulatory Factors (GRFs)?

GRFs, which bind to sites scattered throughout the genome within promoters, would not only play a key role in regulating gene expression but also partition the genome in functionally independent domains.In Saccharomyces cerevisiae, a group of more than 200 co-regulated genes (Ribi genes) is involved in ribosome biogenesis. This regulon has been shown to rely on a small set of transcriptional regulators (mainly Abf1, but also Reb1, Tbf1 and Rap1) referred to as general regulatory factors (GRFs) because of their widespread binding and action at many promoters and other specialized genomic regions.General regulatory factors (GRFs) as genome partitioners GRFs, which bind to sites scattered throughout the genome within promoters, would not only play a key role in regulating gene expression but also partition the genome in functionally independent domains. Abf1 and Rap1 are general regulatory factors (GRFs) that contribute to transcriptional activation of a large number of genes, as well as to replication, silencing and telomere structure in yeast. We speculate that an important function of general regulatory factors such as Reb1p is to establish and maintain proper transcription start sites at promoters, and that when binding of such factors is compromised, resulting effects on mRNA translation may be an underappreciated aspect of gene regulation studies. We found that nucleosomes and specific DNA-binding proteins, including the general regulatory factors Reb1p, Rap1p, and Abf1p, and Pol III transcription factors enhance the efficiency of NNS termination by physically blocking Pol II progression. In the model organism Saccharomyces cerevisiae, these regions are adjacent to binding sites for general regulatory transcription factors, and the Reb1 protein is commonly bound to promoter DNA near such regions. Here, we use high resolution tiling arrays to examine the contributions of two general regulatory factors, Abf1 and Rap1, to nucleosome occupancy in Saccharomyces cerevisiae. Multiple roles of the general regulatory factor Abf1 in yeast ribosome biogenesis. GRFs, which bind to sites scattered throughout the genome within promoters, would not only play a key role in regulating gene expression but also partition the genome in functionally independent domains.

http://www.ncbi.nlm.nih.gov/pubmed/28130396,http://www.ncbi.nlm.nih.gov/pubmed/11369969,http://www.ncbi.nlm.nih.gov/pubmed/1295944,http://www.ncbi.nlm.nih.gov/pubmed/22123662,http://www.ncbi.nlm.nih.gov/pubmed/24650116,http://www.ncbi.nlm.nih.gov/pubmed/21045362,http://www.ncbi.nlm.nih.gov/pubmed/24686796,http://www.ncbi.nlm.nih.gov/pubmed/6270614,http://www.ncbi.nlm.nih.gov/pubmed/21886730,http://www.ncbi.nlm.nih.gov/pubmed/26275628,http://www.ncbi.nlm.nih.gov/pubmed/28761605

Which virus can be diagnosed with the monospot test?

Epstein-Barr virus (EBV) can be detected with the monospot test. EBV is a highly prevalent virus, transmitted via saliva, which often causes asymptomatic infection in children but frequently results in infectious mononucleosis in adolescents.

http://www.ncbi.nlm.nih.gov/pubmed/28709498

Why is the Fyn kinase considered a promising therapeutic target for Alzheimer's Disease?

Fyn is an attractive target for AD therapeutics, not only based on its activation by Aβ via cellular prion protein but also due to its known interaction with tau, uniquely linking the two key pathologies in AD.

http://www.ncbi.nlm.nih.gov/pubmed/28874668

What is the link between TADs and GRBs?

Topologically associating domains (TADs) are ancient features that coincide with Metazoan clusters of extreme noncoding conservation (aka GRBs).Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

http://www.ncbi.nlm.nih.gov/pubmed/12824372

What is Target Explorer?

Target Explorer is an automated tool for the identification of new target genes for a specified set of transcription factors. It was specifically designed for the well-annotated Drosophila melanogaster genome, but most options can be used for sequences from other genomes as well. Target Explorer is available at http://trantor.bioc.columbia.edu/Target_Explorer/

http://www.ncbi.nlm.nih.gov/pubmed/12200417

Can the yeast protein Abf1 act as insulator?

Saccharomyces cerevisiae Rap1p and Abf1p proteins are endowed with a potent insulating capacityyesSaccharomyces cerevisiae Rap1p and Abf1p proteins are endowed with a potent insulating capacity.

http://www.ncbi.nlm.nih.gov/pubmed/25115546

What does the human IVIG treatment for Alzheimer's disease contain?

Human intravenous immunoglobulin (IVIG) is a mixture of polyclonal IgG antibodies isolated and pooled from thousands of healthy human donors.

http://www.ncbi.nlm.nih.gov/pubmed/28293277

Is there any linear-time and linear-space algorithm for the computation of avoided words in biological sequences?

Yes. There is a linear-time and linear-space algorithm for the computation of avoided words of length k in a given sequence x.

http://www.ncbi.nlm.nih.gov/pubmed/23836714,http://www.ncbi.nlm.nih.gov/pubmed/28589221,http://www.ncbi.nlm.nih.gov/pubmed/19915560,http://www.ncbi.nlm.nih.gov/pubmed/21314938,http://www.ncbi.nlm.nih.gov/pubmed/26081484,http://www.ncbi.nlm.nih.gov/pubmed/27010248,http://www.ncbi.nlm.nih.gov/pubmed/28680098,http://www.ncbi.nlm.nih.gov/pubmed/25181302,http://www.ncbi.nlm.nih.gov/pubmed/27052166

What is the mechanism of the auxin-inducible degron system?

Fusion of inducible degradation signals, so-called degrons, to cellular proteins is an elegant method of controlling protein levels in vivo. The auxin-inducible degron (AID) system allows the rapid and reversible proteolysis of proteins of interest, and enables the generation of conditional mutants of budding yeast. Strategies that use ubiquitin-mediated protein degradation to eliminate the product of a gene of interest, such as heat-inducible degron (td) and auxin-inducible degron (AID), are powerful methods for constructing conditional mutants. Auxin-inducible degron (AID) technology allows rapid depletion of proteins in animal cells and fungi, but its application to human cells has been limited by the difficulties of tagging endogenous proteins. The auxin-inducible degron harbors great potential for dynamic protein depletion in yeast. Here, we thoroughly and quantitatively characterize the auxin-inducible degron in single yeast cells.Plants have evolved a unique system in which the plant hormone auxin directly induces rapid degradation of the AUX/IAA family of transcription repressors by a specific form of the SCF E3 ubiquitin ligase. Other eukaryotes lack the auxin response but share the SCF degradation pathway, allowing the transplantation of the auxin-inducible degron (AID) system into nonplant cells and the use of a small molecule to conditionally control protein stability.

http://www.ncbi.nlm.nih.gov/pubmed/8469500,http://www.ncbi.nlm.nih.gov/pubmed/18558055,http://www.ncbi.nlm.nih.gov/pubmed/16719870,http://www.ncbi.nlm.nih.gov/pubmed/25477907,http://www.ncbi.nlm.nih.gov/pubmed/21977942,http://www.ncbi.nlm.nih.gov/pubmed/12010076,http://www.ncbi.nlm.nih.gov/pubmed/3965026,http://www.ncbi.nlm.nih.gov/pubmed/25815650,http://www.ncbi.nlm.nih.gov/pubmed/9614412,http://www.ncbi.nlm.nih.gov/pubmed/18937649,http://www.ncbi.nlm.nih.gov/pubmed/21393451,http://www.ncbi.nlm.nih.gov/pubmed/6859802

Which bacteria causes erythrasma?

Corynebacterium minutissimum is the bacteria that leads to cutaneous eruptions of erythrasma and is the most common cause of interdigital foot infections.

http://www.ncbi.nlm.nih.gov/pubmed/28623093,http://www.ncbi.nlm.nih.gov/pubmed/25748404,http://www.ncbi.nlm.nih.gov/pubmed/16237566,http://www.ncbi.nlm.nih.gov/pubmed/11799392,http://www.ncbi.nlm.nih.gov/pubmed/18520775,http://www.ncbi.nlm.nih.gov/pubmed/23359635,http://www.ncbi.nlm.nih.gov/pubmed/27411420,http://www.ncbi.nlm.nih.gov/pubmed/16816006,http://www.ncbi.nlm.nih.gov/pubmed/24589093,http://www.ncbi.nlm.nih.gov/pubmed/27813696,http://www.ncbi.nlm.nih.gov/pubmed/22378147

Mutations in which gene cause Schimke immune-osseous dysplasia?

SMARCAL1, also known as HARP, is an ATP-dependent annealing helicase that stabilizes replication forks during DNA damage. Mutations in this gene are the cause of Schimke immune-osseous dysplasia, an autosomal recessive disorder characterized by T-cell immunodeficiency and growth dysfunctions. Mutations in this gene are the cause of Schimke immune-osseous dysplasia (SIOD), an autosomal recessive disorder characterized by T-cell immunodeficiency and growth dysfunctions. SMARCAL1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A-Like 1), also known as HARP, is an ATP-dependent annealing helicase that stabilizes replication forks during DNA damage.Smarcal1 , also known as harp, is an atp-dependent annealing helicase that stabilizes replication forks during dna damage. Mutations in this gene are the cause of schimke immune-osseous dysplasia , an autosomal recessive disorder characterized by t-cell immunodeficiency and growth dysfunctions. Mutations in this gene are the cause of Schimke immune-osseous dysplasia (SIOD), an autosomal recessive disorder characterized by T-cell immunodeficiency and growth dysfunctions. SMARCAL1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A-Like 1), also known as HARP, is an ATP-dependent annealing helicase that stabilizes replication forks during DNA damage. Mutations in this gene are the cause of Schimke immune-osseous dysplasia , an autosomal recessive disorder characterized by T-cell immunodeficiency and growth dysfunctions. SMARCAL1 , also known as HARP, is an ATP-dependent annealing helicase that stabilizes replication forks during DNA damage. SMARCAL1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A-Like 1), also known as HARP, is an ATP-dependent annealing helicase that stabilizes replication forks during DNA damage. Mutations in this gene are the cause of Schimke immune-osseous dysplasia (SIOD), an autosomal recessive disorder characterized by T-cell immunodeficiency and growth dysfunctions.

http://www.ncbi.nlm.nih.gov/pubmed/27521725,http://www.ncbi.nlm.nih.gov/pubmed/17854667,http://www.ncbi.nlm.nih.gov/pubmed/27458589,http://www.ncbi.nlm.nih.gov/pubmed/1656290,http://www.ncbi.nlm.nih.gov/pubmed/28361164,http://www.ncbi.nlm.nih.gov/pubmed/9452242,http://www.ncbi.nlm.nih.gov/pubmed/28936073

What is the most common histological diagnosis of "butterfly glioma"?

Butterfly glioma is glioblastoma multiforme invading corpus callosum .

http://www.ncbi.nlm.nih.gov/pubmed/23691404,http://www.ncbi.nlm.nih.gov/pubmed/18286821,http://www.ncbi.nlm.nih.gov/pubmed/22434056,http://www.ncbi.nlm.nih.gov/pubmed/24171835,http://www.ncbi.nlm.nih.gov/pubmed/24980921,http://www.ncbi.nlm.nih.gov/pubmed/23117075,http://www.ncbi.nlm.nih.gov/pubmed/27973931,http://www.ncbi.nlm.nih.gov/pubmed/26076791,http://www.ncbi.nlm.nih.gov/pubmed/28981939,http://www.ncbi.nlm.nih.gov/pubmed/21949351,http://www.ncbi.nlm.nih.gov/pubmed/22876593,http://www.ncbi.nlm.nih.gov/pubmed/19606488,http://www.ncbi.nlm.nih.gov/pubmed/27617132,http://www.ncbi.nlm.nih.gov/pubmed/28075445,http://www.ncbi.nlm.nih.gov/pubmed/27785401

Which chromosomes are implicated in the Emanuel syndrome?

Emanuel syndrome is associated with supernumerary chromosome t(11;22)(q23;q11), which consists of the extra genetic material from chromosomes 11 and 22.

http://www.ncbi.nlm.nih.gov/pubmed/22109108,http://www.ncbi.nlm.nih.gov/pubmed/24553142,http://www.ncbi.nlm.nih.gov/pubmed/25182241

Is a CpG island methylator phenotype involved in ependymomas?

Although devoid of recurrent single nucleotide variants and focal copy number aberrations, poor-prognosis hindbrain ependymomas exhibit a CpG island methylator phenotypeyesAlthough devoid of recurrent single nucleotide variants and focal copy number aberrations, poor-prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype Supratentorial and spinal pediatric ependymomas display a hypermethylated phenotype which includes the loss of tumor suppressor genes involved in the control of cell growth and death.Although devoid of recurrent single nucleotide variants and focal copy number aberrations, poor-prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype Although no recurrently mutated genes were found throughout these groups of ependymomas, PFA exhibited a CpG island methylator phenotype, PFB was associated with extensive chromosomal aberrations, and the C11orf95-RELA fusion gene was frequently observed in supratentorial ependymomas. Supratentorial and spinal pediatric ependymomas display a hypermethylated phenotype which includes the loss of tumor suppressor genes involved in the control of cell growth and death. Although devoid of recurrent single nucleotide variants and focal copy number aberrations, poor-prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype.

http://www.ncbi.nlm.nih.gov/pubmed/28985562

Are loop domains preserved upon cohesin loss?

No. Degradation of cohesin leads to elimination of loop domains. Neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation but does affect a significant minority of active genes.

http://www.ncbi.nlm.nih.gov/pubmed/29043067

Which workflow in Bioconductor has been developed for accessing human RNA-seq samples?

The recount2 resource is composed of over 70,000 uniformly processed human RNA-seq samples spanning TCGA and SRA, including GTEx.

http://www.ncbi.nlm.nih.gov/pubmed/24014378

What does VBP15 do to skeletal muscle?

VBP15 protects and promotes efficient repair of skeletal muscle cells. Potent inhibition of NF-κB is mediated through protein interactions of the glucocorticoid receptor, however VBP15 shows significantly reduced hormonal receptor transcriptional activity. In DMD model mice it improves muscle strength, live-imaging and pathology through both preventive and post-onset intervention regimens.

http://www.ncbi.nlm.nih.gov/pubmed/27988142,http://www.ncbi.nlm.nih.gov/pubmed/27993828

What is filgotinib?

Filgotinib is an oral selective Janus kinase inhibitor. It has been tested in patients with rheumatoid arthritis and Chroni's disease, and has been shown to be safe and efficacious.

http://www.ncbi.nlm.nih.gov/pubmed/27814676

What is Q-nexus?

Q-nexus is a comprehensive and efficient analysis pipeline designed for ChIP-nexus.

http://www.ncbi.nlm.nih.gov/pubmed/29039115,http://www.ncbi.nlm.nih.gov/pubmed/28887358,http://www.ncbi.nlm.nih.gov/pubmed/28751490,http://www.ncbi.nlm.nih.gov/pubmed/28935694,http://www.ncbi.nlm.nih.gov/pubmed/29058636,http://www.ncbi.nlm.nih.gov/pubmed/29143249

What is the mechanism of action of Tisagenlecleucel?

Tisagenlecleucel CD19-directed chimeric antigen receptor T cells (CART19) product that cause reprogramming a patient's own T cells with a transgene encoding a chimeric antigen receptor to identify and eliminate CD19-expressing cells. Its is is approved for children and young adults with relapsed or refractory B-cell acute lymphoblastic leukemia.

http://www.ncbi.nlm.nih.gov/pubmed/7916404,http://www.ncbi.nlm.nih.gov/pubmed/9010406,http://www.ncbi.nlm.nih.gov/pubmed/21174521,http://www.ncbi.nlm.nih.gov/pubmed/10993496,http://www.ncbi.nlm.nih.gov/pubmed/27843288,http://www.ncbi.nlm.nih.gov/pubmed/26894521,http://www.ncbi.nlm.nih.gov/pubmed/26218905,http://www.ncbi.nlm.nih.gov/pubmed/9147893,http://www.ncbi.nlm.nih.gov/pubmed/17406640,http://www.ncbi.nlm.nih.gov/pubmed/27613247,http://www.ncbi.nlm.nih.gov/pubmed/9177303,http://www.ncbi.nlm.nih.gov/pubmed/21346843,http://www.ncbi.nlm.nih.gov/pubmed/22390282,http://www.ncbi.nlm.nih.gov/pubmed/20809775,http://www.ncbi.nlm.nih.gov/pubmed/24167936,http://www.ncbi.nlm.nih.gov/pubmed/7999980,http://www.ncbi.nlm.nih.gov/pubmed/11906302,http://www.ncbi.nlm.nih.gov/pubmed/26448041,http://www.ncbi.nlm.nih.gov/pubmed/9309689,http://www.ncbi.nlm.nih.gov/pubmed/27756254,http://www.ncbi.nlm.nih.gov/pubmed/28991104,http://www.ncbi.nlm.nih.gov/pubmed/20632027,http://www.ncbi.nlm.nih.gov/pubmed/16523300,http://www.ncbi.nlm.nih.gov/pubmed/11329546,http://www.ncbi.nlm.nih.gov/pubmed/12031765,http://www.ncbi.nlm.nih.gov/pubmed/23113023,http://www.ncbi.nlm.nih.gov/pubmed/10758737,http://www.ncbi.nlm.nih.gov/pubmed/1449769,http://www.ncbi.nlm.nih.gov/pubmed/21694444,http://www.ncbi.nlm.nih.gov/pubmed/21734595,http://www.ncbi.nlm.nih.gov/pubmed/8605641

What is LHON, also known as Lebers syndrome?

Leber's hereditary optic neuropathy (LHON) is a common inherited mitochondrial disorder that is characterized by the degeneration of the optic nerves, leading to vision loss.

http://www.ncbi.nlm.nih.gov/pubmed/27605105

What is the ReliableGenome?

The increasing adoption of clinical whole-genome resequencing (WGS) demands for highly accurate and reproducible variant calling (VC) methods. The observed discordance between state-of-the-art VC pipelines, however, indicates that the current practice still suffers from non-negligible numbers of false positive and negative SNV and INDEL calls that were shown to be enriched among discordant calls but also in genomic regions with low sequence complexity. ReliableGenome is a method for partitioning genomes into high and low concordance regions with respect to a set of surveyed VC pipelines. It combines call sets derived by multiple pipelines from arbitrary numbers of datasets and interpolates expected concordance for genomic regions without data.

http://www.ncbi.nlm.nih.gov/pubmed/23509369,http://www.ncbi.nlm.nih.gov/pubmed/18995839,http://www.ncbi.nlm.nih.gov/pubmed/19285159,http://www.ncbi.nlm.nih.gov/pubmed/23989959

List polyubiquitin binding proteins involved in NF-kappaB signaling.

NEMO A20 ABIN-1 ABIN-2 optineurin p62

http://www.ncbi.nlm.nih.gov/pubmed/12548530

What are the prednisone side effects in DMD patients?

Side effects of prednisone in DMD patients include reduced growth rate and increase in body weight.

http://www.ncbi.nlm.nih.gov/pubmed/24260525,http://www.ncbi.nlm.nih.gov/pubmed/28327663,http://www.ncbi.nlm.nih.gov/pubmed/23754700

Which is the specificity of deubiquitinase USP25?

Ubiquitin Specific Protease 25 (USP25), a member of the deubiquitinase family, is involved in several disease-related signal pathways including myogenesis, immunity and protein degradation. It specially catalyzes the hydrolysis of the K48-linked and K63-linked polyubiquitin chains.

http://www.ncbi.nlm.nih.gov/pubmed/12776909,http://www.ncbi.nlm.nih.gov/pubmed/28282278,http://www.ncbi.nlm.nih.gov/pubmed/29135930,http://www.ncbi.nlm.nih.gov/pubmed/12799851

Is Loss of function one of the cardinal signs of inflammation?

Functio Laesa also known as loss of function is considered to be the 5th cardinal sign of inflammation.

http://www.ncbi.nlm.nih.gov/pubmed/26321255

Does the association of PARP1 and CTCF follow a circadian rhythm?

Synchronization of the circadian rhythm by serum shock induces oscillations in PARP1-CTCF interactions, which is accompanied by oscillating recruitment of circadian loci to the lamina, followed by the acquisition of repressive H3K9me2 marks and transcriptional attenuation. Furthermore, depletion of H3K9me2/3, inhibition of PARP activity by olaparib, or downregulation of PARP1 or CTCF expression counteracts both recruitment to the envelope and circadian transcription. PARP1- and CTCF-regulated contacts between circadian loci and the repressive chromatin environment at the lamina therefore mediate circadian transcriptional plasticity.Synchronization of the circadian rhythm by serum shock induces oscillations in PARP1-CTCF interactions, which is accompanied by oscillating recruitment of circadian loci to the lamina, followed by the acquisition of repressive H3K9me2 marks and transcriptional attenuation PARP1- and CTCF-regulated contacts between circadian loci and the repressive chromatin environment at the lamina therefore mediate circadian transcriptional plasticity.Synchronization of the circadian rhythm by serum shock induces oscillations in PARP1-CTCF interactions, which is accompanied by oscillating recruitment of circadian loci to the lamina, followed by the acquisition of repressive H3K9me2 marks and transcriptional attenuation here we uncovered an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains . Parp1- and ctcf-regulated contacts between circadian loci to the lamina, followed by the acquisition of repressive h3k9me2 marks and transcriptional attenuation here we uncovered an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains . PARP1- and CTCF-regulated contacts between circadian loci and the repressive chromatin environment at the lamina therefore mediate circadian transcriptional plasticity. Synchronization of the circadian rhythm by serum shock induces oscillations in PARP1-CTCF interactions, which is accompanied by oscillating recruitment of circadian loci to the lamina, followed by the acquisition of repressive H3K9me2 marks and transcriptional attenuation. Uncovered an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains . PARP1- and CTCF-regulated contacts between circadian loci and the repressive chromatin environment at the lamina therefore mediate circadian transcriptional plasticity. Synchronization of the circadian rhythm by serum shock induces oscillations in PARP1-CTCF interactions, which is accompanied by oscillating recruitment of circadian loci to the lamina, followed by the acquisition of repressive H3K9me2 marks and transcriptional attenuation. here we uncovered an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains (LADs). PARP1- and CTCF-regulated contacts between circadian loci and the repressive chromatin environment at the lamina therefore mediate circadian transcriptional plasticity. yesSynchronization of the circadian rhythm by serum shock induces oscillations in PARP1-CTCF interactions, which is accompanied by oscillating recruitment of circadian loci to the lamina, followed by the acquisition of repressive H3K9me2 marks and transcriptional attenuation. PARP1- and CTCF-regulated contacts between circadian loci and the repressive chromatin environment at the lamina therefore mediate circadian transcriptional plasticity. Here we uncovered an inter-chromosomal network connecting active loci enriched in circadian genes to repressed lamina-associated domains. Synchronization of the circadian rhythm by serum shock induces oscillations in PARP1-CTCF interactions, which is accompanied by oscillating recruitment of circadian loci to the lamina, followed by the acquisition of repressive H3K9me2 marks and transcriptional attenuation. PARP1- and CTCF-regulated contacts between circadian loci and the repressive chromatin environment at the lamina therefore mediate circadian transcriptional plasticity.

http://www.ncbi.nlm.nih.gov/pubmed/23133621,http://www.ncbi.nlm.nih.gov/pubmed/19366428,http://www.ncbi.nlm.nih.gov/pubmed/14996219,http://www.ncbi.nlm.nih.gov/pubmed/17080288,http://www.ncbi.nlm.nih.gov/pubmed/8914512

What induces Arabidopsis ROF1 expression?

The abundance of ROF1 increased several-fold under stress conditions such as wounding, heat stress or exposure to elevated NaCl levels.

http://www.ncbi.nlm.nih.gov/pubmed/26276636,http://www.ncbi.nlm.nih.gov/pubmed/26499245,http://www.ncbi.nlm.nih.gov/pubmed/26527277,http://www.ncbi.nlm.nih.gov/pubmed/27940490,http://www.ncbi.nlm.nih.gov/pubmed/28536180,http://www.ncbi.nlm.nih.gov/pubmed/25497547

What is the preferred orientation of CTCF binding sites for chromatin looping?

chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs "facing" one another.As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. Recent studies identified a correlation between the orientation of CTCF-binding sites and chromatin loops. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function.

http://www.ncbi.nlm.nih.gov/pubmed/27655365,http://www.ncbi.nlm.nih.gov/pubmed/12100810,http://www.ncbi.nlm.nih.gov/pubmed/12693559,http://www.ncbi.nlm.nih.gov/pubmed/11562617,http://www.ncbi.nlm.nih.gov/pubmed/25687145,http://www.ncbi.nlm.nih.gov/pubmed/23558266

Does erythromycin increase risk of hypertrophic pyloric stenosis?

Yes, post-natal erythromycin exposure is associated with increased risk of hypertrophic pyloric stenosis. The association is stronger when exposure occurs in the first 2 weeks of life.

http://www.ncbi.nlm.nih.gov/pubmed/25505609

How many amino acids does davunetide consist of?

Davunetide or NAP is an eight amino acid peptide.

http://www.ncbi.nlm.nih.gov/pubmed/28903484,http://www.ncbi.nlm.nih.gov/pubmed/27617908,http://www.ncbi.nlm.nih.gov/pubmed/27255916,http://www.ncbi.nlm.nih.gov/pubmed/26649774,http://www.ncbi.nlm.nih.gov/pubmed/27612318,http://www.ncbi.nlm.nih.gov/pubmed/29028266,http://www.ncbi.nlm.nih.gov/pubmed/26874353,http://www.ncbi.nlm.nih.gov/pubmed/28344082,http://www.ncbi.nlm.nih.gov/pubmed/28344080,http://www.ncbi.nlm.nih.gov/pubmed/27892769

Can a circRNA be translated into protein?

Circ-ZNF609 is associated with heavy polysomes, and it is translated into a protein in a splicing-dependent and cap-independent manner, providing an example of a protein-coding circRNA in eukaryotes. Circular RNAs (circRNAs) represent a large class of noncoding RNAs (ncRNAs) that have recently emerged as regulators of gene expression However, whether circRNAs encode functional proteins remains elusive, although translation of several circRNAs was recently reportedΜost circRNAs were not associated with translating ribosomes, therefore, circRNAs were deemed to be noncoding. However, the latest research findings revealed that some circRNAs could generate proteins in vivo, which expands the landscape of transcriptome and proteome

http://www.ncbi.nlm.nih.gov/pubmed/17346703,http://www.ncbi.nlm.nih.gov/pubmed/19106226,http://www.ncbi.nlm.nih.gov/pubmed/23099887,http://www.ncbi.nlm.nih.gov/pubmed/17223284

What is the phenomenon of gene kissing?

Clustering of genes with similar expression patterns constitutes a phenomenon sometimes called "gene kissing."This positioning can also result in the clustering of genes with similar expression patterns, a phenomenon sometimes called "gene kissing." This positioning can also result in the clustering of genes with similar expression patterns, a phenomenon sometimes called "gene kissing." We speculate that our findings might provide insight into other types of gene kissing, some of which also require cis-acting DNA sequences and trans-acting proteins.

http://www.ncbi.nlm.nih.gov/pubmed/9389696,http://www.ncbi.nlm.nih.gov/pubmed/19073821,http://www.ncbi.nlm.nih.gov/pubmed/19013120,http://www.ncbi.nlm.nih.gov/pubmed/8097946,http://www.ncbi.nlm.nih.gov/pubmed/26299174,http://www.ncbi.nlm.nih.gov/pubmed/15523923,http://www.ncbi.nlm.nih.gov/pubmed/29142973,http://www.ncbi.nlm.nih.gov/pubmed/23551149,http://www.ncbi.nlm.nih.gov/pubmed/25331409,http://www.ncbi.nlm.nih.gov/pubmed/8113408

What protein is the most common cause of hereditary renal amyloidosis?

The most common cause of hereditary renal amyloidosis is over expression of a mutant form of the Fibrinogen A Alpha protein

http://www.ncbi.nlm.nih.gov/pubmed/28043681

What are the side effects of deflazacort in DMD patients?

The side effects observed in DMD patients following deflazacort treatment include growth failure and weight gain, facial fullness, blood pressure, bone health, cataracts, gastrointestinal symptoms, behavior, hypertrichosis, and need for medication interventions.