{ "Contributors": [ "Species-800" ], "Source": [ "Species-800" ], "URL": [ "https://huggingface.co/datasets/species_800" ], "Categories": [ "Named Entity Recognition" ], "Definition": [ "Given a sentence, you need to recognize the name of the organism. There might be several correct answers. If it does not exist, you need to output \"There is no related enetity.\"." ], "Reasoning": [], "Input_language": [ "English" ], "Output_language": [ "English" ], "Instruction_language": [ "English" ], "Domains": [ "Medical Knowledge" ], "Positive Examples": [], "Negative Examples": [], "Instances": [ { "input": "Methanoregula formicica sp. nov., a methane - producing archaeon isolated from methanogenic sludge.", "output": "Methanoregula formicica." }, { "input": "A novel methane - producing archaeon, strain SMSP ( T ), was isolated from an anaerobic, propionate - degrading enrichment culture that was originally obtained from granular sludge in a mesophilic upflow anaerobic sludge blanket ( UASB ) reactor used to treat a beer brewery effluent.", "output": "SMSP ( T )." }, { "input": "Cells were non - motile, blunt - ended, straight rods, 1. 0 - 2. 6 mum long by 0. 5 mum wide; cells were sometimes up to 7 mum long.", "output": "There is no related enetity." }, { "input": "Asymmetrical cell division was observed in rod - shaped cells.", "output": "There is no related enetity." }, { "input": "Coccoid cells ( 0. 5 - 1. 0 mum in diameter ) were also observed in mid - to late - exponential phase cultures.", "output": "There is no related enetity." }, { "input": "Growth was observed between 10 and 40 ^ 0C ( optimum, 30 - 33 ^ 0C ) and pH 7. 0 and 7. 6 ( optimum, pH 7. 4 ).", "output": "There is no related enetity." }, { "input": "The G + C content of the genomic DNA was 56. 2 mol %.", "output": "There is no related enetity." }, { "input": "The strain utilized formate and hydrogen for growth and methane production.", "output": "There is no related enetity." }, { "input": "Based on comparative sequence analyses of the 16S rRNA and mcrA ( encoding the alpha subunit of methyl - coenzyme M reductase, a key enzyme in the methane - producing pathway ) genes, strain SMSP ( T ) was affiliated with group E1 / E2 within the order Methanomicrobiales.", "output": "SMSP ( T )." }, { "input": "The closest relative based on both 16S rRNA and mcrA gene sequences was Methanoregula boonei 6A8 ( T ) ( 96. 3 % 16S rRNA gene sequence similarity, 85. 4 % deduced McrA amino acid sequence similarity ).", "output": "Methanoregula boonei 6A8." }, { "input": "The percentage of 16S rRNA gene sequence similarity indicates that strain SMSP ( T ) and Methanoregula boonei 6A8 ( T ) represent different species within the same genus.", "output": "SMSP ( T ), Methanoregula boonei 6A8." }, { "input": "This is supported by our findings of shared phenotypic properties, including cell morphology and growth temperature range, and phenotypic differences in substrate usage and pH range.", "output": "There is no related enetity." }, { "input": "Based on these genetic and phenotypic properties, we propose that strain SMSP ( T ) represents a novel species of the genus Methanoregula, for which we propose the name Methanoregula formicica sp. nov., with the type strain SMSP ( T ) ( = NBRC 105244 ( T ) = DSM 22288 ( T ) ).", "output": "SMSP ( T ), Methanoregula formicica, SMSP ( T )." }, { "input": "Characterizing the role of the microtubule binding protein Bim1 in Cryptococcus neoformans.", "output": "Cryptococcus neoformans." }, { "input": "During sexual development the human fungal pathogen Cryptococcus neoformans undergoes a developmental transition from yeast - form growth to filamentous growth.", "output": "human, Cryptococcus neoformans." }, { "input": "This transition requires cellular restructuring to form a filamentous dikaryon.", "output": "There is no related enetity." }, { "input": "Dikaryotic growth also requires tightly controlled nuclear migration to ensure faithful replication and dissemination of genetic material to spore progeny.", "output": "There is no related enetity." }, { "input": "Although the gross morphological changes that take place during dikaryotic growth are largely known, the molecular underpinnings that control this process are uncharacterized.", "output": "There is no related enetity." }, { "input": "Here we identify and characterize a C. neoformans homolog of the Saccharomyces cerevisiae BIM1 gene, and establish the importance of BIM1 for proper filamentous growth of C. neoformans.", "output": "C . neoformans, Saccharomyces cerevisiae, C . neoformans." }, { "input": "Deletion of BIM1 leads to truncated sexual development filaments, a severe defect in diploid formation, and a block in monokaryotic fruiting.", "output": "There is no related enetity." }, { "input": "Our findings lead to a model consistent with a critical role for BIM1 in both filament integrity and nuclear congression that is mediated through the microtubule cytoskeleton.", "output": "There is no related enetity." }, { "input": "Serinicoccus profundi sp. nov., an actinomycete isolated from deep - sea sediment, and emended description of the genus Serinicoccus.", "output": "Serinicoccus profundi sp . nov .." }, { "input": "A Gram - reaction - positive bacterial strain of the genus Serinicoccus, designated MCCC 1A05965 ( T ), was isolated from a deep - sea ( 5368 m ) sediment of the Indian Ocean.", "output": "MCCC 1A05965." }, { "input": "Comparison of 16S rRNA gene sequences revealed that the isolate shared 97. 6 % sequence similarity with Serinicoccus marinus JC1078 ( T ), the type strain of the only described species of the genus Serinicoccus.", "output": "Serinicoccus marinus." }, { "input": "The DNA - DNA relatedness between these two strains was 46. 2 % ( standard deviation 1. 86 % ).", "output": "There is no related enetity." }, { "input": "The cell wall contained alanine, glycine, serine, l - ornithine and glutamic acid, which corresponds to the description of the genus Serinicoccus.", "output": "There is no related enetity." }, { "input": "The acyl type of the glycan chain of the peptidoglycan was glycolyl.", "output": "There is no related enetity." }, { "input": "Other characteristics of strain MCCC 1A05965 ( T ) were consistent with those of the genus Serinicoccus.", "output": "MCCC 1A05965." }, { "input": "Cells were coccoid, moderately halophilic, oxidase - negative, catalase - positive and non - spore - forming.", "output": "There is no related enetity." }, { "input": "The major menaquinone was MK - 8 ( H ( 4 ) ).", "output": "There is no related enetity." }, { "input": "The predominant cellular fatty acids were iso - C ( 15: 0 ) ( 34. 7 % ) and iso - C ( 16: 0 ) ( 17. 0 % ).", "output": "There is no related enetity." }, { "input": "The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unknown glycolipid.", "output": "There is no related enetity." }, { "input": "The DNA G + C content was 72 mol %.", "output": "There is no related enetity." }, { "input": "Strain MCCC 1A05965 ( T ) ( = 0714S6 - 1 ( T ) = DSM 21363 ( T ) = CGMCC 4. 5582 ( T ) ) is assigned as the type strain of a novel species, for which the name Serinicoccus profundi sp. nov.", "output": "MCCC 1A05965, Serinicoccus profundi sp . nov." }, { "input": "is proposed.", "output": "There is no related enetity." }, { "input": "Proposal of Mingxiaea gen. nov. for the anamorphic basidiomycetous yeast species in the Bulleribasidium clade ( Tremellales ) based on molecular phylogenetic analysis, with six new combinations and four novel species.", "output": "yeast." }, { "input": "The distinction and monophyletic property of the basidiomycetous yeast species in the Bulleribasidium clade of the order Tremellales was resolved by molecular phylogenetic analysis based on the combined sequences of the 18S rRNA gene, internal transcribed spacer ( ITS ) region including 5. 8S rRNA gene and 26S rRNA gene D1 / D2 domain.", "output": "yeast." }, { "input": "The addition to the clade of new anamorphic species identified among ballistoconidium - forming yeasts isolated from China confirmed and strengthened the separation of this clade from other clades or lineages in the order Tremellales.", "output": "yeasts." }, { "input": "A new anamorphic genus, Mingxiaea gen. nov.", "output": "There is no related enetity." }, { "input": "( type species Mingxiaea variabilis comb. nov. ) is therefore proposed to accommodate the anamorphic species in the Bulleribasidium clade.", "output": "There is no related enetity." }, { "input": "Six new combinations are proposed for the described species of this clade which were formerly assigned to the genus Bullera.", "output": "There is no related enetity." }, { "input": "Four novel species in the new genus were identified among 16 ballistoconidium - forming yeast strains isolated from plant leaves collected in Hainan province, southern China, by D1 / D2 and ITS sequence analyses.", "output": "yeast." }, { "input": "The novel species are described as Mingxiaea sanyaensis sp. nov.", "output": "There is no related enetity." }, { "input": "( type strain SY - 3. 23 ( T ) = AS 2. 3623 ( T ) = CBS 11408 ( T ) ), Mingxiaea hainanensis ( type strain WZS - 8. 13 ( T ) = AS 2. 4161 ( T ) = CBS 11409 ( T ) ), Mingxiaea foliicola ( type strain WZS - 8. 14 ( T ) = AS 2. 3518 ( T ) = CBS 11407 ( T ) ) and Mingxiaea wuzhishanensis ( type strain WZS - 29. 8 ( T ) = AS 2. 4163 ( T ) = CBS 11411 ( T ) ).", "output": "There is no related enetity." }, { "input": "Scardovia wiggsiae sp. nov., isolated from the human oral cavity and clinical material, and emended descriptions of the genus Scardovia and Scardovia inopinata.", "output": "Scardovia wiggsiae, human, Scardovia inopinata." }, { "input": "Six strains of anaerobic, pleomorphic Gram - positive bacilli, isolated from the human oral cavity and an infected arm wound, were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group.", "output": "human." }, { "input": "16S rRNA gene sequence analysis revealed that the isolates were most closely related to Scardovia inopinata CCUG 35729 ( T ) ( 94. 8 - 94. 9 % 16S rRNA gene sequence similarity ).", "output": "Scardovia inopinata." }, { "input": "The isolates were saccharolytic and produced acetic and lactic acids as end products of fermentation.", "output": "There is no related enetity." }, { "input": "The major fatty acids were C ( 16: 0 ) ( 49. 8 % ) and C ( 18: 1 ) omega9c ( 35. 8 % ).", "output": "There is no related enetity." }, { "input": "Polar lipid analysis revealed a variety of glycolipids, diphosphatidylglycerol, an unidentified phospholipid and an unidentified phosphoglycolipid.", "output": "There is no related enetity." }, { "input": "No respiratory quinones were detected.", "output": "There is no related enetity." }, { "input": "The peptidoglycan was of the type A4alpha L - Lys - Thr - Glu, with L - lysine partially replaced by L - ornithine.", "output": "There is no related enetity." }, { "input": "The DNA G + C content of one of the strains, C1A _ 55 ( T ) (, ) was 55 mol %.", "output": "There is no related enetity." }, { "input": "A novel species, Scardovia wiggsiae sp. nov., is proposed to accommodate the six isolates, with the type strain C1A _ 55 ( T ) ( = DSM 22547 ( T ) = CCUG 58090 ( T ) ).", "output": "Scardovia wiggsiae." }, { "input": "Flavobacterium ponti sp. nov., isolated from seawater.", "output": "Flavobacterium ponti sp . nov .." }, { "input": "A Gram - stain - negative, non - flagellated, non - gliding, yellow - pigmented and rod - shaped bacterial strain, designated GSW - R14 ( T ), was isolated from seawater of Geoje Island in the South Sea, Korea.", "output": "GSW - R14." }, { "input": "Strain GSW - R14 ( T ) grew optimally at 25 ^ 0C, at pH 7. 0 - 8. 0 and in the presence of 2 % ( w / v ) NaCl.", "output": "GSW - R14." }, { "input": "Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GSW - R14 ( T ) belonged to the genus Flavobacterium, joining Flavobacterium gelidilacus LMG 21477 ( T ) by a bootstrap resampling value of 100 %.", "output": "GSW - R14, Flavobacterium gelidilacus." }, { "input": "Strain GSW - R14 ( T ) exhibited 97. 6 % 16S rRNA gene sequence similarity to F. gelidilacus LMG 21477 ( T ) and similarities of 91. 2 - 95. 2 % to other members of the genus Flavobacterium.", "output": "GSW - R14, F . gelidilacus." }, { "input": "Strain GSW - R14 ( T ) contained MK - 6 as the predominant menaquinone.", "output": "GSW - R14." }, { "input": "The fatty acid profile of strain GSW - R14 ( T ) was similar to that of F. gelidilacus LMG 21477 ( T ).", "output": "GSW - R14, F . gelidilacus." }, { "input": "The DNA G + C content of strain GSW - R14 ( T ) was 31. 4 mol % and its DNA - DNA relatedness with F. gelidilacus LMG 21477 ( T ) was 31 %.", "output": "GSW - R14, F . gelidilacus." }, { "input": "Strain GSW - R14 ( T ) could be distinguished from F. gelidilacus and the other species of the genus Flavobacterium by its phylogenetic and genetic distinctiveness and by several phenotypic properties.", "output": "GSW - R14, F . gelidilacus." }, { "input": "On the basis of these data, strain GSW - R14 ( T ) is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium ponti sp. nov.", "output": "GSW - R14, Flavobacterium ponti sp . nov .." }, { "input": "is proposed; the type strain is GSW - R14 ( T ) ( = KCTC 22802 ( T ) = CCUG 58402 ( T ) ).", "output": "GSW - R14." }, { "input": "Thermasporomyces composti gen. nov., sp. nov., a thermophilic actinomycete isolated from compost.", "output": "Thermasporomyces composti gen . nov . , sp . nov .." }, { "input": "A thermophilic, Gram - positive bacterium that formed a branched vegetative mycelium was isolated from compost.", "output": "There is no related enetity." }, { "input": "The strain, designated I3 ( T ), grew at temperatures between 35 and 62 ^ 0C, with optimum growth at 50 - 55 ^ 0C.", "output": "There is no related enetity." }, { "input": "No growth was observed below 29 ^ 0C or above 65 ^ 0C.", "output": "There is no related enetity." }, { "input": "The pH range for growth was 5. 7 - 10. 0, the pH for optimum growth was 7. 0 and no growth was observed below pH 5. 6 or above pH 10. 8.", "output": "There is no related enetity." }, { "input": "The DNA G + C content of strain I3 ( T ) was 69. 2 mol %.", "output": "There is no related enetity." }, { "input": "The major fatty acids found were C ( 15: 0 ) iso ( 14. 2 % ), C ( 15: 0 ) anteiso ( 12. 1 % ), C ( 17: 0 ) iso ( 16. 3 % ) and C ( 17: 0 ) anteiso ( 21. 7 % ).", "output": "There is no related enetity." }, { "input": "The major menaquinones were MK - 9 ( H ( 4 ) ), MK - 10 ( H ( 4 ) ) and MK - 11 ( H ( 4 ) ).", "output": "There is no related enetity." }, { "input": "The cell wall contained glutamic acid, glycine, alanine and ll - diaminopimelic acid in a molar ratio of 1. 0: 3. 9: 0. 6: 0. 5.", "output": "There is no related enetity." }, { "input": "The polar lipids consisted of ninhydrin - positive phosphoglycolipids, phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid.", "output": "There is no related enetity." }, { "input": "The cell - wall sugars were rhamnose and arabinose.", "output": "There is no related enetity." }, { "input": "16S rRNA gene sequence analysis assigned this actinomycete to the family Nocardioidaceae, but its 16S rRNA gene sequence shared no more than 95. 5 % similarity with those of other members of the family.", "output": "There is no related enetity." }, { "input": "The chemotaxonomic and phenotypic characteristics of strain I3 ( T ) differed in some respects from those of members of the genus Actinopolymorpha, the most closely related genus.", "output": "There is no related enetity." }, { "input": "Therefore, strain I3 ( T ) represents a novel species in a new genus of the family Nocardioidaceae, for which the name Thermasporomyces composti gen. nov., sp. nov.", "output": "Thermasporomyces composti gen . nov . , sp . nov .." }, { "input": "is proposed.", "output": "There is no related enetity." }, { "input": "The type strain of the type species is I3 ( T ) ( = JCM 16421 ( T ) = DSM 22891 ( T ) ).", "output": "JCM 16421 ( T )." }, { "input": "Phycicoccus cremeus sp. nov., isolated from forest soil, and emended description of the genus Phycicoccus.", "output": "There is no related enetity." }, { "input": "A bacterial strain, designated V2M29 ( T ), was isolated from forest soil collected in the Changbai Mountains, Heilongjiang Province, China.", "output": "There is no related enetity." }, { "input": "Cells of strain V2M29 ( T ) were Gram - positive, rod - shaped ( 0. 5 - 0. 8 mum in diameter and 1. 5 - 2. 0 mum in length ), strictly aerobic and non - motile.", "output": "There is no related enetity." }, { "input": "Colonies produced on R2A agar plates were creamy, smooth, circular and 0. 3 - 0. 8 mm in diameter.", "output": "There is no related enetity." }, { "input": "Strain V2M29 ( T ) grew at 14 - 35 ^ 0C ( optimum, 29 ^ 0C ), at pH 4. 1 - 10. 0 ( optimum, pH 7. 0 - 8. 0 ) and in the presence of 0 - 7. 0 % ( w / v ) NaCl ( optimum, 0 - 2. 0 % ).", "output": "There is no related enetity." }, { "input": "Strain V2M29 ( T ) contained MK - 8 ( H ( 4 ) ) as the major respiratory quinone and iso - C ( 15: 0 ) ( 20. 9 % ), iso - C ( 16: 0 ) ( 18. 5 % ), C ( 17: 1 ) omega8c ( 16. 7 % ) and 10 - methyl - C ( 17: 0 ) ( 9. 2 % ) as the major cellular fatty acids.", "output": "There is no related enetity." }, { "input": "The cell - wall peptidoglycan type was based on meso - 2, 6 - diaminopimelic acid and the acyl type of the muramic acid was acetyl.", "output": "There is no related enetity." }, { "input": "Diphosphatidylglycerol, phosphatidylinositol and six unknown glycolipids were the major polar lipids.", "output": "There is no related enetity." }, { "input": "The G + C content of the DNA was 72. 0 mol % ( T ( m ) ).", "output": "There is no related enetity." }, { "input": "16S rRNA gene sequence analysis indicated that strain V2M29 ( T ) was phylogenetically related to members of the genus Phycicoccus, with sequence similarities ranging from 96. 6 - 97. 8 %.", "output": "There is no related enetity." }, { "input": "The DNA - DNA relatedness values of strain V2M29 ( T ) to Phycicoccus dokdonensis DS - 8 ( T ) and Phycicoccus bigeumensis DSM 19264 ( T ) were 32. 5 + / - 3. 3 % and 29. 2 + / - 2. 3 %, respectively.", "output": "Phycicoccus dokdonensis DS - 8 ( T ), Phycicoccus bigeumensis DSM 19264 ( T )." }, { "input": "Based on these results, it is concluded that strain V2M29 ( T ) represents a novel species of the genus Phycicoccus, for which the name Phycicoccus cremeus sp. nov.", "output": "There is no related enetity." }, { "input": "is proposed, with V2M29 ( T ) ( = CGMCC 1. 6963 ( T ) = NBRC 104261 ( T ) ) as the type strain.", "output": "There is no related enetity." }, { "input": "Streptomyces hyderabadensis sp. nov., an actinomycete isolated from soil.", "output": "Streptomyces hyderabadensis sp . nov .." }, { "input": "A novel actinomycete, designated strain OU - 40 ( T ), was isolated from farm soil collected from the Hyderabad region of Andhra Pradesh, southern India.", "output": "OU - 40." }, { "input": "The strain was found to have morphological and chemotaxonomic characteristics typical of species of the genus Streptomyces.", "output": "There is no related enetity." }, { "input": "Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain OU - 40 ( T ) belonged to the genus Streptomyces, and was related most closely to Streptomyces pactum NBRC 13433 ( T ) ( 99. 0 % sequence similarity ), Streptomyces olivaceus NBRC 12805 ( T ) ( 99. 0 % ) and Streptomyces parvulus NBRC 13193 ( T ) ( 98. 8 % ).", "output": "OU - 40, Streptomyces pactum, Streptomyces olivaceus, Streptomyces parvulus." }, { "input": "Strain OU - 40 ( T ) could be distinguished from the type strains of its closest phylogenetic relatives based on levels of DNA - DNA relatedness and comparison of morphological and phenotypic data.", "output": "OU - 40." }, { "input": "It is therefore concluded that strain OU - 40 ( T ) represents a novel species of the genus Streptomyces, for which the name Streptomyces hyderabadensis sp. nov.", "output": "OU - 40, Streptomyces hyderabadensis sp . nov .." }, { "input": "is proposed.", "output": "There is no related enetity." }, { "input": "The type strain is OU - 40 ( T ) ( = CCTCC AA 209024 ( T ) = PCM 2692 ( T ) ).", "output": "OU - 40." }, { "input": "Gordonia humi sp. nov., isolated from soil.", "output": "Gordonia humi sp . nov .." }, { "input": "A Gram - stain - positive, non - endospore - forming actinobacterium ( CC - 12301 ( T ) ) was isolated from soil attached to a spawn used in the laboratory to grow the edible mushroom Agaricus brasiliensis.", "output": "CC - 12301 ( T ), Agaricus brasiliensis." }, { "input": "Based on 16S rRNA gene sequence similarities, strain CC - 12301 ( T ) was shown to belong to the genus Gordonia and was most closely related to the type strains of Gordonia hydrophobica ( 97. 6 % similarity ), Gordonia terrae ( 97. 5 % ), Gordonia amarae ( 97. 5 % ) and Gordonia malaquae ( 97. 4 % ).", "output": "CC - 12301 ( T ), Gordonia hydrophobica, Gordonia terrae, Gordonia amarae, Gordonia malaquae." }, { "input": "The quinone system was determined to consist predominantly of menaquinone MK - 9 ( H ( 2 ) ), minor amounts of MK - 8 ( H ( 2 ) ) and MK - 7 ( H ( 2 ) ).", "output": "There is no related enetity." }, { "input": "The polar lipid profile consisted of the major compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of two phosphatidylinositol mannosides and phosphatidylinositol and minor amounts of phosphatidylglycerol, three unidentified glycolipids, two phosphoglycolipids and a phospholipid.", "output": "There is no related enetity." }, { "input": "Mycolic acids were present.", "output": "There is no related enetity." }, { "input": "These chemotaxonomic traits and the major fatty acids, which were C ( 16: 1 ) cis9, C ( 16: 0 ), C ( 18: 1 ) and tuberculostearic acid ( 10 - methyl C ( 18: 0 ) ), supported the affiliation of strain CC - 12301 ( T ) to the genus Gordonia.", "output": "CC - 12301 ( T )." }, { "input": "The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain CC - 12301 ( T ) from the most closely related Gordonia species.", "output": "CC - 12301 ( T )." }, { "input": "Strain CC - 12301 ( T ) therefore represents a novel species, for which the name Gordonia humi sp. nov.", "output": "CC - 12301 ( T ), Gordonia humi sp . nov .." }, { "input": "is proposed, with the type strain CC - 12301 ( T ) ( = DSM 45298 ( T ) = CCM 7727 ( T ) ).", "output": "CC - 12301 ( T )." }, { "input": "Methanoregula boonei gen. nov., sp. nov., an acidiphilic methanogen isolated from an acidic peat bog.", "output": "Methanoregula boonei gen . nov . , sp . nov .." }, { "input": "A novel acidiphilic, hydrogenotrophic methanogen, designated strain 6A8 ( T ), was isolated from an acidic ( pH 4. 0 - 4. 5 ) and ombrotrophic ( rain - fed ) bog located near Ithaca, NY, USA.", "output": "6A8." }, { "input": "Cultures were dimorphic, containing thin rods ( 0. 2 - 0. 3 mum in diameter and 0. 8 - 3. 0 mum long ) and irregular cocci ( 0. 2 - 0. 8 mum in diameter ).", "output": "There is no related enetity." }, { "input": "The culture utilized H ( 2 ) / CO ( 2 ) to produce methane but did not utilize formate, acetate, methanol, ethanol, 2 - propanol, butanol or trimethylamine.", "output": "There is no related enetity." }, { "input": "Optimal growth conditions were near pH 5. 1 and 35 ^ 0C.", "output": "There is no related enetity." }, { "input": "The culture grew in basal medium containing as little as 0. 43 mM Na ( + ) and growth was inhibited completely by 50 mM NaCl.", "output": "There is no related enetity." }, { "input": "To our knowledge, strain 6A8 ( T ) is one of the most acidiphilic ( lowest pH optimum ) and salt - sensitive methanogens in pure culture.", "output": "6A8." }, { "input": "Acetate, coenzyme M, vitamins and yeast extract were required for growth.", "output": "There is no related enetity." }, { "input": "It is proposed that a new genus and species be established for this organism, Methanoregula boonei gen. nov., sp. nov.", "output": "Methanoregula boonei gen . nov . , sp . nov .." }, { "input": "The type strain of Methanoregula boonei is 6A8 ( T ) ( = DSM 21154 ( T ) = JCM 14090 ( T ) ).", "output": "Methanoregula boonei, 6A8." }, { "input": "Marinobacterium coralli sp. nov., isolated from mucus of coral ( Mussismilia hispida ).", "output": "Marinobacterium coralli sp . nov ., Mussismilia hispida." }, { "input": "A Gram - negative, aerobic bacterium, designated R - 40509 ( T ), was isolated from mucus of the reef builder coral ( Mussismilia hispida ) located in the Sao Sebastiao Channel, Sao Paulo, Brazil.", "output": "R - 40509, Mussismilia hispida." }, { "input": "The strain was oxidase - positive and catalase - negative, and required Na ( + ) for growth.", "output": "There is no related enetity." }, { "input": "Its phylogenetic position was in the genus Marinobacterium and the closest related species were Marinobacterium sediminicola, Marinobacterium maritimum and Marinobacterium stanieri; the isolate exhibited 16S rRNA gene sequence similarities of 97. 5 - 98. 0 % with the type strains of these species.", "output": "Marinobacterium sediminicola, Marinobacterium maritimum, Marinobacterium stanieri." }, { "input": "16S rRNA gene sequence similarities with other type strains of the genus Marinobacterium were below 96 %.", "output": "There is no related enetity." }, { "input": "DNA - DNA hybridizations between strain R - 40509 ( T ) and the type strains of the phylogenetically closest species of the genus Marinobacterium revealed less than 70 % DNA - DNA relatedness, supporting the novel species status of the strain.", "output": "R - 40509." }, { "input": "Phenotypic characterization revealed that the strain was able to grow at 15 - 42 ^ 0C and in medium containing up to 9 % NaCl.", "output": "There is no related enetity." }, { "input": "The isolate could be differentiated from phenotypically related species by several features, including its ability to utilize d - alanine, l - alanine, bromosuccinic acid, Beta - hydroxybutyric acid and alpha - ketovaleric acid, but not acetate or l - arabinose.", "output": "There is no related enetity." }, { "input": "It produced acetoin ( Voges - Proskauer ), but did not have esterase lipase ( C8 ) or catalase activities.", "output": "There is no related enetity." }, { "input": "It possessed C ( 18: 1 ) omega7c ( 35 % ), summed feature 3 ( iso - C ( 15: 0 ) 2 - OH and / or C ( 16: 1 ) omega7c; 25 % ) and C ( 16: 0 ) ( 22 % ) as major cellular fatty acids.", "output": "There is no related enetity." }, { "input": "The DNA G + C content was 58. 5 mol %.", "output": "There is no related enetity." }, { "input": "The name Marinobacterium coralli sp. nov.", "output": "Marinobacterium coralli sp . nov .." }, { "input": "is proposed to accommodate this novel isolate; the type strain is R - 40509 ( T ) ( = LMG 25435 ( T ) = CAIM 1449 ( T ) ).", "output": "R - 40509, LMG 25435 ( T, CAIM 1449 ( T )." }, { "input": "Amnibacterium kyonggiense gen. nov., sp. nov., a new member of the family Microbacteriaceae.", "output": "Amnibacterium kyonggiense gen . nov . , sp . nov .." }, { "input": "A Gram - positive, non - motile bacterium, designated KSL51201 - 037 ( T ), was isolated from Anyang stream, Republic of Korea, and was characterized using a polyphasic taxonomic approach.", "output": "KSL51201 - 037 ( T )." }, { "input": "Comparative 16S rRNA gene sequence analysis showed that strain KSL51201 - 037 ( T ) belonged to the family Microbacteriaceae of the class Actinobacteria and exhibited 96. 9 % gene sequence similarity to Labedella gwakjiensis KSW2 - 17 ( T ), 96. 0 % to Leifsonia ginsengi wged11 ( T ) and 95. 9 % to Microterricola viridarii KV - 677 ( T ).", "output": "KSL51201 - 037 ( T ), Labedella gwakjiensis KSW2 - 17 ( T ), Leifsonia ginsengi wged11 ( T ), Microterricola viridarii KV - 677 ( T )." }, { "input": "The G + C content of the genomic DNA was 72. 7 mol %.", "output": "There is no related enetity." }, { "input": "Strain KSL51201 - 037 ( T ) had l - 2, 4 - diaminobutyric acid as the diagnostic cell - wall diamino acid, MK - 11 and MK - 12 as the major menaquinones, anteiso - C ( 15: 0 ) ( 47. 8 % ) and iso - C ( 16: 0 ) ( 24. 0 % ) as the major fatty acids and phosphatidylglycerol and three unknown phospholipids as the major polar lipids.", "output": "KSL51201 - 037 ( T )." }, { "input": "On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, it is suggested that strain KSL51201 - 037 ( T ) represents a novel species of a new genus in the family Microbacteriaceae for which the name Amnibacterium kyonggiense gen. nov., sp. nov.", "output": "KSL51201 - 037 ( T ), Amnibacterium kyonggiense gen . nov . , sp . nov .." }, { "input": "is proposed.", "output": "There is no related enetity." }, { "input": "The type strain of the type species is KSL51201 - 037 ( T ) ( = KEMC 51201 - 037 ( T ) = JCM 16463 ( T ) ).", "output": "KSL51201 - 037 ( T )." }, { "input": "Miniimonas arenae gen. nov., sp. nov., an actinobacterium isolated from sea sand.", "output": "Miniimonas arenae." }, { "input": "A Gram - positive, non - motile, coccoid - to rod - shaped, non - spore - forming bacterium, designated strain YM18 - 15 ( T ), was isolated from sea sand and studied using a polyphasic taxonomic approach.", "output": "YM18 - 15." }, { "input": "Strain YM18 - 15 ( T ) grew under both aerobic and anaerobic conditions.", "output": "YM18 - 15." }, { "input": "The cell - wall peptidoglycan type was A4Beta and ornithine was the diagnostic diamino acid.", "output": "There is no related enetity." }, { "input": "The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unknown phospholipid, MK - 8 ( H ( 4 ) ) was the major menaquinone and the predominant fatty acids were anteiso - C ( 15: 0 ) and C ( 16: 0 ).", "output": "There is no related enetity." }, { "input": "The DNA G + C content was 74. 2 mol %.", "output": "There is no related enetity." }, { "input": "High 16S rRNA gene sequence similarities ( 96. 3 - 97. 3 % ) were found with the sequences of the type strains of the three genera of the family Beutenbergiaceae.", "output": "There is no related enetity." }, { "input": "Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YM18 - 15 ( T ) formed a clade with Serinibacter salmoneus, Salana multivorans and Beutenbergia cavernae.", "output": "YM18 - 15, Serinibacter salmoneus, Salana multivorans, Beutenbergia cavernae." }, { "input": "Strain YM18 - 15 ( T ) differed from these three type strains in chemotaxonomic characteristics and in 16S rRNA gene signature nucleotides.", "output": "YM18 - 15." }, { "input": "Based on genetic and chemotaxonomic evidence, it is suggested that strain YM18 - 15 ( T ) represents a novel species of a new genus within the family Beutenbergiaceae, for which the name Miniimonas arenae gen. nov., sp. nov.", "output": "YM18 - 15, Miniimonas arenae." }, { "input": "is proposed.", "output": "There is no related enetity." }, { "input": "The type strain of the type species is YM18 - 15 ( T ) ( = NBRC 106267 ( T ) = KCTC 19750 ( T ) = MBIC 08348 ( T ) ).", "output": "YM18 - 15." }, { "input": "Anoxybacillus tengchongensis sp. nov. and Anoxybacillus eryuanensis sp. nov., facultatively anaerobic, alkalitolerant bacteria from hot springs.", "output": "Anoxybacillus tengchongensis, Anoxybacillus eryuanensis." }, { "input": "Two novel thermophilic, spore - forming bacterial strains, T - 11 ( T ) and E - 112 ( T ), were isolated from hot springs in Tengchong and Eryuan counties of Yunnan province in south - west China.", "output": "T - 11, E - 112." }, { "input": "The strains were Gram - stain - positive rods, occurring singly or in chains.", "output": "There is no related enetity." }, { "input": "Growth of strain T - 11 ( T ) was observed between 30 and 75 ^ 0C ( optimum 50 ^ 0C ) and at pH 7 - 11 ( optimum pH 8. 5 ), while the temperature range for strain E - 112 ( T ) was 35 - 70 ^ 0C ( optimum 55 ^ 0C ) and the pH range was 7. 0 - 11. 0 ( optimum pH 8. 0 ).", "output": "T - 11, E - 112." }, { "input": "The DNA G + C contents of strains T - 11 ( T ) and E - 112 ( T ) were 41. 1 and 42. 6 mol %, respectively.", "output": "T - 11, E - 112." }, { "input": "On the basis of 16S rRNA gene sequence similarity, the two strains were shown to be related most closely to Anoxybacillus species.", "output": "There is no related enetity." }, { "input": "The chemotaxonomic characteristics [ predominant isoprenoid quinone menaquinone 7 ( MK - 7 ); major fatty acids iso - C ( 15: 0 ) and iso - C ( 17: 0 ) ] also supported the affiliation of strains T - 11 ( T ) and E - 112 ( T ) to the genus Anoxybacillus.", "output": "T - 11, E - 112." }, { "input": "The results of DNA - DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains T - 11 ( T ) and E - 112 ( T ) from Anoxybacillus species with validly published names.", "output": "T - 11, E - 112." }, { "input": "Strains T - 11 ( T ) and E - 112 ( T ) therefore represent two novel species, for which the names Anoxybacillus tengchongensis sp. nov.", "output": "T - 11, E - 112, Anoxybacillus tengchongensis." }, { "input": "( type strain T - 11 ( T ) = CCTCC AB209237 ( T ) = KCTC 13721 ( T ) ) and Anoxybacillus eryuanensis sp. nov.", "output": "T - 11, Anoxybacillus eryuanensis." }, { "input": "( type strain E - 112 ( T ) = CCTCC AB209236 ( T ) = KCTC 13720 ( T ) ) are proposed.", "output": "E - 112." }, { "input": "Neisseria wadsworthii sp. nov. and Neisseria shayeganii sp. nov., isolated from clinical specimens.", "output": "Neisseria wadsworthii, Neisseria shayeganii." }, { "input": "An analysis of 16S rRNA gene sequences from archived clinical reference specimens has identified two novel Neisseria species.", "output": "There is no related enetity." }, { "input": "For each species, two strains from independent sources were identified.", "output": "There is no related enetity." }, { "input": "Amongst species with validly published names, the closest species to the newly identified organisms were Neisseria canis, N. dentiae, N. zoodegmatis, N. animaloris and N. weaveri.", "output": "Neisseria canis, N . dentiae, N . zoodegmatis, N . animaloris, N . weaveri." }, { "input": "DNA - DNA hybridization studies demonstrated that the newly identified isolates represent species that are distinct from these nearest neighbours.", "output": "There is no related enetity." }, { "input": "Analysis of partial 23S rRNA gene sequences for the newly identified strains and their nearest neighbours provided additional support for the species designation.", "output": "There is no related enetity." }, { "input": "Bayesian analysis of 16S rRNA gene sequences suggested that the newly identified isolates belong to distinct but related species of the genus Neisseria, and are members of a clade that includes N. dentiae, N. bacilliformis and N. canis.", "output": "N . dentiae, N . bacilliformis, N . canis." }, { "input": "The predominant cellular fatty acids [ 16: 0, summed feature 3 ( 16: 1omega7c and / or iso - 15: 0 2 - OH ) and 18: 1omega7c ], as well as biochemical and morphological analyses further support the designation of Neisseria wadsworthii sp. nov.", "output": "Neisseria wadsworthii." }, { "input": "( type strain 9715 ( T ) = DSM 22247 ( T ) = CIP 109934 ( T ) ) and Neisseria shayeganii sp. nov.", "output": "9715, Neisseria shayeganii." }, { "input": "( type strain 871 ( T ) = DSM 22246 ( T ) = CIP 109933 ( T ) ).", "output": "871." }, { "input": "Spirochaeta perfilievii sp. nov., an oxygen - tolerant, sulfide - oxidizing, sulfur - and thiosulfate - reducing spirochaete isolated from a saline spring.", "output": "There is no related enetity." }, { "input": "A novel strain of fermenting, aerotolerant, chemo - organoheterotrophic spirochaete designated P ( T ) was isolated from a sulfur ' Thiodendron ' mat in a saline spring at the Staraya Russa resort ( Novgorod Region, Russia ).", "output": "There is no related enetity." }, { "input": "Cells of strain P ( T ) exhibited a helical shape.", "output": "There is no related enetity." }, { "input": "The spirochaete required sulfide in the growth medium and was able to oxidize it non - enzymically to elemental sulfur via the interaction of H ( 2 ) O ( 2 ) with sulfide and deposit it in the periplasmic space.", "output": "There is no related enetity." }, { "input": "Growth occurred at 4 - 32 ^ 0C ( optimum at 28 - 30 ^ 0C ), pH 6. 0 - 8. 5 ( optimum pH 7. 0 - 7. 5 ), and in 0. 1 - 1 M NaCl ( optimum 0. 35 M ).", "output": "There is no related enetity." }, { "input": "The isolate used several sugars and polysaccharides as carbon or energy sources but did not use peptides, amino acids, organic acids or alcohols.", "output": "There is no related enetity." }, { "input": "The products of glucose fermentation were formate, acetate, ethanol, pyruvate, CO ( 2 ) and H ( 2 ).", "output": "There is no related enetity." }, { "input": "The genomic DNA G + C content was 41. 7 mol %.", "output": "There is no related enetity." }, { "input": "16S rRNA gene sequence analysis showed that strain P ( T ) fell within a group of species in the genus Spirochaeta, including Spirochaeta litoralis, S. isovalerica and S. cellobiosiphila, with which it shared less then 89 % sequence similarity.", "output": "Spirochaeta litoralis, S . isovalerica, S . cellobiosiphila." }, { "input": "On the basis of its morphology, physiology and other phenotypic properties, as well as its phylogenetic position, the new isolate is considered to represent a novel species of the genus Spirochaeta, for which the name Spirochaeta perfilievii sp. nov.", "output": "There is no related enetity." }, { "input": "is proposed.", "output": "There is no related enetity." }, { "input": "The type strain is P ( T ) ( = DSM 19205 ( T ) = VKM B - 2514 ( T ) ).", "output": "There is no related enetity." }, { "input": "Sporosalibacterium faouarense gen. nov., sp. nov., a moderately halophilic bacterium isolated from oil - contaminated soil.", "output": "There is no related enetity." }, { "input": "A novel strictly anaerobic, moderately halophilic and mesophilic bacterium, designated strain SOL3f37 ( T ), was isolated from a hydrocarbon - polluted soil surrounding a deep petroleum environment located in south Tunisia.", "output": "There is no related enetity." }, { "input": "Cells of strain SOL3f37 ( T ) stained Gram - positive and were motile, straight and spore - forming.", "output": "There is no related enetity." }, { "input": "Strain SOL3f37 ( T ) had a typical Gram - positive - type cell - wall structure, unlike the thick, multilayered cell wall of its closest relative Clostridiisalibacter paucivorans.", "output": "Clostridiisalibacter paucivorans." }, { "input": "The major fatty acids were iso - C ( 15: 0 ) ( 41 % ), iso - C ( 14: 0 ) 3 - OH and / or iso - C ( 15: 0 ) dimethyl acetal ( 21. 6 % ), iso - C ( 13: 0 ) ( 4. 4 % ), anteiso - C ( 15: 0 ) ( 3. 9 % ) and iso - C ( 15: 1 ) ( 2. 8 % ).", "output": "There is no related enetity." }, { "input": "Strain SOL3f37 ( T ) grew between 20 and 48 ^ 0C ( optimum 40 ^ 0C ) and at pH 6. 2 - 8. 1 ( optimum pH 6. 9 ).", "output": "There is no related enetity." }, { "input": "Strain SOL3f37 ( T ) required at least 0. 5 NaCl l ( - 1 ) and grew in the presence of NaCl concentrations up to 150 g l ( - 1 ) ( optimum 40 g l ( - 1 ) ).", "output": "There is no related enetity." }, { "input": "Yeast extract ( 2 g l ( - 1 ) ) was required for degradation of pyruvate, fumarate, fructose, glucose and mannitol.", "output": "There is no related enetity." }, { "input": "Also, strain SOL3f37 ( T ) grew heterotrophically on yeast extract, peptone and bio - Trypticase, but was unable to grow on Casamino acids.", "output": "yeast." }, { "input": "Sulfate, thiosulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced.", "output": "There is no related enetity." }, { "input": "The DNA G + C content was 30. 7 mol %.", "output": "There is no related enetity." }, { "input": "Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SOL3f37 ( T ) was a member of the family Clostridiaceae in the order Clostridiales; strain SOL3f37 ( T ) was related to members of various genera of the family Clostridiaceae.", "output": "There is no related enetity." }, { "input": "It exhibited highest 16S rRNA gene sequence similarity ( 93. 4 % ) with Clostridiisalibacter paucivorans 37HS60 ( T ), 91. 8 % with Thermohalobacter berrensis CTT3 ( T ) and 91. 7 % with Caloranaerobacter azorensis MV1087 ( T ).", "output": "Clostridiisalibacter paucivorans, Thermohalobacter berrensis, Caloranaerobacter azorensis." }, { "input": "On the basis of genotypic, phenotypic and phylogenetic data, it is suggested that strain SOL3f37 ( T ) represents a novel species in a new genus.", "output": "There is no related enetity." }, { "input": "The name Sporosalibacterium faouarense gen. nov., sp. nov.", "output": "There is no related enetity." }, { "input": "is proposed, with SOL3f37 ( T ) ( = DSM 21485 ( T ) = JCM 15487 ( T ) ) as the type strain of Sporosalibacterium faouarense.", "output": "There is no related enetity." }, { "input": "Streptomyces lacticiproducens sp. nov., a lactic acid - producing streptomycete isolated from the rhizosphere of tomato plants.", "output": "tomato." }, { "input": "A novel actinomycete, designated strain GIMN4. 001 ( T ), was isolated from the rhizosphere of tomato plants grown in Guangzhou, China.", "output": "tomato." }, { "input": "The strain produced greyish white aerial mycelia, lactic acid and a large quantity of double diamond - shaped crystals on potato dextrose agar and yeast extract - malt extract agar.", "output": "potato, yeast." }, { "input": "The colour of the substrate mycelium was not sensitive to pH.", "output": "There is no related enetity." }, { "input": "Microscopic observations revealed that strain GIMN4. 001 ( T ) produced verticillate chains of cylindrical spores.", "output": "There is no related enetity." }, { "input": "Chemotaxonomic data confirmed that strain GIMN4. 001 ( T ) belonged to the genus Streptomyces.", "output": "There is no related enetity." }, { "input": "Melanin pigments were not produced.", "output": "There is no related enetity." }, { "input": "No antibacterial activity was observed against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis or Candida albicans, but inhibitory activity was observed against Penicillium citrinum.", "output": "Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Candida albicans, Penicillium citrinum." }, { "input": "16S rRNA gene sequence analysis revealed that strain GIMN4. 001 ( T ) was related most closely to Streptomyces morookaense ATCC 19166 ( T ) ( 98. 9 % similarity ) and Streptomyces lavenduligriseus ATCC 13306 ( T ) ( 98. 7 % ).", "output": "Streptomyces morookaense, ATCC 19166 ( T ), Streptomyces lavenduligriseus, ATCC 13306 ( T )." }, { "input": "Levels of DNA - DNA relatedness between strain GIMN4. 001 ( T ) and the type strains of these species were low ( 14 - 20 % ).", "output": "There is no related enetity." }, { "input": "Furthermore, strain GIMN4. 001 ( T ) could be differentiated from S. morookaense, S. lavenduligriseus and other closely related species of the genus Streptomyces based on morphological, physiological and biochemical characteristics.", "output": "S . morookaense." }, { "input": "On the basis of its physiological and molecular properties, strain GIMN4. 001 ( T ) is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces lacticiproducens sp. nov.", "output": "There is no related enetity." }, { "input": "is proposed.", "output": "There is no related enetity." }, { "input": "The type strain is GIMN4. 001 ( T ) ( = CCTCC M208214 ( T ) = NRRL B - 24800 ( T ) ).", "output": "There is no related enetity." }, { "input": "An rpoB signature sequence provides unique resolution for the molecular typing of cyanobacteria.", "output": "There is no related enetity." }, { "input": "The use of morphological characters for the classification of cyanobacteria has often led to ambiguous strain assignment.", "output": "There is no related enetity." }, { "input": "In the past two decades, the availability of sequences, such as those of the 16S rRNA, nif, cpc and rpoC1 genes, and the use of metagenomics, has steadily increased and has made the reconstruction of evolutionary relationships of some cyanobacterial groups possible in addition to improving strain assignment.", "output": "There is no related enetity." }, { "input": "Conserved indels ( insertions / deletions ) are present in all cyanobacterial RpoB ( Beta subunit of RNA polymerase ) sequences presently available in public databases.", "output": "There is no related enetity." }, { "input": "These indels are located in the Rpb2 _ 6 domain of RpoB, which is involved in DNA binding and DNA - directed RNA polymerase activity.", "output": "There is no related enetity." }, { "input": "They are variable in length ( 6 - 44 aa ) and sequence, and form part of what appears to be a longer signature sequence ( 43 - 81 aa ).", "output": "There is no related enetity." }, { "input": "Indeed, a number of these sequences turn out to be distinctive among several strains of a given genus and even among strains of a given species.", "output": "There is no related enetity." }, { "input": "These signature sequences can thus be used to identify cyanobacteria at a subgenus level and can be useful molecular markers to establish the taxonomic positions of cyanobacterial isolates in laboratory cultures, and / or to assess cyanobacterial biodiversity in space and time in natural ecosystems.", "output": "There is no related enetity." }, { "input": "Auritidibacter ignavus gen. nov., sp. nov., of the family Micrococcaceae isolated from an ear swab of a man with otitis externa, transfer of the members of the family Yaniellaceae Li et al.", "output": "Auritidibacter ignavus gen . nov . , sp . nov .." }, { "input": "2008 to the family Micrococcaceae and emended description of the suborder Micrococcineae.", "output": "There is no related enetity." }, { "input": "A Gram - reaction - positive, aerobic, catalase - positive, non - spore - forming, rod - shaped bacterium designated IMMIB L - 1656 ( T ) was isolated from an ear swab of a man and characterized using a polyphasic approach.", "output": "IMMIB L - 1656 ( T )." }, { "input": "16S rRNA gene sequence analysis indicated that strain IMMIB L - 1656 ( T ) is related to members of the family Micrococcaceae ( & lt; 95. 1 % sequence similarity ).", "output": "IMMIB L - 1656 ( T )." }, { "input": "Anaylsis using different phylogenetic algorithms consistently grouped strain IMMIB L - 1656 ( T ) with members of the genus Yaniella.", "output": "IMMIB L - 1656 ( T )." }, { "input": "The organism posessed a cell - wall murein based on L - lysine ( variation A4alpha, type L - Lys - Gly - L - Glu ), MK - 10 as the predominant menaquinone and long - chain cellular fatty acids of straight - chain and branched - chain saturated types ( with iso - C ( 15: 0 ) and anteiso - C ( 17: 0 ) predominating ).", "output": "There is no related enetity." }, { "input": "The polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol in addition to unknown glycolipids.", "output": "There is no related enetity." }, { "input": "The DNA G + C content was 59. 7 mol %.", "output": "There is no related enetity." }, { "input": "Based on its distinctive genotypic and phenotypic characteristics, strain IMMIB L - 1656 ( T ) represents a novel species in a novel genus, for which the name Auritidibacter ignavus gen. nov., sp. nov.", "output": "IMMIB L - 1656 ( T ), Auritidibacter ignavus gen . nov . , sp . nov .." }, { "input": "is proposed.", "output": "There is no related enetity." }, { "input": "We also propose that members of the family Yaniellaceae be transferred to the family Micrococcaceae with amendments to the description of the suborder Micrococcineae.", "output": "There is no related enetity." }, { "input": "The type strain of Auritidibacter ignavus is IMMIB L - 1656 ( T ) ( = DSM 45359 ( T ) = CCUG 57943 ( T ) ).", "output": "Auritidibacter ignavus, IMMIB L - 1656 ( T ), DSM 45359 ( T ), CCUG 57943 ( T )." }, { "input": "Flavobacterium beibuense sp. nov., isolated from marine sediment.", "output": "There is no related enetity." }, { "input": "A taxonomic study was carried out on strain F44 - 8 ( T ), which was isolated from a crude - oil - degrading consortium, enriched from marine sediment of the Beibu Gulf, PR China.", "output": "There is no related enetity." }, { "input": "The 16S rRNA gene sequence of strain F44 - 8 ( T ) showed highest similarities to those of Flavobacterium frigoris LMG 21922 ( T ) ( 93. 3 % ), Flavobacterium terrae R2A1 - 13 ( T ) ( 93. 3 % ) and Flavobacterium gelidilacus LMG 21477 ( T ) ( 93. 1 % ).", "output": "Flavobacterium frigoris LMG 21922 ( T ), Flavobacterium terrae R2A1 - 13 ( T ), Flavobacterium gelidilacus LMG 21477 ( T )." }, { "input": "Sequence similarities to other members of the genus Flavobacterium were & lt; 93. 0 %.", "output": "There is no related enetity." }, { "input": "The dominant fatty acids of strain F44 - 8 ( T ) were iso - C ( 15: 0 ), summed feature 3 ( iso - C ( 15: 0 ) 2 - OH and / or C ( 16: 1 ) omega7c ), iso - C ( 15: 1 ) G and iso - C ( 17: 0 ) 3 - OH.", "output": "There is no related enetity." }, { "input": "The DNA G + C content of strain F44 - 8 ( T ) was 38. 6 mol %.", "output": "There is no related enetity." }, { "input": "These results are consistent with characteristics of members of the genus Flavobacterium.", "output": "There is no related enetity." }, { "input": "Strain F44 - 8 ( T ) could, however, be readily distinguished from all known Flavobacterium species by a number of phenotypic features.", "output": "There is no related enetity." }, { "input": "Therefore, according to the phenotypic and 16S rRNA gene sequence data, strain F44 - 8 ( T ) represents a novel species in the genus Flavobacterium, for which the name Flavobacterium beibuense sp. nov.", "output": "There is no related enetity." }, { "input": "is proposed ( type strain F44 - 8 ( T ) = CCTCC AB 209067 ( T ) = LMG 25233 ( T ) = MCCC 1A02877 ( T ) ).", "output": "There is no related enetity." }, { "input": "Fungal secondary metabolites - strategies to activate silent gene clusters.", "output": "There is no related enetity." }, { "input": "Filamentous fungi produce a multitude of low molecular weight bioactive compounds.", "output": "There is no related enetity." }, { "input": "The increasing number of fungal genome sequences impressively demonstrated that their biosynthetic potential is far from being exploited.", "output": "There is no related enetity." }, { "input": "In fungi, the genes required for the biosynthesis of a secondary metabolite are clustered.", "output": "There is no related enetity." }, { "input": "Many of these bioinformatically newly discovered secondary metabolism gene clusters are silent under standard laboratory conditions.", "output": "There is no related enetity." }, { "input": "Consequently, no product can be found.", "output": "There is no related enetity." }, { "input": "This review summarizes the current strategies that have been successfully applied during the last years to activate these silent gene clusters in filamentous fungi, especially in the genus Aspergillus.", "output": "There is no related enetity." }, { "input": "The techniques take advantage of genome mining, vary from the simple search for compounds with bioinformatically predicted physicochemical properties up to methods that exploit a probable interaction of microorganisms.", "output": "There is no related enetity." }, { "input": "Until now, the majority of successful approaches have been based on molecular biology like the generation of gene & quot; knock outs & quot;, promoter exchange, overexpression of transcription factors or other pleiotropic regulators.", "output": "There is no related enetity." }, { "input": "Moreover, strategies based on epigenetics opened a new avenue for the elucidation of the regulation of secondary metabolite formation and will certainly continue to play a significant role for the elucidation of cryptic natural products.", "output": "There is no related enetity." }, { "input": "The conditions under which a given gene cluster is naturally expressed are largely unknown.", "output": "There is no related enetity." }, { "input": "One technique is to attempt to simulate the natural habitat by co - cultivation of microorganisms from the same ecosystem.", "output": "There is no related enetity." }, { "input": "This has already led to the activation of silent gene clusters and the identification of novel compounds in Aspergillus nidulans.", "output": "Aspergillus nidulans." }, { "input": "These simulation strategies will help discover new natural products in the future, and may also provide fundamental new insights into microbial communication.", "output": "There is no related enetity." }, { "input": "Compartmentalization and molecular traffic in secondary metabolism: a new understanding of established cellular processes.", "output": "There is no related enetity." }, { "input": "Great progress has been made in understanding the regulation of expression of genes involved in secondary metabolism.", "output": "There is no related enetity." }, { "input": "Less is known about the mechanisms that govern the spatial distribution of the enzymes, cofactors, and substrates that mediate catalysis of secondary metabolites within the cell.", "output": "There is no related enetity." }, { "input": "Filamentous fungi in the genus Aspergillus synthesize an array of secondary metabolites and provide useful systems to analyze the mechanisms that mediate the temporal and spatial regulation of secondary metabolism in eukaryotes.", "output": "There is no related enetity." }, { "input": "For example, aflatoxin biosynthesis in Aspergillus parasiticus has been studied intensively because this mycotoxin is highly toxic, mutagenic, and carcinogenic in humans and animals.", "output": "Aspergillus parasiticus, humans." }, { "input": "Using aflatoxin synthesis to illustrate key concepts, this review focuses on the mechanisms by which sub - cellular compartmentalization and intra - cellular molecular traffic contribute to the initiation and completion of secondary metabolism within the cell.", "output": "There is no related enetity." }, { "input": "We discuss the recent discovery of aflatoxisomes, specialized trafficking vesicles that participate in the compartmentalization of aflatoxin synthesis and export of the toxin to the cell exterior; this work provides a new and clearer understanding of how cells integrate secondary metabolism into basic cellular metabolism via the intra - cellular trafficking machinery.", "output": "There is no related enetity." }, { "input": "The lipid language of plant - fungal interactions.", "output": "There is no related enetity." }, { "input": "Lipid mediated cross - kingdom communication between hosts and pathogens is a rapidly emerging field in molecular plant - fungal interactions.", "output": "There is no related enetity." }, { "input": "Amidst our growing understanding of fungal and plant chemical cross - talk lies the distinct, yet little studied, role for a group of oxygenated lipids derived from polyunsaturated fatty acids, termed oxylipins.", "output": "There is no related enetity." }, { "input": "Endogenous fungal oxylipins are known for their roles in carrying out pathogenic strategies to successfully colonize their host, reproduce, and synthesize toxins.", "output": "There is no related enetity." }, { "input": "While plant oxylipins also have functions in reproduction and development, they are largely recognized as agents that facilitate resistance to pathogen attack.", "output": "There is no related enetity." }, { "input": "Here we review the composition and endogenous functions of oxylipins produced by both plants and fungi and introduce evidence which suggests that fungal pathogens exploit host oxylipins to facilitate their own virulence and pathogenic development.", "output": "There is no related enetity." }, { "input": "Specifically, we describe how fungi induce plant lipid metabolism to utilize plant oxylipins in order to promote G - protein - mediated regulation of sporulation and mycotoxin production in the fungus.", "output": "There is no related enetity." }, { "input": "The use of host - ligand mimicry ( i. e. coronatine ) to manipulate plant defense responses that benefit the fungus are also implicated.", "output": "There is no related enetity." }, { "input": "Treatment non - adherence in teenage and young adult patients with cancer.", "output": "There is no related enetity." }, { "input": "Adhering to treatment can be a significant issue for many patients diagnosed with chronic health conditions and this has been reported to be greater during the adolescent years.", "output": "There is no related enetity." }, { "input": "However, little is known about treatment adherence in teenage and young adult ( TYA ) patients with cancer.", "output": "There is no related enetity." }, { "input": "To increase awareness of the adherence challenges faced by these patients, we have reviewed the published work.", "output": "There is no related enetity." }, { "input": "The available evidence suggests that a substantial proportion of TYA patients with cancer do have difficulties, with reports that up to 63 % of patients do not adhere to their treatment regimens.", "output": "There is no related enetity." }, { "input": "However, with inconsistent findings across studies, the true extent of non - adherence for these young patients is still unclear.", "output": "There is no related enetity." }, { "input": "Furthermore, it is apparent that there are many components of the cancer treatment regimen that have yet to be assessed in relation to patient adherence.", "output": "There is no related enetity." }, { "input": "Factors that have been shown to affect treatment adherence in TYA patients include patient emotional functioning ( depression and self - esteem ), patient health beliefs ( perceived illness severity and vulnerability ), and family environment ( parental support and parent - child concordance ).", "output": "There is no related enetity." }, { "input": "Strategies that foster greater patient adherence are also identified.", "output": "There is no related enetity." }, { "input": "These strategies are multifactorial, targeting not only the patient, but the health professional, family, and treatment regimen.", "output": "There is no related enetity." }, { "input": "This review highlights the lack of interventional studies addressing treatment adherence in TYA patients with cancer, with only one such intervention being identified: a video game intervention focusing on behavioural issues related to cancer treatment and care.", "output": "There is no related enetity." }, { "input": "Methodological issues in measuring adherence are addressed and suggestions for improving the design of future adherence studies highlighted, of which there is a great need.", "output": "There is no related enetity." }, { "input": "Monovalent cations regulate expression and activity of the Hak1 potassium transporter in Debaryomyces hansenii.", "output": "Debaryomyces hansenii." }, { "input": "Debaryomyces hansenii was able to grow in a medium containing residual amounts of K ( + ), indicating the activity of high affinity K ( + ) transporters.", "output": "Debaryomyces hansenii." }, { "input": "Transcriptional regulation analysis of the genes encoding the two potassium uptake systems in D. hansenii revealed that while DhTRK1 is not regulated at transcriptional level, expression of DhHAK1 required starvation in the absence of K ( + ) and Na ( + ) and was not affected by changes in membrane potential.", "output": "D . hansenii." }, { "input": "Rb ( + ) transport in cells expressing DhHAK1 was activated by external Na ( + ) or acidic pH and inhibited by high pH.", "output": "There is no related enetity." }, { "input": "We propose a K ( + ) - H ( + ) symporter that, under certain conditions may work as a K ( + ) - Na ( + ) transporter, as the mechanism driving K ( + ) influx mediated by DhHak1p.", "output": "There is no related enetity." }, { "input": "Isocitrate dehydrogenase - 1 mutations: a fundamentally new understanding of diffuse glioma?", "output": "There is no related enetity." }, { "input": "The discovery of somatic mutations in the gene encoding isocitrate dehydrogenase - 1 ( IDH1 ) in glioblastomas was remarkable because the enzyme was not previously identified with any known oncogenic pathway.", "output": "There is no related enetity." }, { "input": "IDH1 is mutated in up to 75 % of grade II and grade III diffuse gliomas.", "output": "There is no related enetity." }, { "input": "Apart from acute myeloid leukaemia, other tumour types do not carry IDH1 mutations.", "output": "There is no related enetity." }, { "input": "Mutations in a homologous gene, IDH2, have also been identified, although they are much rarer.", "output": "There is no related enetity." }, { "input": "Although TP53 mutations and 1p / 19q codeletions are mutually exclusive in gliomas, in both of these genotypes IDH1 mutations are common.", "output": "There is no related enetity." }, { "input": "IDH1 and IDH2 mutations are early events in the development of gliomas.", "output": "There is no related enetity." }, { "input": "Moreover, IDH1 and IDH2 mutations are a major prognostic marker for overall and progression - free survival in grade II - IV gliomas.", "output": "There is no related enetity." }, { "input": "Mutated IDH1 has an altered catalytic activity that results in the accumulation of 2 - hydroxyglutarate.", "output": "There is no related enetity." }, { "input": "Molecularly, IDH1 and IDH2 mutations are heterozygous, affect only a single codon, and rarely occur together.", "output": "There is no related enetity." }, { "input": "Because IDH1 does not belong to a traditional oncogenic pathway and is specifically and commonly mutated in gliomas, the altered enzymatic activity of IDH1 may provide a fundamentally new understanding of diffuse glioma.", "output": "There is no related enetity." }, { "input": "Characterization of the GPI - anchored endo Beta - 1, 3 - glucanase Eng2 of Aspergillus fumigatus.", "output": "Aspergillus fumigatus." }, { "input": "A GPI - anchored endo Beta - 1, 3 - glucanase of Aspergillus fumigatus was characterized.", "output": "Aspergillus fumigatus." }, { "input": "The enzyme encoded by ENG2 ( AFUA _ 2g14360 ) belongs to the glycoside hydrolase family 16 ( GH16 ).", "output": "There is no related enetity." }, { "input": "The activity was characterized using a recombinant protein produced by Pichiapastoris.", "output": "Pichiapastoris." }, { "input": "The recombinant enzyme preferentially acts on soluble Beta - 1, 3 - glucans.", "output": "There is no related enetity." }, { "input": "Enzymatic analysis of the endoglucanase activity using Carboxymethyl - Curdlan - Remazol Brilliant Blue ( CM - Curdlan - RBB ) as a substrate revealed a wide temperature optimum of 24 - 40 ^ 0C, a pH optimum of 5. 0 - 6. 5 and a K ( m ) of 0. 8 mg ml ( - 1 ).", "output": "There is no related enetity." }, { "input": "HPAEC analysis of the products formed by Eng2 when acting on different oligo - Beta - 1, 3 - glucans confirmed the predicted endoglucanase activity and also revealed a transferase activity for oligosaccharides of a low degree of polymerization.", "output": "There is no related enetity." }, { "input": "The growth phenotype of the Afeng2 mutant was identical to that of the wt strain.", "output": "There is no related enetity." }, { "input": "Measuring impact in the Millennium Development Goal era and beyond: a new approach to large - scale effectiveness evaluations.", "output": "There is no related enetity." }, { "input": "Evaluation of large - scale programmes and initiatives aimed at improvement of health in countries of low and middle income needs a new approach.", "output": "There is no related enetity." }, { "input": "Traditional designs, which compare areas with and without a given programme, are no longer relevant at a time when many programmes are being scaled up in virtually every district in the world.", "output": "There is no related enetity." }, { "input": "We propose an evolution in evaluation design, a national platform approach that: uses the district as the unit of design and analysis; is based on continuous monitoring of different levels of indicators; gathers additional data before, during, and after the period to be assessed by multiple methods; uses several analytical techniques to deal with various data gaps and biases; and includes interim and summative evaluation analyses.", "output": "There is no related enetity." }, { "input": "This new approach will promote country ownership, transparency, and donor coordination while providing a rigorous comparison of the cost - effectiveness of different scale - up approaches.", "output": "There is no related enetity." }, { "input": "UreA, the major urea / H + symporter in Aspergillus nidulans.", "output": "Aspergillus nidulans." }, { "input": "We report here the characterization of UreA, a high - affinity urea / H + symporter of Aspergillus nidulans.", "output": "Aspergillus nidulans." }, { "input": "The deletion of the encoding gene abolishes urea transport at low substrate concentrations, suggesting that in these conditions UreA is the sole transport system specific for urea in A. nidulans.", "output": "A . nidulans." }, { "input": "The ureA gene is not inducible by urea or its precursors, but responds to nitrogen metabolite repression, necessitating for its expression the AreA GATA factor.", "output": "There is no related enetity." }, { "input": "In contrast to what was observed for other transporters in A. nidulans, repression by ammonium is also operative during the isotropic growth phase.", "output": "A . nidulans." }, { "input": "The activity of UreA is down - regulated post - translationally by ammonium - promoted endocytosis.", "output": "There is no related enetity." }, { "input": "A number of homologues of UreA have been identified in A. nidulans and other Aspergilli, which cluster in four groups, two of which contain the urea transporters characterized so far in fungi and plants.", "output": "A . nidulans." }, { "input": "This phylogeny may have arisen by gene duplication events, giving place to putative transport proteins that could have acquired novel, still unidentified functions.", "output": "There is no related enetity." }, { "input": "The Candida albicans Rgd1 is a RhoGAP protein involved in the control of filamentous growth.", "output": "Candida albicans." }, { "input": "Rho proteins are essential regulators of polarized growth in eukaryotic cells.", "output": "There is no related enetity." }, { "input": "These proteins are down - regulated in vivo by specific Rho GTPase Activating Proteins ( RhoGAP ).", "output": "There is no related enetity." }, { "input": "We investigated the role of Rgd1 RhoGAP, encoded by the Candida albicans RGD1 gene.", "output": "Candida albicans." }, { "input": "We demonstrated that CaCdc42, CaRho3 and CaRho4 proteins had an intrinsic GTPase activity and that CaRgd1 stimulates in vitro GTP hydrolysis of these GTPases.", "output": "There is no related enetity." }, { "input": "Deletion of RGD1 in C. albicans results in sensitivity to low pH as already described for rgd1Delta in Saccharomyces cerevisiae.", "output": "C . albicans, Saccharomyces cerevisiae." }, { "input": "The role of Rgd1 in survival at low pH is conserved in the two yeast species as the CaRGD1 gene complements the Scrgd1Delta sensitivity.", "output": "There is no related enetity." }, { "input": "By tagging the RhoGAP with GFP, we found that CaRgd1 is localized at the tip and cortex of growing cells and during cytokinesis at the septation sites in yeast and filamentous forms.", "output": "There is no related enetity." }, { "input": "We investigated the effect of CaRgd1 on the control of the polarized growth.", "output": "There is no related enetity." }, { "input": "Removing CaRGD1 alleles increased filamentous growth and cells lacking CaRgd1 presented longer germ tubes.", "output": "There is no related enetity." }, { "input": "Conversely, RGD1 overexpression restricted hyphae growth.", "output": "There is no related enetity." }, { "input": "Our results demonstrate that Rgd1 is critical for filamentous formation in C. albicans especially for filamentous elongation.", "output": "C . albicans." }, { "input": "Surface and flagella morphology of the motile form of Chromera velia revealed by field - emission scanning electron microscopy.", "output": "Chromera velia." }, { "input": "Chromera velia ( Chromerida; Alveolata ) is an autotrophic protist isolated from stony corals.", "output": "Chromera velia." }, { "input": "Ch. velia possesses a chloroplast thought to be most closely related to the apicoplasts of non - photosynthetic apicomplexa.", "output": "Ch . velia." }, { "input": "Phylogenetic analyses place Ch. velia as a close relative of parasitic apicomplexa and predatory colpodellids.", "output": "Ch . velia." }, { "input": "We have used field - emission scanning electron microscopy of cells sputter - coated with gold or chromium and non - coated cells to characterise the surface ultrastructure of the motile form of Ch. velia.", "output": "Ch . velia." }, { "input": "In overall morphology the biflagellated Ch. velia cells resemble the colpodellid Colpodella edax, but with some notable differences.", "output": "Ch . velia, Colpodella edax." }, { "input": "The ventral side of the flagellated Ch. velia cell has two grooves extending from the anterior flagella insertion point with a ridge rising towards the anterior apex of the cell.", "output": "Ch . velia." }, { "input": "The anterior flagellum is shorter than the posterior flagellum and possesses a distinct, small curved appendage.", "output": "There is no related enetity." }, { "input": "The insertion point of the anterior flagellum is partly enclosed by a flap extending from the cell.", "output": "There is no related enetity." }, { "input": "The posterior flagellum is approximately four times the length of the cell and possesses mastigonemes.", "output": "There is no related enetity." }, { "input": "The combination of coating techniques proved superior to the commonly used gold coating to determine fine surface ultrastructure.", "output": "There is no related enetity." }, { "input": "This new ultrastructural information for Ch. velia allowed us to emend its diagnosis.", "output": "Ch . velia." }, { "input": "Stress - induced pseudocyst formation - - a newly identified mechanism of protection against organic solvents in acanthamoebae of the T4 genotype.", "output": "T4." }, { "input": "Differentiation into highly resistant double - walled cysts is a major mechanism allowing amphizoic acanthamoebae to survive under long - lasting, unfavourable environmental conditions.", "output": "There is no related enetity." }, { "input": "We found that relatively low concentrations of methanol, acetone or DMSO stimulate prompt Acanthamoeba differentiation into a rounded cyst - like stage with a single envelope.", "output": "There is no related enetity." }, { "input": "To address whether this rapid response differs from the encystment, time - dependent changes in cell surface characteristics and cyst - specific gene expression were monitored in encystating cells and cells differentiating under methanol treatment using microscopic, lectin - binding, PCR and resistance studies.", "output": "There is no related enetity." }, { "input": "In contrast to the encystment: ( 1 ) a single - layered amorphous mannose / glucose coat was the only envelope assembled on the surface of the solvent - treated cells, ( 2 ) the cyst - specific protein ( CSP21 ) was not expressed, ( 3 ) the coat did not protect cells against acidic pH and ( 4 ) in solvent - free encystment medium, the coated cells did not assemble the double - layered wall, thus indicating that these cells were not immature cysts.", "output": "There is no related enetity." }, { "input": "These findings lead us to specify a terminal stage of rapid Acanthamoeba differentiation elicited by acute organic solvent stress as & quot; pseudocyst & quot;, and to suggest that encystation and pseudocyst formation are distinct stress responses.", "output": "There is no related enetity." }, { "input": "Moreover, the possibility exists that pseudocysts might form in response to certain contact lens solutions thus increasing resistance of acanthamoebae to disinfecting agents.", "output": "There is no related enetity." }, { "input": "Possible roles of phospholipase A ( 2 ) in the biological activities of Acanthamoeba castellanii ( T4 Genotype ).", "output": "Acanthamoeba castellanii." }, { "input": "Using phospholipases A ( 2 ) - specific spectrophotometric assays, it was shown that A. castellanii lysates and their conditioned medium exhibit phospholipase activities.", "output": "A . castellanii." }, { "input": "The extracellular levels of PLA ( 2 ) detected were significantly reduced compared with the cell - associated enzyme ( P & lt; 0. 05 ).", "output": "There is no related enetity." }, { "input": "Sphinganine, a PLA ( 2 ) inhibitor showed robust amoebistatic properties but had no effect on the viability of A. castellanii.", "output": "A . castellanii." }, { "input": "The potency of sphinganine was demonstrated effectively towards purified PLA ( 2 ) derived from porcine pancreas.", "output": "There is no related enetity." }, { "input": "Using sphinganine, it was observed that PLA ( 2 ) is involved in neither binding nor cytotoxicity of the human brain microvascular endothelial cells due to A. castellanii.", "output": "human, A . castellanii." }, { "input": "Unlike as was the case for Dictyostelium amoebae, PLA ( 2 ) appeared to be involved in A. castellanii phagocytosis of the fluorescently - labelled polystyrene beads.", "output": "A . castellanii." }, { "input": "Horseradish peroxidase was used as a tracer molecule to develop assays to study pinocytosis in A. castellanii.", "output": "Horseradish, A . castellanii." }, { "input": "The findings revealed that sphinganine impedes phagocytosis but augments pinocytosis in A. castellanii suggesting distinct nature of processes.", "output": "A . castellanii." }, { "input": "A complete understanding of the role of phospholipases in the biology and pathogenesis of A. castellanii infections will determine their potential as therapeutic targets.", "output": "A . castellanii." }, { "input": "The roles played by Aspergillus nidulans apoptosis - inducing factor ( AIF ) - like mitochondrial oxidoreductase ( AifA ) and NADH - ubiquinone oxidoreductases ( NdeA - B and NdiA ) in farnesol resistance.", "output": "Aspergillus nidulans." }, { "input": "Farnesol ( FOH ) is a nonsterol isoprenoid produced by dephosphorylation of farnesyl pyrophosphate, a catabolite of the cholesterol biosynthetic pathway.", "output": "There is no related enetity." }, { "input": "These isoprenoids inhibit proliferation and induce apoptosis.", "output": "There is no related enetity." }, { "input": "Here, we show that Aspergillus nidulans AifA encoding the apoptosis - inducing factor ( AIF ) - like mitochondrial oxidoreductase plays a role in the function of the mitochondrial Complex I. Additionally, we demonstrated that ndeA - B and ndiA encode external and internal alternative NADH dehydrogenases, respectively, that have a function in FOH resistance.", "output": "Aspergillus nidulans." }, { "input": "When exposed to FOH, the DeltaaifA and DeltandeA strains have increased ROS production while DeltandeB, DeltandeA DeltandeB, and DeltandiA mutant strains showed the same ROS accumulation than in the absence of FOH.", "output": "There is no related enetity." }, { "input": "We observed several compensatory mechanisms affecting the differential survival of these mutants to FOH.", "output": "There is no related enetity." }, { "input": "Regulation of secondary metabolism by chromatin structure and epigenetic codes.", "output": "There is no related enetity." }, { "input": "Chromatin, composed of DNA wrapped around an octamer of histones, is the relevant substrate for all genetic processes in eukaryotic nuclei.", "output": "There is no related enetity." }, { "input": "Changes in chromatin structure are associated with the activation and silencing of gene transcription and reversible post - translational modifications of histones are now known to direct chromatin structure transitions.", "output": "There is no related enetity." }, { "input": "Recent studies in several fungal species have identified a chromatin - based regulation of secondary metabolism ( SM ) gene clusters representing an upper - hierarchical level for the coordinated control of large chromosomal elements.", "output": "There is no related enetity." }, { "input": "Regulation by chromatin transition processes provides a mechanistic model to explain how different SM clusters located at dispersed genomic regions can be simultaneously silenced during primary metabolism.", "output": "There is no related enetity." }, { "input": "Activation of SM clusters has been shown to be associated with increased acetylation of histones H3 and H4 and, consequently, inhibition of histone de - acetylase activities also leads to increased production of secondary metabolites.", "output": "There is no related enetity." }, { "input": "New findings suggest that SM clusters are silenced by heterochromatic histone marks and that the & quot; closed & quot; heterochromatic structures are reversed during SM activation.", "output": "There is no related enetity." }, { "input": "This process is mediated by the conserved activator of SM, LaeA.", "output": "There is no related enetity." }, { "input": "Despite the increase in knowledge about these processes, much remains to be learned from chromatin - level regulation of SM.", "output": "There is no related enetity." }, { "input": "For example, which proteins & quot; position & quot; the chromatin restructuring signal onto SM clusters or how exactly LaeA works to mediate the low level of heterochromatic marks inside different clusters remain open questions.", "output": "There is no related enetity." }, { "input": "Answers to these and other chromatin - related questions would certainly complete our understanding of SM gene regulation and signaling and, because for many predicted SM clusters corresponding products have not been identified so far, anti - silencing strategies would open new ways for the identification of novel bioactive substances.", "output": "There is no related enetity." }, { "input": "Conservation of POPs, the plant organellar DNA polymerases, in eukaryotes.", "output": "There is no related enetity." }, { "input": "POPs, plant organellar DNA polymerases, have been isolated from various photosynthetic eukaryotes.", "output": "There is no related enetity." }, { "input": "Previously, we purified the native POP of Cyanidioschyzon merolae ( CmPOP ) from whole cellular extracts and showed that CmPOP has DNA polymerase activity with a high processivity and a 3 ' - 5 ' exonuclease activity, and its expression is related to cell proliferation.", "output": "Cyanidioschyzon merolae." }, { "input": "In rice, the recombinant protein of POP has activities found in CmPOP, and high fidelity of POP has also been demonstrated.", "output": "rice." }, { "input": "These facts suggest that POPs are involved in the replication of organellar genomes.", "output": "There is no related enetity." }, { "input": "POPs are also conserved in most non - opisthokont eukaryotes, which lack DNA polymerase gamma ( Polgamma ), a mitochondrial replication enzyme in opisthokonts ( fungi and animals ).", "output": "There is no related enetity." }, { "input": "The ciliate Tetrahymena thermophila contains a single gene for a putative POP ( TetPOP ).", "output": "Tetrahymena thermophila." }, { "input": "Immunoblot analysis demonstrated that TetPOP is localized in mitochondria, and TetPOP has been purified from mitochondria through a column chromatography series.", "output": "There is no related enetity." }, { "input": "Sensitivity to phosphonoacetate and dideoxyTTP was examined in POPs ( TetPOP and CmPOP ) or POP - containing organelles ( chloroplasts of Arabidopsis ) and other polymerases ( DNA polymerase I and mitochondria of rat liver, which contain Polgamma ), and the results suggest that high sensitivity to phosphonoacetate is unique to POPs in Family - A DNA polymerases.", "output": "Arabidopsis, rat." }, { "input": "Finally, we propose a model for the succession of organellar DNA polymerases.", "output": "There is no related enetity." }, { "input": "Identification of a mastigoneme protein from Phytophthora nicotianae.", "output": "Phytophthora nicotianae." }, { "input": "Tripartite tubular hairs ( mastigonemes ) on the anterior flagellum of protists in the stramenopile taxon are responsible for reversing the thrust of flagellar beat and for cell motility.", "output": "There is no related enetity." }, { "input": "Immunoprecipitation experiments using antibodies directed towards mastigonemes on the flagella of zoospores of Phytophthora nicotianae have facilitated the cloning of a gene encoding a mastigoneme shaft protein in this Oomycete.", "output": "Phytophthora nicotianae." }, { "input": "Expression of the gene, designated PnMas2, is up - regulated during asexual sporulation, a period during which many zoospore components are synthesized.", "output": "There is no related enetity." }, { "input": "Analysis of the sequence of the PnMas2 protein has revealed that, like other stramenopile mastigoneme proteins, PnMas2 has an N - terminal secretion signal and contains four cysteine - rich epidermal growth factor ( EGF ) - like domains.", "output": "There is no related enetity." }, { "input": "Evidence from non - denaturing gels indicates that PnMas2 forms large oligomeric complexes, most likely through disulphide bridging.", "output": "There is no related enetity." }, { "input": "Bioinformatic analysis has revealed that Phytophthora species typically contain three or four putative mastigoneme proteins containing the four EGF - like domains.", "output": "There is no related enetity." }, { "input": "These proteins are similar in sequence to mastigoneme proteins in other stramenopile protists including the algae Ochromonas danica, Aureococcus anophagefferens and Scytosiphon lomentaria and the diatoms Thalassiosira pseudonana and T. weissflogii.", "output": "Ochromonas danica, Aureococcus anophagefferens, Scytosiphon lomentaria, Thalassiosira pseudonana, T . weissflogii." }, { "input": "Prasinoderma singularis sp. nov.", "output": "There is no related enetity." }, { "input": "( Prasinophyceae, Chlorophyta ), a solitary coccoid Prasinophyte from the South - East Pacific Ocean.", "output": "There is no related enetity." }, { "input": "During the BIOSOPE cruise in the South - East Pacific Ocean in 2004, several unidentified strains of prasinophytes were isolated into culture.", "output": "There is no related enetity." }, { "input": "Of these, nine strains composed a group for which the partial 18S rRNA gene sequence was related to Prasinoderma coloniale.", "output": "Prasinoderma coloniale." }, { "input": "The ultrastructure, morphology, division process, pigment composition, genome size and molecular genetic phylogeny of these nine strains were investigated, using P. coloniale as a reference.", "output": "P . coloniale." }, { "input": "The 18S rRNA gene sequence of P. singularis sp. nov.", "output": "There is no related enetity." }, { "input": "shares only 96. 9 % of identity with that of P. coloniale and contains a conserved insertion of 567bp length not recorded in P. coloniale.", "output": "P . coloniale, P . coloniale." }, { "input": "When compared to P. coloniale, P. singularis sp. nov.", "output": "P . coloniale." }, { "input": "is morphologically characterized by the absence of colonies, smaller cells with a thinner cell wall, and a second cell type with a different cell covering.", "output": "There is no related enetity." }, { "input": "Dependence between volumes of protoplast and lorica in lugol - fixed tintinnid ciliates.", "output": "There is no related enetity." }, { "input": "The relationship between the volume of tintinnid loricae and protoplasts was studied on the basis of bulk data derived from samples collected in a range of temperate environments: riverine, lacustrine, estuarine, and marine.", "output": "There is no related enetity." }, { "input": "All organisms were fixed with acid Lugol solution ( 0. 5 - 1. 0 % ).", "output": "There is no related enetity." }, { "input": "The dependence was described with the allometric equation: VL = 2. 74xVP ( 1. 03 ), where VL and VP are volumes [ mum ( 3 ) ] of loricae and protoplasts, respectively.", "output": "There is no related enetity." }, { "input": "The dependence was highly significant ( p & lt; 0. 001, n = 417, R ( 2 ) = 0. 85 ).", "output": "There is no related enetity." }, { "input": "On average, protoplasts occupied 31 % of the lorica volume.", "output": "There is no related enetity." }, { "input": "One species, Helicostomella subulata, was omitted from the calculations and treated separately since this ciliate has a relatively large lorica.", "output": "There is no related enetity." }, { "input": "The relationship identified between lorica and protoplast volumes permits recalculating incomplete data if protoplasts are the only body part measured.", "output": "There is no related enetity." }, { "input": "PRP8 intein in Ajellomycetaceae family pathogens: sequence analysis, splicing evaluation and homing endonuclease activity.", "output": "There is no related enetity." }, { "input": "Inteins are intervening sequences that are transcribed and translated with flanking host protein sequences and then self - excised by protein splicing.", "output": "There is no related enetity." }, { "input": "Bi - functional inteins also contain a homing endonuclease responsible for their genetic mobility.", "output": "There is no related enetity." }, { "input": "The PRP8 intein, the most widespread among fungi, occurs in important pathogens such as Histoplasma capsulatum and Paracoccidioides brasiliensis, from the Ajellomycetaceae family.", "output": "Histoplasma capsulatum, Paracoccidioides brasiliensis." }, { "input": "Herein, we describe the bi - functional PRP8 intein in two other Ajellomycetacean pathogens, Blastomyces dermatitidis and Emmonsia parva.", "output": "Blastomyces dermatitidis, Emmonsia parva." }, { "input": "Sequence analysis and experimental evidence suggest that the homing endonuclease from PbrPRP8 is inactive.", "output": "There is no related enetity." }, { "input": "The splicing activity of the PRP8 intein from the B. dermatitidis, E. parva and P. brasiliensis species complex was demonstrated in a non - native protein context in Escherichia coli.", "output": "B . dermatitidis, E . parva, P . brasiliensis species complex, Escherichia coli." }, { "input": "Since the PRP8 intein is located in a functionally essential nuclear protein, it can be considered a promising therapeutic target for anti - fungal drugs, because inhibition of intein splicing should inhibit proliferation of intein - containing pathogens.", "output": "There is no related enetity." }, { "input": "Barcoding Tetrahymena: discriminating species and identifying unknowns using the cytochrome c oxidase subunit I ( cox - 1 ) barcode.", "output": "There is no related enetity." }, { "input": "DNA barcoding using the mitochondrial cytochromecoxidase subunit I ( cox - 1 ) gene has recently gained popularity as a tool for species identification of a variety of taxa.", "output": "There is no related enetity." }, { "input": "The primary objective of our research was to explore the efficacy of using cox - 1 barcoding for species identification within the genus Tetrahymena.", "output": "There is no related enetity." }, { "input": "We first increased intraspecific sampling for Tetrahymena canadensis, Tetrahymena hegewischi, Tetrahymena pyriformis, Tetrahymena rostrata, Tetrahymena thermophila, and Tetrahymena tropicalis.", "output": "Tetrahymena canadensis, Tetrahymena hegewischi, Tetrahymena pyriformis, Tetrahymena rostrata, Tetrahymena thermophila, Tetrahymena tropicalis." }, { "input": "Increased sampling efforts show that intraspecific sequence divergence is typically less than 1 %, though it may be more in some species.", "output": "There is no related enetity." }, { "input": "The barcoding also showed that some strains might be misidentified or mislabeled.", "output": "There is no related enetity." }, { "input": "We also used cox - 1 barcodes to provide species identifications for 51 unidentified environmental isolates, with a success rate of 98 %.", "output": "There is no related enetity." }, { "input": "Thus, cox - 1 barcoding is an invaluable tool for protistologists, especially when used in conjunction with morphological studies.", "output": "There is no related enetity." }, { "input": "Facing unknowns: living cultures ( Pirum gemmata gen. nov., sp. nov., and Abeoforma whisleri, gen. nov., sp. nov. ) from invertebrate digestive tracts represent an undescribed clade within the unicellular Opisthokont lineage ichthyosporea ( Mesomycetozoea ).", "output": "Pirum gemmata gen . nov . , sp . nov ., Abeoforma whisleri , gen . nov . , sp . nov .." }, { "input": "During a culture - based survey of opisthokonts living in marine invertebrate digestive tracts, we isolated two new eukaryotes that differed from described taxa by more than 10 % in their small subunit ribosomal DNA sequences.", "output": "There is no related enetity." }, { "input": "Phylogenetic analysis showed that the two isolates represented a divergent clade of ichthyosporeans known previously only from environmental clone sequences.", "output": "There is no related enetity." }, { "input": "We used light and electron microscopy to describe the isolates as new genera and species Pirum gemmata and Abeoforma whisleri.", "output": "Pirum gemmata, Abeoforma whisleri." }, { "input": "A. whisleri had a complex life cycle that remains incompletely known but involved walled spherical cells, plasmodia and amoebae.", "output": "A . whisleri." }, { "input": "Asexual reproduction occurred via dispersal amoebae, endospores, binary fission and budding.", "output": "There is no related enetity." }, { "input": "In contrast P. gemmata had a less complex life cycle with no amoeboid or plasmodial stages.", "output": "P . gemmata." }, { "input": "Both species had membrane - bound tubular extensions of the cytoplasm embedded in the inner layers of their cell walls.", "output": "There is no related enetity." }, { "input": "By comparing P. gemmata and A. whisleri to other ichthyosporea we speculate on the characters that may have been present in the ancestral ichthyosporean.", "output": "P . gemmata, A . whisleri." }, { "input": "P. gemmata and A. whisleri illustrate the unique and diverse forms that can be found by capturing taxa belonging to divergent and uncultured lineages.", "output": "P . gemmata, A . whisleri." }, { "input": "Does climate warming stimulate or inhibit soil protist communities?", "output": "There is no related enetity." }, { "input": "A test on testate amoebae in high - arctic tundra with free - air temperature increase.", "output": "There is no related enetity." }, { "input": "Soil testate amoebae assemblages in a grassland area at Zackenberg ( Northeast Greenland ) were subjected to simulated climate - warming during the growing season using the Free - Air Temperature Increase technique.", "output": "There is no related enetity." }, { "input": "Samples were collected in upper ( 0 - 3cm ) and deeper ( 3 - 6cm ) soil horizons.", "output": "There is no related enetity." }, { "input": "Mean temperature elevations at 2. 5 and 7. 5 cm depth were 2. 58 + / - SD 1. 11 and 2. 13 + / - SD 0. 77 ^ 0C, respectively, and did not differ significantly.", "output": "There is no related enetity." }, { "input": "Soil moisture in the top 11cm was not affected by the warming.", "output": "There is no related enetity." }, { "input": "During the manipulation, the densities of living amoebae and empty shells were higher in the experimental plots but only in the upper layer.", "output": "There is no related enetity." }, { "input": "Possibly, testate amoebae in the deeper layer were limited by other factors, suggesting that warming enhances the carrying capacity only in favourable conditions.", "output": "There is no related enetity." }, { "input": "Species richness, on the other hand, was only increased in the deeper horizon.", "output": "There is no related enetity." }, { "input": "Warming did not change the percentage of individuals belonging to small - sized species in any of the living assemblages, contrary to our expectation that those species would quickly increase their density.", "output": "There is no related enetity." }, { "input": "However, in the empty shell assemblages, the proportion of small - sized individuals in the experimental plots was higher in both layers, indicating a rapid, transient increase in small amoebae before the first sampling date.", "output": "There is no related enetity." }, { "input": "Changes in successional state of testate amoebae assemblages in response to future climate change might thus be ephemeral, whereas alterations in density and species richness might be more sustained.", "output": "There is no related enetity." }, { "input": "Characterization of the Aspergillus nidulans biotin biosynthetic gene cluster and use of the bioDA gene as a new transformation marker.", "output": "Aspergillus nidulans." }, { "input": "The genes involved in the biosynthesis of biotin were identified in the hyphal fungus Aspergillus nidulans through homology searches and complementation of Escherichia coli biotin - auxotrophic mutants.", "output": "Aspergillus nidulans, Escherichia coli." }, { "input": "Whereas the 7, 8 - diaminopelargonic acid synthase and dethiobiotin synthetase are encoded by distinct genes in bacteria and the yeast Saccharomyces cerevisiae, both activities are performed in A. nidulans by a single enzyme, encoded by the bifunctional gene bioDA.", "output": "yeast, Saccharomyces cerevisiae, A . nidulans." }, { "input": "Such a bifunctional bioDA gene is a genetic feature common to numerous members of the ascomycete filamentous fungi and basidiomycetes, as well as in plants and oomycota.", "output": "There is no related enetity." }, { "input": "However, unlike in other eukaryota, the three bio genes contributing to the four enzymatic steps from pimeloyl - CoA to biotin are organized in a gene cluster in pezizomycotina.", "output": "There is no related enetity." }, { "input": "The A. nidulans auxotrophic mutants biA1, biA2 and biA3 were all found to have mutations in the 7, 8 - diaminopelargonic acid synthase domain of the bioDA gene.", "output": "A . nidulans." }, { "input": "Although biotin auxotrophy is an inconvenient marker in classical genetic manipulations due to cross - feeding of biotin, transformation of the biA1 mutant with the bioDA gene from either A. nidulans or Aspergillus fumigatus led to the recovery of well - defined biotin - prototrophic colonies.", "output": "A . nidulans, Aspergillus fumigatus." }, { "input": "The usefulness of bioDA gene as a novel and robust transformation marker was demonstrated in co - transformation experiments with a green fluorescent protein reporter, and in the efficient deletion of the laccase ( yA ) gene via homologous recombination in a mutant lacking non - homologous end - joining activity.", "output": "There is no related enetity." }, { "input": "Regulation of virulence factors, carbon utilization and virulence by SNF1 in Cryptococcus neoformans JEC21 and divergent actions of SNF1 between cryptococcal strains.", "output": "Cryptococcus neoformans JEC21." }, { "input": "We describe here the functions of a Snf1 / AMPK homolog in the human pathogenic yeast Cryptococcus neoformans, strain JEC21.", "output": "JEC21." }, { "input": "We found that JEC21 SNF1 is a key regulator for the biosynthesis of the major virulence factors, stress resistance and alternative carbon source utilization.", "output": "JEC21." }, { "input": "Disruption of JEC21 SNF1 results in defects of laccase activity and capsule production, sensitivity to cation stress.", "output": "JEC21." }, { "input": "Especially, we found that JEC21 SNF1 is essential for growth at elevated temperature and for thermotolerance.", "output": "JEC21." }, { "input": "To our knowledge, a role for Snf1 proteins in thermotolerance has not been reported.", "output": "There is no related enetity." }, { "input": "Furthermore, we observed a functional divergence between JEC21 SNF1 and its equivalent from serotype A strain H99.", "output": "H99." }, { "input": "A high temperature is needed for H99 SNF1 to function in stress response and carbon source preference, but not for the JEC21 SNF1.", "output": "H99, JEC21." }, { "input": "Our results confirmed a critical role of JEC21 SNF1 in regulation of stress response and virulence.", "output": "JEC21." }, { "input": "Revelation of divergent actions of SNF1 may help to understand the evolution of cryptococcal pathogenesis and provides insights into the strain - associated biosynthesis of virulence factors.", "output": "There is no related enetity." }, { "input": "Gout therapeutics: new drugs for an old disease.", "output": "There is no related enetity." }, { "input": "The approval of febuxostat, a non - purine - analogue inhibitor of xanthine oxidase, by the European Medicines Agency and the US Food and Drug Administration heralds a new era in the treatment of gout.", "output": "There is no related enetity." }, { "input": "The use of modified uricases to rapidly reduce serum urate concentrations in patients with otherwise untreatable gout is progressing.", "output": "There is no related enetity." }, { "input": "Additionally, advances in our understanding of the transport of uric acid in the renal proximal tubule and the inflammatory response to monosodium urate crystals are translating into potential new treatments.", "output": "There is no related enetity." }, { "input": "In this Review, we focus on the clinical trials of febuxostat.", "output": "There is no related enetity." }, { "input": "We also review results from studies of pegloticase, a pegylated uricase in development, and we summarise data for several other pipeline drugs for gout, such as the selective uricosuric drug RDEA594 and various interleukin - 1 inhibitors.", "output": "There is no related enetity." }, { "input": "Finally, we issue a word of caution about the proper use of the new drugs and the already available drugs for gout.", "output": "There is no related enetity." }, { "input": "At a time of important advances, we need to recommit ourselves to a rational approach to the treatment of gout.", "output": "There is no related enetity." }, { "input": "Carry - over effects as drivers of fitness differences in animals.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Carry - over effects occur when processes in one season influence the success of an individual in the following season.", "output": "There is no related enetity." }, { "input": "This phenomenon has the potential to explain a large amount of variation in individual fitness, but so far has only been described in a limited number of species.", "output": "There is no related enetity." }, { "input": "This is largely due to difficulties associated with tracking individuals between periods of the annual cycle, but also because of a lack of research specifically designed to examine hypotheses related to carry - over effects.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We review the known mechanisms that drive carry - over effects, most notably macronutrient supply, and highlight the types of life histories and ecological situations where we would expect them to most often occur.", "output": "There is no related enetity." }, { "input": "We also identify a number of other potential mechanisms that require investigation, including micronutrients such as antioxidants.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We propose a series of experiments designed to estimate the relative contributions of extrinsic and intrinsic quality effects in the pre - breeding season, which in turn will allow an accurate estimation of the magnitude of carry - over effects.", "output": "There is no related enetity." }, { "input": "To date this has proven immensely difficult, and we hope that the experimental frameworks described here will stimulate new avenues of research vital to advancing our understanding of how carry - over effects can shape animal life histories.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "We also explore the potential of state - dependent modelling as a tool for investigating carry - over effects, most notably for its ability to calculate optimal rates of acquisition of a multitude of resources over the course of the annual cycle, and also because it allows us to vary the strength of density - dependent relationships which can alter the magnitude of carry - over effects in either a synergistic or agonistic fashion.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "In conclusion carry - over effects are likely to be far more widespread than currently indicated, and they are likely to be driven by a multitude of factors including both macro - and micronutrients.", "output": "There is no related enetity." }, { "input": "For this reason they could feasibly be responsible for a large amount of the observed variation in performance among individuals, and consequently warrant a wealth of new research designed specifically to decompose components of variation in fitness attributes related to processes across and within seasons.", "output": "There is no related enetity." }, { "input": "General factors important for the formation of structured biofilm - like yeast colonies.", "output": "yeast." }, { "input": "The lifestyle of wild and laboratory yeast strains significantly differs.", "output": "yeast." }, { "input": "In contrast to the smooth colonies of laboratory strains, wild Saccharomyces cerevisiae strains form biofilm - like, strikingly structured colonies possessing distinctive traits enabling them to better survive in hostile environments in the wild.", "output": "Saccharomyces cerevisiae." }, { "input": "Here, comparing three sets of strains forming differently structured colonies ( fluffy, semi - fluffy and smooth ), each derived from ancestors with distinct genetic backgrounds isolated from natural settings ( BR - 88, BR - 99 and BR - 103 ), we specified the factors essential for the formation of structured colonies, i. e. for the lifestyle most likely to be preferred in the wild.", "output": "There is no related enetity." }, { "input": "The ability to form an abundant extracellular matrix ( ECM ) is one of the features typical for structured colonies.", "output": "There is no related enetity." }, { "input": "ECM influences colony architecture and many other physiological properties, such as the capability to retain water in a 2 - fold surplus to wet cell biomass.", "output": "There is no related enetity." }, { "input": "ECM composition, however, differs among distinct strains, depending on their particular genetic background.", "output": "There is no related enetity." }, { "input": "We further show that the expression of certain genes ( AQY1, FLO11 ) is also strictly related to the particular colony morphology, being highest in the most structured colonies.", "output": "There is no related enetity." }, { "input": "Flo11p adhesin, important for cell - cell and cell - surface adhesion, is essential for the formation of fluffy colonies and thus significantly contributes to the phenotype variability of wild yeast strains.", "output": "yeast." }, { "input": "On the other hand, surprisingly, neither the cell shape nor budding pattern nor the ability to form pseudohyphae directly influences the formation of three - dimensional fluffy colony architecture.", "output": "There is no related enetity." }, { "input": "Parallel evolution of cytochrome b mediated bifenazate resistance in the citrus red mite Panonychus citri.", "output": "citrus red mite, Panonychus citri." }, { "input": "Bifenazate is a recently developed acaricide that is mainly used to control spider mites on a variety of crops.", "output": "There is no related enetity." }, { "input": "Although first thought to be a neurotoxin, genetic evidence obtained from bifenazate resistant Tetranychus urticae strains suggested an alternative mode of action as a Qo pocket inhibitor of the mitochondrial complex III.", "output": "Tetranychus urticae." }, { "input": "In this study, we reveal how bifenazate resistance in strains of Panonychus citri is maternally inherited and can confer cross - resistance to the known Qo inhibitor acequinocyl.", "output": "Panonychus citri." }, { "input": "The mitochondrial genome of P. citri was sequenced and Qo pocket mutations were shown to be linked with the resistant trait.", "output": "P . citri." }, { "input": "Parallel evolution of cytochrome b mediated bifenazate resistance corroborates the alternative mode of action and yet again illustrates that care should be taken when employing Qo inhibitors as crop protection compounds.", "output": "There is no related enetity." }, { "input": "Wildlife diseases: from individuals to ecosystems.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "We review our ecological understanding of wildlife infectious diseases from the individual host to the ecosystem scale, highlighting where conceptual thinking lacks verification, discussing difficulties and challenges, and offering potential future research directions.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "New molecular approaches hold potential to increase our understanding of parasite interactions within hosts.", "output": "There is no related enetity." }, { "input": "Also, advances in our knowledge of immune systems makes immunological parameters viable measures of parasite exposure, and useful tools for improving our understanding of causal mechanisms.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Studies of transmission dynamics have revealed the importance of heterogeneity in host behaviour and physiology, and of contact processes operating at different spatial and temporal scales.", "output": "There is no related enetity." }, { "input": "An important future challenge is to determine the key transmission mechanisms maintaining the persistence of different types of diseases in the wild.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Regulation of host populations is too complex to consider parasite effects in isolation from other factors.", "output": "There is no related enetity." }, { "input": "One solution is to seek a unified understanding of the conditions under which ( and the ecological rules determining when ) population scale impacts of parasites can occur.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Good evidence now shows that both direct effects of parasites, and trait mediated indirect effects, frequently mediate the success of invasive species and their impacts on recipient communities.", "output": "There is no related enetity." }, { "input": "A wider exploration of these effects is now needed.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "At the ecosystem scale, research is needed to characterize the circumstances and conditions under which both fluxes in parasite biomass, and trait mediated effects, are significant in ecosystem processes, and to demonstrate that parasites do indeed increase ' ecosystem health '.", "output": "There is no related enetity." }, { "input": "7.", "output": "There is no related enetity." }, { "input": "There is a general need for more empirical testing of predictions and subsequent development of theory in the classic research cycle.", "output": "There is no related enetity." }, { "input": "Experimental field studies, meta - analyses, the collection and analysis of long - term data sets, and data constrained modelling, will all be key to advancing our understanding.", "output": "There is no related enetity." }, { "input": "8.", "output": "There is no related enetity." }, { "input": "Finally, we are only now beginning to understand the importance of cross - scale interactions associated with parasitism.", "output": "There is no related enetity." }, { "input": "Such interactions may offer key insights into bigger picture questions such as when and how different regulatory factors are important, when disease can cause species extinctions, and what characteristics are indicative of functionally resilient ecosystems.", "output": "There is no related enetity." }, { "input": "Can we predict indirect interactions from quantitative food webs? - - an experimental approach.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Shared enemies may link the dynamics of their prey.", "output": "There is no related enetity." }, { "input": "Recently, quantitative food webs have been used to infer that herbivorous insect species attacked by the same major parasitoid species will affect each other negatively through apparent competition.", "output": "There is no related enetity." }, { "input": "Nonetheless, theoretical work predicts several alternative outcomes, including positive effects.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "In this paper, we use an experimental approach to link food web patterns to realized population dynamics.", "output": "There is no related enetity." }, { "input": "First, we construct a quantitative food web for three dominant leaf miner species on the oak Quercus robur.", "output": "Quercus robur." }, { "input": "We then measure short - and long - term indirect effects by increasing leaf miner densities on individual trees.", "output": "There is no related enetity." }, { "input": "Finally, we test whether experimental results are consistent with natural leaf miner dynamics on unmanipulated trees.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "The quantitative food web shows that all leaf miner species share a minimum of four parasitoid species.", "output": "There is no related enetity." }, { "input": "While only a small fraction of the parasitoid pool is shared among Tischeria ekebladella and each of two Phyllonorycter species, the parasitoid communities of the congeneric Phyllonorycter species overlap substantially.", "output": "Tischeria ekebladella." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Based on the structure of the food web, we predict strong short - and long - term indirect interactions between the Phyllonorycter species, and limited interactions between them and T. ekebladella.", "output": "T . ekebladella." }, { "input": "As T. ekebladella is the main source of its own parasitoids, we expect to find intraspecific density - dependent parasitism in this species.", "output": "T . ekebladella." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Consistent with these predictions, parasitism in T. ekebladella was high on trees with high densities of conspecifics in the previous generation.", "output": "T . ekebladella." }, { "input": "Among leaf miner species sharing more parasitoids, we found positive rather than negative interactions among years.", "output": "There is no related enetity." }, { "input": "No short - term indirect interactions ( i. e. indirect interactions within a single generation ) were detected.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "Overall, this study is the first to experimentally demonstrate that herbivores with overlapping parasitoid communities may exhibit independent population dynamics - or even apparent mutualism.", "output": "There is no related enetity." }, { "input": "Hence, it proves the potential for versatile indirect interactions in nature, and suggests that the link between patterns in food web structure and realized population dynamics should be verified by rigorous experiments.", "output": "There is no related enetity." }, { "input": "Comparison of transcriptional and translational changes caused by long - term menadione exposure in Aspergillus nidulans.", "output": "Aspergillus nidulans." }, { "input": "Under long - term oxidative stress caused by menadione sodium bisulfite, genome - wide transcriptional and proteome - wide translational changes were compared in Aspergillus nidulans vegetative cells.", "output": "Aspergillus nidulans." }, { "input": "The comparison of proteomic and DNA microarray expression data demonstrated that global gene expression changes recorded with either flip - flop or dendrimer cDNA labeling techniques supported proteome changes moderately with 40 % and 34 % coincidence coefficients, respectively.", "output": "There is no related enetity." }, { "input": "Enzyme levels in the glycolytic pathway were alternating, which was a direct consequence of fluctuating gene expression patterns.", "output": "There is no related enetity." }, { "input": "Surprisingly, enzymes in the vitamin B2 and B6 biosynthetic pathways were repressed concomitantly with the repression of some protein folding chaperones and nuclear transport elements.", "output": "There is no related enetity." }, { "input": "Under long - term oxidative stress, the peroxide - detoxifying peroxiredoxins and cytochrome c peroxidase were replaced by thioredoxin reductase, a nitroreductase and a flavohemoprotein, and protein degradation became predominant to eliminate damaged proteins.", "output": "There is no related enetity." }, { "input": "Contrasting impacts of climate - driven flowering phenology on changes in alien and native plant species distributions.", "output": "There is no related enetity." }, { "input": "* Plant phenology is particularly sensitive to climate and a key indicator of environmental change.", "output": "There is no related enetity." }, { "input": "Globally, first flowering dates ( FFDs ) have advanced by several days per decade in response to recent climate warming, but, while earlier flowering should allow plant distributions to increase, a link between FFD and range changes has not been observed.", "output": "There is no related enetity." }, { "input": "* Here I show for 347 species that the extent to which FFD has responded to climate warming is linked to the degree to which their relative distributions have changed over 30 yr across the British Isles.", "output": "There is no related enetity." }, { "input": "* Native plant species whose phenology did not track climate change declined in distribution, whereas species that became more widespread all exhibited earlier flowering.", "output": "There is no related enetity." }, { "input": "In contrast, alien neophytes showed both a stronger phenological response to warming and a more marked increase in distribution, but no link between the two.", "output": "There is no related enetity." }, { "input": "* These trends were consistent both for relative changes in the national distribution and for local abundance.", "output": "There is no related enetity." }, { "input": "At the national scale, the more recently an alien species became established in Britain, the more likely it was to increase in distribution irrespective of FFD, suggesting that recent changes in alien species distributions are decoupled from climate and driven by other factors.", "output": "There is no related enetity." }, { "input": "A root is a root is a root?", "output": "There is no related enetity." }, { "input": "Water uptake rates of Citrus root orders.", "output": "There is no related enetity." }, { "input": "Knowledge about the physiological function of root orders is scant.", "output": "There is no related enetity." }, { "input": "In this study, a system to monitor the water flux among root orders was developed using miniaturized chambers.", "output": "There is no related enetity." }, { "input": "Different root orders of 4 - year - old Citrus volkameriana trees were analysed with respect to root morphology and water flux.", "output": "Citrus volkameriana." }, { "input": "The eight root orders showed a broad overlap in diameter, but differences in tissue densities and specific root area ( SRA ) were clearly distinguishable.", "output": "There is no related enetity." }, { "input": "Thirty per cent of the root branch biomass but 50 % of the surface area ( SA ) was possessed by the first root order, while the fifth accounted for 5 % of the SA ( 20 % biomass ).", "output": "There is no related enetity." }, { "input": "The root order was identified as a determinant of water flux.", "output": "There is no related enetity." }, { "input": "First - order roots showed a significantly higher rate of water uptake than the second and third root orders, whereas the fourth and fifth root orders showed water excess.", "output": "There is no related enetity." }, { "input": "The water excess suggested the occurrence of hydraulic redistribution ( HR ) as a result of differences in osmotic potentials.", "output": "There is no related enetity." }, { "input": "We suggest that plants may utilize hydraulic redistribution to prevent coarse root desiccation and / or to increase nutrient acquisition.", "output": "There is no related enetity." }, { "input": "Our study showed that the novel ' miniature depletion chamber ' method enabled direct measurement of water fluxes per root order and can be a major tool for future studies on root order traits.", "output": "There is no related enetity." }, { "input": "Increased intracellular H2O2 availability preferentially drives glutathione accumulation in vacuoles and chloroplasts.", "output": "There is no related enetity." }, { "input": "One biochemical response to increased H2O2 availability is the accumulation of glutathione disulphide ( GSSG ), the disulphide form of the key redox buffer glutathione.", "output": "There is no related enetity." }, { "input": "It remains unclear how this potentially important oxidative stress response impacts on the different sub - cellular glutathione pools.", "output": "There is no related enetity." }, { "input": "We addressed this question by using two independent in situ glutathione labelling techniques in Arabidopsis wild type ( Col - 0 ) and the GSSG - accumulating cat2 mutant.", "output": "There is no related enetity." }, { "input": "A comparison of in situ labelling with monochlorobimane ( MCB ) and in vitro labelling with monobromobimane ( MBB ) revealed that, whereas in situ labelling of Col - 0 leaf glutathione was complete within 2 h incubation, about 50 % of leaf glutathione remained inaccessible to MCB in cat2.", "output": "There is no related enetity." }, { "input": "High - performance liquid chromatography ( HPLC ) and enzymatic assays showed that this correlated tightly with the glutathione redox state, pointing to significant in vivo pools of GSSG in cat2 that were unavailable for MCB labelling.", "output": "There is no related enetity." }, { "input": "Immunogold labelling of leaf sections to estimate sub - cellular glutathione distribution showed that the accumulated GSSG in cat2 was associated with only a minor increase in cytosolic glutathione but with a 3 - and 10 - fold increase in plastid and vacuolar pools, respectively.", "output": "There is no related enetity." }, { "input": "The data are used to estimate compartment - specific glutathione concentrations under optimal and oxidative stress conditions, and the implications for redox homeostasis and signalling are discussed.", "output": "There is no related enetity." }, { "input": "Fungal secondary metabolites as modulators of interactions with insects and other arthropods.", "output": "There is no related enetity." }, { "input": "Fungi share a diverse co - evolutionary history with animals, especially arthropods.", "output": "There is no related enetity." }, { "input": "In this review, we focus on the role of secondary metabolism in driving antagonistic arthropod - fungus interactions, i. e., where fungi serve as a food source to fungal grazers, compete with saprophagous insects, and attack insects as hosts for growth and reproduction.", "output": "There is no related enetity." }, { "input": "Although a wealth of studies on animal - fungus interactions point to a crucial role of secondary metabolites in deterring animal feeding and resisting immune defense strategies, causal evidence often remains to be provided.", "output": "There is no related enetity." }, { "input": "Moreover, it still remains an unresolved puzzle as to what extent the tight regulatory control of secondary metabolite formation in some model fungi represents an evolved chemical defense system favored by selective pressure through animal antagonists.", "output": "There is no related enetity." }, { "input": "Given these gaps in knowledge, we highlight some co - evolutionary aspects of secondary metabolism, such as induced response, volatile signaling, and experimental evolution, which may help in deciphering the ecological importance and evolutionary history of secondary metabolite production in fungi.", "output": "There is no related enetity." }, { "input": "A multispecies perspective on ecological impacts of climatic forcing.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "In the prevailing context of concerns over climate change and its potential impacts on ecosystems, evaluating ecological consequences of climatic forcing has become a critical issue.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Historical data on the abundance of organisms have been extensively used to characterize the ecological effects of climatic forcing through specific weather and / or climatic variables, with most of the studies confined to single population models.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "However, population responses to environmental fluctuations typically depend upon positive and negative feedbacks induced by interactions with other species.", "output": "There is no related enetity." }, { "input": "It is therefore important to integrate the insights gained from single population approaches into a multispecies perspective.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Here we combine the hierarchical Bayesian modelling approach with the state - space formulation to extend the scope of previously proposed models of population dynamics under climatic forcing to multi - species systems.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "We use our model to analyse long - term macro - moth ( Lepidoptera ) community data from the Rothamsted Insect Survey network in the UK, using winter rainfall and winter temperature as environmental covariates.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "The effects of the two weather variables were consistent across species, being negative for winter rainfall and positive for winter temperature.", "output": "There is no related enetity." }, { "input": "The two weather variables jointly explained 15 - 40 % of the total environmental variation affecting the dynamics of individual species, and could explain up to 90 % of covariances in species dynamics.", "output": "There is no related enetity." }, { "input": "7.", "output": "There is no related enetity." }, { "input": "The contribution of interspecific interactions to community - level variation was found to be weak compared to the contributions of environmental forcing and intraspecific interactions.", "output": "There is no related enetity." }, { "input": "Cross - talk between light and glucose regulation controls toxin production and morphogenesis in Aspergillus nidulans.", "output": "Aspergillus nidulans." }, { "input": "Light is a major environmental stimulus that has a broad effect on organisms, triggering a cellular response that results in an optimal adaptation enhancing fitness and survival.", "output": "There is no related enetity." }, { "input": "In fungi, light affects growth, and causes diverse morphological changes such as those leading to reproduction.", "output": "There is no related enetity." }, { "input": "Light can also affect fungal metabolism, including the biosynthesis of natural products.", "output": "There is no related enetity." }, { "input": "In this study we show that in Aspergillus nidulans the effect of light on the production of the sterigmatocystin ( ST ) toxin depends on the glucose concentration.", "output": "Aspergillus nidulans." }, { "input": "In cultures grown with 1 % glucose and exposed to light, ST production was lower than when grown in the dark.", "output": "There is no related enetity." }, { "input": "This lower ST production coincided with an elevated rate of cellular damage with partial loss of nuclear integrity and vacuolated cytoplasm.", "output": "There is no related enetity." }, { "input": "However, in cultures grown with 2 % glucose these effects were reversed and light enhanced ST production.", "output": "There is no related enetity." }, { "input": "Glucose abundance also affected the light - dependent subcellular localization of the VeA ( velvet ) protein, a key regulator necessary for normal light - dependent morphogenesis and secondary metabolism in Aspergilli and other fungal genera.", "output": "There is no related enetity." }, { "input": "The role of other VeA - associated proteins, particularly the blue - light - sensing proteins LreA and LreB ( WC - 1 and WC - 2 orthologs ), on conidiation could also be modified by the abundance of glucose.", "output": "There is no related enetity." }, { "input": "We also show that LreA and LreB, as well as the phytochrome FphA, modulate not only the synthesis of sterigmatocystin, but also the production of the antibiotic penicillin.", "output": "There is no related enetity." }, { "input": "Characterization of the developmental regulator FlbE in Aspergillus fumigatus and Aspergillus nidulans.", "output": "Aspergillus fumigatus, Aspergillus nidulans." }, { "input": "Several upstream developmental activators control asexual development ( conidiation ) in Aspergillus.", "output": "There is no related enetity." }, { "input": "In this study, we characterize one of such activators called flbE in Aspergillus fumigatus and Aspergillus nidulans.", "output": "Aspergillus fumigatus, Aspergillus nidulans." }, { "input": "The predicted FlbE protein is composed of 222 and 201 aa in A. fumigatus and A. nidulans, respectively.", "output": "A . fumigatus, A . nidulans." }, { "input": "While flbE is transiently expressed during early phase of growth in A. nidulans, it is somewhat constitutively expressed during the lifecycle of A. fumigatus.", "output": "A . nidulans, A . fumigatus." }, { "input": "The deletion of flbE causes reduced conidiation and delayed expression of brlA and vosA in both species.", "output": "There is no related enetity." }, { "input": "Moreover, FlbE is necessary for salt - induced development in liquid submerged culture in A. fumigatus.", "output": "A . fumigatus." }, { "input": "The A. nidulans flbE null mutation is fully complemented by A. fumigatus flbE, indicating a functional conservancy of FlbE in Aspergillus.", "output": "A . nidulans, A . fumigatus." }, { "input": "Both the deletion and overexpression of flbE in A. nidulans result in developmental defects, enhanced autolysis, precocious cell death, and delayed expression of brlA / vosA, suggesting that balanced activity of FlbE is crucial for proper growth and development.", "output": "A . nidulans." }, { "input": "Importantly, the N - terminal portion of FlbE exhibits the trans - activation ability in yeast, whereas the C - terminal half negatively affects its activity.", "output": "yeast." }, { "input": "Site - directed mutagenesis of certain conserved N - terminal amino acids abolishes the ability of trans - activation, overexpression - induced autolysis, and complementing the null mutation.", "output": "There is no related enetity." }, { "input": "Finally, overexpression of flbD, but not flbB or flbC, restores conidiation in A. nidulans DeltaflbE, generally supporting the current genetic model for developmental regulation.", "output": "A . nidulans." }, { "input": "Dinoflagellates associated with freshwater sponges from the ancient lake baikal.", "output": "There is no related enetity." }, { "input": "Dinoflagellates are a diverse group of protists that are common in both marine and freshwater environments.", "output": "There is no related enetity." }, { "input": "While the biology of marine dinoflagellates has been the focus of several recent studies, their freshwater relatives remain little - investigated.", "output": "There is no related enetity." }, { "input": "In the present study we explore the diversity of dinoflagellates in Lake Baikal by identifying and analyzing dinoflagellate sequences for 18S rDNA and ITS - 2 from total DNA extracted from three species of endemic Baikalian sponges ( Baikalospongia intermedia, Baikalospongia recta and Lubomirskia incrustans ).", "output": "Baikalospongia intermedia, Baikalospongia recta, Lubomirskia incrustans." }, { "input": "Phylogenetic analyses of these sequences revealed extensive dinoflagellate diversity in Lake Baikal.", "output": "There is no related enetity." }, { "input": "We found two groups of sequences clustering within the order Suessiales, known for its symbiotic relationships with various invertebrates.", "output": "There is no related enetity." }, { "input": "Thus they may be regarded as potential symbionts of Baikalian sponges.", "output": "There is no related enetity." }, { "input": "In addition, Gyrodinium helveticum, representatives from the genus Gymnodinium, dinoflagellates close to the family Pfiesteriaceae, and a few dinoflagellates without definite affiliation were detected.", "output": "Gyrodinium helveticum." }, { "input": "No pronounced difference in the distribution of dinoflagellates among the studied sponges was found, except for the absence of the Piscinoodinium - like dinoflagellates in L. incrustans.", "output": "There is no related enetity." }, { "input": "To the best of our knowledge, this is the first study of the diversity of dinoflagellates in freshwater sponges, the first systematic investigation of dinoflagellate molecular diversity in Lake Baikal and the first finding of members of the order Suessiales as symbionts of freshwater invertebrates.", "output": "There is no related enetity." }, { "input": "Transcription factors BmPOUM2 and BmBetaFTZ - F1 are involved in regulation of the expression of the wing cuticle protein gene BmWCP4 in the silkworm, Bombyx mori.", "output": "silkworm, Bombyx mori." }, { "input": "In Bombyx mori, the wing cuticle protein gene BmWCP4 is expressed specifically in the epidermis at the onset and mid - stage of pupation and is responsible for the formation of the pupal cuticle during the larval - pupal metamorphosis.", "output": "Bombyx mori." }, { "input": "The gene consists of four exons and three introns and is present as a single copy in the genome.", "output": "There is no related enetity." }, { "input": "Its expression was up - regulated by 20 - hydroxyecdysone ( 20E ) and the 20E - induced expression was suppressed by juvenile hormone ( JH ) III.", "output": "There is no related enetity." }, { "input": "The upstream regulatory sequence region of the BmWCP4 gene was cloned and the regulatory elements responsible for 20E induction were identified.", "output": "There is no related enetity." }, { "input": "Two cis - regulatory elements ( CREs ) bound by the transcription factors BmPOUM2 and BmBetaFTZ - F1 were identified that mediated 20E - regulated expression of this gene.", "output": "There is no related enetity." }, { "input": "An electrophoretic mobility shift assay detected two nuclear proteins isolated from the epidermis and the BmN cell line that specifically bound to the POU and BetaFTZ - F1 CREs, respectively.", "output": "There is no related enetity." }, { "input": "BmPOUM2 recombinant protein explicitly bound to the POU CRE.", "output": "There is no related enetity." }, { "input": "Developmental and 20E - induced expression of the BmWCP4, BmPOUM2 and BmBetaFTZ - F1 genes showed that BmPOUM2 and BmBetaFTZ - F1 were initially expressed, followed by BmWCP4.", "output": "There is no related enetity." }, { "input": "These data suggest that the 20E - induced expression of BmWCP4 is mediated by the transcription factors BmPOUM2 and BmBetaFTZ - F1 binding to their CREs in the regulatory sequence region of the BmWCP4 gene.", "output": "There is no related enetity." }, { "input": "Drought limitation of photosynthesis differs between C3and C4grass species in a comparative experiment.", "output": "There is no related enetity." }, { "input": "Phylogenetic analyses show that C4 grasses typically occupy drier habitats than their C3 relatives, but recent experiments comparing the physiology of closely related C3 and C4 species have shown that advantages of C4 photosynthesis can be lost under drought.", "output": "There is no related enetity." }, { "input": "We tested the generality of these paradoxical findings in grass species representing the known evolutionary diversity of C4 NADP - me and C3 photosynthetic types.", "output": "There is no related enetity." }, { "input": "Our experiment investigated the effects of drought on leaf photosynthesis, water potential, nitrogen, chlorophyll content and mortality.", "output": "There is no related enetity." }, { "input": "C4 grasses in control treatments were characterized by higher CO2 assimilation rates and water potential, but lower stomatal conductance and nitrogen content.", "output": "There is no related enetity." }, { "input": "Under drought, stomatal conductance declined more dramatically in C3 than C4 species, and photosynthetic water - use and nitrogen - use efficiency advantages held by C4 species under control conditions were each diminished by 40 %.", "output": "There is no related enetity." }, { "input": "Leaf mortality was slightly higher in C4 than C3 grasses, but leaf condition under drought otherwise showed no dependence on photosynthetic - type.", "output": "There is no related enetity." }, { "input": "This phylogenetically controlled experiment suggested that a drought - induced reduction in the photosynthetic performance advantages of C4 NADP - me relative to C3 grasses is a general phenomenon.", "output": "There is no related enetity." }, { "input": "OsRAN2, essential for mitosis, enhances cold tolerance in rice by promoting export of intranuclear tubulin and maintaining cell division under cold stress.", "output": "rice." }, { "input": "With global climate change, abnormally low temperatures have affected the world ' s rice production.", "output": "rice." }, { "input": "Many genes have been shown to be essential for molecular improvement of rice cold - tolerance traits.", "output": "rice." }, { "input": "However, less is known about the molecular cellular mechanism of their response to cold stress.", "output": "There is no related enetity." }, { "input": "Here, we investigated OsRAN2 involved in regulation of cell division during cold stress in rice.", "output": "rice." }, { "input": "Expression of OsRAN2 was increased under cold treatment, but not during salt and drought stress.", "output": "There is no related enetity." }, { "input": "The mean root mitotic index was closely related to the expression level of OsRAN2.", "output": "There is no related enetity." }, { "input": "Knockdown transgenic rice lines showed an aberrant organization of spindles during mitosis and stunted growth during development.", "output": "rice." }, { "input": "Overexpression of OsRAN2 enhanced cold tolerance in rice.", "output": "rice." }, { "input": "The transgenic rice overexpressing OsRAN2 showed maintained cell division, decreased proportion of cells with intranuclear tubulin and formation of a normal nuclear envelope under the cold condition.", "output": "rice." }, { "input": "Our study suggests a mechanism for OsRAN2 in regulating cold resistance in rice by maintaining cell division through promoting the normal export of intranuclear tubulin at the end of mitosis.", "output": "rice." }, { "input": "This insight could help improve the cold - tolerance trait in rice.", "output": "rice." }, { "input": "Drought increases freezing tolerance of both leaves and xylem of Larrea tridentata.", "output": "Larrea tridentata." }, { "input": "Drought and freezing are both known to limit desert plant distributions, but the interaction of these stressors is poorly understood.", "output": "There is no related enetity." }, { "input": "Drought may increase freezing tolerance in leaves while decreasing it in the xylem, potentially creating a mismatch between water supply and demand.", "output": "There is no related enetity." }, { "input": "To test this hypothesis, we subjected Larrea tridentata juveniles grown in a greenhouse under well - watered or drought conditions to minimum temperatures ranging from - 8 to - 24 ^ 0C.", "output": "Larrea tridentata." }, { "input": "We measured survival, leaf retention, gas exchange, cell death, freezing point depression and leaf - specific xylem hydraulic conductance ( k1 ).", "output": "There is no related enetity." }, { "input": "Drought - exposed plants exhibited smaller decreases in gas exchange after exposure to - 8 ^ 0C compared to well - watered plants.", "output": "There is no related enetity." }, { "input": "Drought also conferred a significant positive effect on leaf, xylem and whole - plant function following exposure to - 15 ^ 0C; drought - exposed plants exhibited less cell death, greater leaf retention, higher k1 and higher rates of gas exchange than well - watered plants.", "output": "There is no related enetity." }, { "input": "Both drought - exposed and well - watered plants experienced 100 % mortality following exposure to - 24 ^ 0C.", "output": "There is no related enetity." }, { "input": "By documenting the combined effects of drought and freezing stress, our data provide insight into the mechanisms determining plant survival and performance following freezing and the potential for shifts in L. tridentata abundance and range in the face of changing temperature and precipitation regimes.", "output": "L . tridentata." }, { "input": "Nitrogen source interacts with ROP signalling in root hair tip - growth.", "output": "There is no related enetity." }, { "input": "Root hairs elongate in a highly polarized manner known as tip growth.", "output": "There is no related enetity." }, { "input": "Overexpression of constitutively active Rho of Plant ( ROP ) / RAC GTPases mutants induces swelling of root hairs.", "output": "There is no related enetity." }, { "input": "Here, we demonstrate that Atrop11 ( CA ) - induced swelling of root hairs depends on the composition of the growth medium.", "output": "There is no related enetity." }, { "input": "Depletion of ammonium allowed normal root hair elongation in Atrop11 ( CA ) plants, induced the development of longer root hairs in wild - type plants and suppressed the effect of Atrop11 ( CA ) expression on actin organization and reactive oxygen species distribution, whereas membrane localization of the protein was not affected.", "output": "There is no related enetity." }, { "input": "Ammonium at concentrations higher than 1 mM and the presence of nitrate were required for induction of swelling.", "output": "There is no related enetity." }, { "input": "Oscillations in wall and cytoplasmic pH are known to accompany tip growth in root hairs, and buffering of the growth medium decreased Atrop11 ( CA ) - induced swelling.", "output": "There is no related enetity." }, { "input": "Fluorescence ratio imaging experiments revealed that in wild - type root hairs, the addition of NH4NO3 to the growth medium induced an increase in the amplitude of extracellular and intracellular pH oscillations and an overall decrease in cytoplasmic pH at the cell apex.", "output": "There is no related enetity." }, { "input": "Based on these results, we suggest a model in which ROP GTPases and nitrogen - dependent pH oscillations function in parallel pathways, creating a positive feedback loop during root hair growth.", "output": "There is no related enetity." }, { "input": "Green - colored plastids in the dinoflagellate genus Lepidodinium are of core chlorophyte origin.", "output": "There is no related enetity." }, { "input": "Most photosynthetic dinoflagellates possess plastids containing chlorophyllsa + c, but species belonging to the genus Lepidodinium are unique in bearing non - canonical plastids containing chlorophyllsa + b.", "output": "There is no related enetity." }, { "input": "According to the pioneering works on pigment composition data, it has been proposed that Lepidodinium plastids were derived from a prasinophyte species, though this hypothesis was not supported by a recent phylogenetic analysis based on an alignment comprised of eight plastid proteins ( Takishita et al. 2008, Gene 410: 26 - 26 ).", "output": "There is no related enetity." }, { "input": "This & quot; 8 - protein & quot; analysis however was insufficient to clarify the origin of Lepidodinium plastids for two major reasons: First, the alignment lacked sufficient evolutionary information to resolve the precise origin of Lepidodinium plastids.", "output": "There is no related enetity." }, { "input": "Second, the taxa considered did not well represent the diversity of Chlorophyta.", "output": "There is no related enetity." }, { "input": "Particularly, prasinophytes were poorly sampled in the alignment.", "output": "There is no related enetity." }, { "input": "In this study, we sequenced plastid - encoded genes from L. chlorophorum, one pedinophyte species, one ulvophyte species, and six prasinophyte species.", "output": "L . chlorophorum." }, { "input": "The 85 sequences newly determined in this study and recent progress in plastid genome sequencing enabled us to prepare an alignment comprised of 11 plastid proteins from green algal taxa that appropriately cover the diversity of Chlorophyta.", "output": "There is no related enetity." }, { "input": "All the analyses of the 11 - protein data set robustly grouped L. chlorophorum with members of the & quot; core chlorophytes. & quot; Thus, we here propose that Lepidodinium plastids are of core chlorophyte origin.", "output": "L . chlorophorum." }, { "input": "Floret initiation, tissue expansion and carbon availability at the meristem of the sunflower capitulum as affected by water or light deficits.", "output": "sunflower." }, { "input": "* The co - ordination between floret initiation and meristem expansion, and their relationships with carbon availability, were studied and quantified in sunflower ( Helianthus annuus ) plants subjected to light or water shortages.", "output": "sunflower, Helianthus annuus." }, { "input": "* Meristem size, number of floret primordia, primordium size, rate of plant biomass accumulation, leaf area, photosynthetic rate, and soluble sugar content in the capitulum were measured until completion of floret initiation.", "output": "There is no related enetity." }, { "input": "* Although treatments differentially affected tissue expansion and biomass acquisition, a common relationship between the final number of florets and the rate and duration of meristem expansion was conserved.", "output": "There is no related enetity." }, { "input": "In the absence of water deficit, changes in relative expansion rate in the meristem paralleled changes in soluble sugar content.", "output": "There is no related enetity." }, { "input": "Water deficit reduced tissue expansion both in leaves and in the capitulum, and induced the accumulation of soluble sugars in the meristem.", "output": "There is no related enetity." }, { "input": "Use of these sugars at re - watering was associated with increased meristem growth and higher floret numbers compared with control plants.", "output": "There is no related enetity." }, { "input": "* Floret initiation and meristem tissue expansion remained strongly co - ordinated under all studied circumstances, and both depended on local carbon availability when water supply was unlimited.", "output": "There is no related enetity." }, { "input": "Transient water deficits favoured reproductive meristem growth and floret production.", "output": "There is no related enetity." }, { "input": "Equations accounting for these results constitute a framework for phenotyping the response to drought.", "output": "There is no related enetity." }, { "input": "A hydraulic explanation for size - specific plant shrinkage: developmental hydraulic sectoriality.", "output": "There is no related enetity." }, { "input": "* While great attention has been paid to the mechanisms controlling plant growth, much less is known about why and how plants shrink.", "output": "There is no related enetity." }, { "input": "The modular design of plants may facilitate the independence of modules if the xylem vasculature is hydraulically sectored.", "output": "There is no related enetity." }, { "input": "We examined the hydraulic connectivity of modules comprising juveniles and adults of the aridland chamaephyte Cryptantha flava ( Boraginaceae ), motivated by the observation that rosette mortality is spatially aggregated in adults, but not in juveniles.", "output": "There is no related enetity." }, { "input": "* We explored spatial patterns of leaf wilting after clipping a single lateral root, tracked physiological dyes taken up by a single root, and measured within - plant variation in leaf water potentials after watering a portion of the root system.", "output": "There is no related enetity." }, { "input": "We then measured xylem anatomical features related to hydraulic connectivity.", "output": "There is no related enetity." }, { "input": "* Our approaches revealed hydraulic integration in juveniles but hydraulic sectoriality in adults.", "output": "There is no related enetity." }, { "input": "We attribute such developmental changes to increasing distances between xylem bundles, and larger xylem lumen and heartwood areas as plants age.", "output": "There is no related enetity." }, { "input": "* We have demonstrated functional sectoriality in a desert chamaephyte, and report the mechanism by which sectoriality occurs, offering a hydraulic explanation for the death of whole plant portions resulting in shrinkage of large plants, and for the high occurrence of this design in deserts.", "output": "There is no related enetity." }, { "input": "Bird community specialization, bird conservation and disturbance: the role of wildfires.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Although niche theory predicts that disturbance should favour generalist species, the community - level implications of this pattern have been sparsely analysed.", "output": "There is no related enetity." }, { "input": "Here, we test the hypothesis that disturbance favours generalist species within communities, analysing effects of wildfires in bird communities in a Mediterranean climate area as a case study.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We use bird occurrence data in more than 500 1 x 1 km squares forming a gradient running from forest to completely burnt areas.", "output": "There is no related enetity." }, { "input": "The level of specialization of bird communities was estimated by means of three complementary species specialization indices, calculated for different landscape gradients and averaged at the community level ( i. e. 1 x 1 km squares ), and mean species rarity.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We also calculated mean habitat preferences along landscape gradients, as well as an index of conservation value and total species richness.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Different estimators of bird community specialization varied in contrasting fashion along the wildfire disturbance gradient, and thus we conclude that it is not justified to expect unique community responses to the sharp variations in habitat characteristics brought by wildfire disturbances.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Burnt areas tended to have rarer and urban - avoider bird species, whereas unburnt forests tended to have larger proportions of forest specialist species.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "The mean conservation value of communities clearly increased towards the burnt extreme of the wildfire disturbance gradient, while this had a negligible effect on species richness.", "output": "There is no related enetity." }, { "input": "7.", "output": "There is no related enetity." }, { "input": "Wildfires seem to play an important role for the maintenance of open - habitat, urban - avoider bird populations in Mediterranean landscapes and also to benefit a set of bird species of unfavourable European conservation status.", "output": "There is no related enetity." }, { "input": "8.", "output": "There is no related enetity." }, { "input": "In this context, it cannot be unambiguously concluded that fire disturbance, even in a context in which fires are greatly favoured by human - related activities, leads to more functionally simplified communities dominated by generalist species.", "output": "There is no related enetity." }, { "input": "Contrasting patterns of individual specialization and trophic coupling in two marine apex predators.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Apex predators are often assumed to be dietary generalists and, by feeding on prey from multiple basal nutrient sources, serve to couple discrete food webs.", "output": "There is no related enetity." }, { "input": "But there is increasing evidence that individual level dietary specialization may be common in many species, and this has not been investigated for many marine apex predators.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Because of their position at or near the top of many marine food webs, and the possibility that they can affect populations of their prey and induce trophic cascades, it is important to understand patterns of dietary specialization in shark populations.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Stable isotope values from body tissues with different turnover rates were used to quantify patterns of individual specialization in two species of ' generalist ' sharks ( bull sharks, Carcharhinus leucas, and tiger sharks, Galeocerdo cuvier ).", "output": "bull sharks, Carcharhinus leucas, tiger sharks, Galeocerdo cuvier." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Despite wide population - level isotopic niche breadths in both species, isotopic values of individual tiger sharks varied across tissues with different turnover rates.", "output": "tiger sharks." }, { "input": "The population niche breadth was explained mostly by variation within individuals suggesting tiger sharks are true generalists.", "output": "tiger sharks." }, { "input": "In contrast, isotope values of individual bull sharks were stable through time and their wide population level niche breadth was explained by variation among specialist individuals.", "output": "bull sharks." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Relative resource abundance and spatial variation in food - predation risk tradeoffs may explain the differences in patterns of specialization between shark species.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "The differences in individual dietary specialization between tiger sharks and bull sharks results in different functional roles in coupling or compartmentalizing distinct food webs.", "output": "tiger sharks, bull sharks." }, { "input": "7.", "output": "There is no related enetity." }, { "input": "Individual specialization may be an important feature of trophic dynamics of highly mobile marine top predators and should be explicitly considered in studies of marine food webs and the ecological role of top predators.", "output": "There is no related enetity." }, { "input": "Genetic mapping of 14 avirulence genes in an EU - B04 x 1639 progeny of Venturia inaequalis.", "output": "There is no related enetity." }, { "input": "Durable resistance to apple scab ( Venturia inaequalis ( Cke ) Wint; anamorph Spilocaea pomi Fries ) is one of the major goals of apple ( Malus ) breeding programs.", "output": "apple, Venturia inaequalis, Spilocaea pomi, apple." }, { "input": "Since current scab resistance breeding is heavily reliant on genes with gene - for - gene relationships, a good understanding of the genetic basis of host - pathogen interactions needs to be developed for this strategy to be successful.", "output": "There is no related enetity." }, { "input": "While the genomic organization of apple scab resistance genes has been studied extensively, little is known about the avirulence genes in the pathogen.", "output": "apple." }, { "input": "The progeny of a cross of European V. inaequalis race ( 1 ) isolate EU - B04 and race ( 1, 2, 8, 9 ) isolate 1639 was used to generate a genetic map based on microsatellite and AFLP markers, and investigated for inheritance of avirulence traits on 20 Malus accessions representing 17 scab resistance genes.", "output": "V . inaequalis." }, { "input": "The accessions comprised scab differential hosts ( 0 ), ( 1 ), ( 2 ), ( 8 ), and ( 9 ), and hosts carrying known as well as not previously reported secondary resistance genes, including some identified in crosses that have resistant accessions ' Geneva ', ' Dolgo ', Malus baccata jackii, M. micromalus, or ' Antonovka ' in their pedigree.", "output": "Malus baccata jackii, M . micromalus." }, { "input": "The latter genes appear to be narrow spectrum genes that showed gene - for - gene relationships as a segregation ratio of Avr: avr = 1: 1 was observed on 12 accessions, while a ratio of 3: 1 was observed on five accessions and a ratio of 7: 1 on one host.", "output": "There is no related enetity." }, { "input": "All progenies were shown to be pathogenic, as all of them were able to infect hosts ( 0 ) and ( 1 ).", "output": "There is no related enetity." }, { "input": "A genetic map consisting of 15 major linkage groups ( LGs ) and spanning 972cM was generated with the aid of 156 markers.", "output": "There is no related enetity." }, { "input": "The map position of 12 avirulence traits was determined: eight avirulence genes mapped into two separate clusters ( 1: AvrVdg2, AvrVv1, AvrVu1, AvrVrjrd; and 2: AvrVu2, AvrVh3. 2, AvrVs1, AvrVu4 ), while four avirulence genes ( AvrRvi8, AvrVv2, AvrVt57 and AvrVsv ) mapped to different LGs.", "output": "There is no related enetity." }, { "input": "AvrRvi2 and AvrRvi9 also are genetically linked, but showed an interaction with AvrRvi8, the nature of which is unclear.", "output": "There is no related enetity." }, { "input": "While AvrRvi8 segregated at 1: 1 ratio, the other two Avrs segregated at 3: 1 ratios.", "output": "There is no related enetity." }, { "input": "However, all progeny avirulent on hosts ( 2 ) and ( 9 ) were also avirulent on host ( 8 ) and further research is required to determine the avirulence gene relationships.", "output": "There is no related enetity." }, { "input": "A further two independently segregating loci, AvrRvi1 and AvrRvi6, identified in previous studies, were mapped by inference based on their known linkage to SSR markers.", "output": "There is no related enetity." }, { "input": "The clustering of avirulence genes in V. inaequalis reflecting the clustering of resistance genes in Malus suggests this pathosystem is a classical example of an & quot; arms race & quot; between host and pathogen.", "output": "There is no related enetity." }, { "input": "This also seems to apply to the narrow spectrum scab resistance genes, which may imply a larger role in plant defense for these genes than has been assumed to date.", "output": "There is no related enetity." }, { "input": "Functional characterization of Arabidopsis thaliana isopropylmalate dehydrogenases reveals their important roles in gametophyte development.", "output": "Arabidopsis thaliana." }, { "input": "* Isopropylmalate dehydrogenases ( IPMDHs ) catalyze the oxidative decarboxylation of 3 - isopropylmalate ( 3 - IPM ) in leucine biosynthesis in microorganisms.", "output": "There is no related enetity." }, { "input": "The Arabidopsis thaliana genome contains three putative IPMDH genes.", "output": "Arabidopsis thaliana." }, { "input": "* IPMDH2 and IPMDH3 proteins exhibited significantly higher activity toward 3 - IPM than IPMDH1, which is indicative of a pivotal role in leucine biosynthesis.", "output": "There is no related enetity." }, { "input": "Single mutants of IPMDH2 or IPMDH3 lacked a discernible phenotype.", "output": "There is no related enetity." }, { "input": "Genetic analysis showed that ipmdh2 ipmdh3 was lethal in male gametophytes and had reduced transmission through female gametophytes.", "output": "There is no related enetity." }, { "input": "The aborted pollen grains were small, abnormal in cellular structure, and arrested in germination.", "output": "There is no related enetity." }, { "input": "In addition, half of the double mutant embryo sacs exhibited slowed development.", "output": "There is no related enetity." }, { "input": "* The IPMDH2 / ipmdh2 ipmdh3 / ipmdh3 genotype exhibited abnormal vegetative phenotypes, suggesting haplo - insufficiency of IPMDH2 in the ipmdh3 background.", "output": "There is no related enetity." }, { "input": "This mutant and a triple mutant containing one allele of IPMDH2 or IPMDH3 had decreased leucine biosynthetic enzyme activities and lower free leucine concentrations.", "output": "There is no related enetity." }, { "input": "The latter mutant showed changes in glucosinolate profiles different from those in the ipmdh1 mutant.", "output": "There is no related enetity." }, { "input": "* The results demonstrate that IPMDH2 and IPMDH3 primarily function in leucine biosynthesis, are essential for pollen development and are needed for proper embryo sac development.", "output": "There is no related enetity." }, { "input": "OsHMA3, a P1B - type of ATPase affects root - to - shoot cadmium translocation in rice by mediating efflux into vacuoles.", "output": "rice." }, { "input": "* The cadmium ( Cd ) over - accumulating rice ( Oryza sativa ) cv Cho - Ko - Koku was previously shown to have an enhanced rate of root - to - shoot Cd translocation.", "output": "rice, Oryza sativa, cv Cho - Ko - Koku." }, { "input": "This trait is controlled by a single recessive allele located at qCdT7.", "output": "There is no related enetity." }, { "input": "* In this study, using positional cloning and transgenic strategies, heavy metal ATPase 3 ( OsHMA3 ) was identified as the gene that controls root - to - shoot Cd translocation rates.", "output": "There is no related enetity." }, { "input": "The subcellular localization and Cd - transporting activity of the gene products were also investigated.", "output": "There is no related enetity." }, { "input": "* The allele of OsHMA3 that confers high root - to - shoot Cd translocation rates ( OsHMA3mc ) encodes a defective P ( 1B ) - ATPase transporter.", "output": "There is no related enetity." }, { "input": "OsHMA3 fused to green fluorescent protein was localized to vacuolar membranes in plants and yeast.", "output": "yeast." }, { "input": "An OsHMA3 transgene complemented Cd sensitivity in a yeast mutant that lacks the ability to transport Cd into vacuoles.", "output": "yeast." }, { "input": "By contrast, OsHMA3mc did not complement the Cd sensitivity of this yeast mutant, indicating that the OsHMA3mc transport function was lost.", "output": "yeast." }, { "input": "* We propose that the root cell cytoplasm of Cd - overaccumulating rice plants has more Cd available for loading into the xylem as a result of the lack of OsHMA3 - mediated transportation of Cd to the vacuoles.", "output": "rice plants." }, { "input": "This defect results in Cd translocation to the shoots in higher concentrations.", "output": "There is no related enetity." }, { "input": "These data demonstrate the importance of vacuolar sequestration for Cd accumulation in rice.", "output": "rice." }, { "input": "Spatial distribution of arsenic and temporal variation of its concentration in rice.", "output": "rice." }, { "input": "* In order to gain insights into the transport and distribution of arsenic ( As ) in intact rice ( Oryza sativa ) plants and its unloading into the rice grain, we investigated the spatial distribution of As and the temporal variation of As concentration in whole rice plants at different growth stages.", "output": "rice, Oryza sativa, rice, rice plants." }, { "input": "To the best of our knowledge, this is the first time that such a study has been performed.", "output": "There is no related enetity." }, { "input": "* Inductively coupled plasma mass spectroscopy ( ICP - MS ) and high - performance liquid chromatography ( HPLC ) - ICP - MS were used to analyze total As concentration and speciation.", "output": "There is no related enetity." }, { "input": "Moreover, synchrotron - based X - ray fluorescence ( SXRF ) was used to investigate in situ As distribution in the leaf, internode, node and grain.", "output": "There is no related enetity." }, { "input": "* Total As concentrations of vegetative tissues increased during the 2 wk after flowering.", "output": "There is no related enetity." }, { "input": "The concentration of dimethylarsinic acid ( DMA ) in the caryopsis decreased progressively with its development, whereas inorganic As concentration remained stable.", "output": "There is no related enetity." }, { "input": "The ratios of As content between neighboring leaves or between neighboring internodes were c.", "output": "There is no related enetity." }, { "input": "0. 6.", "output": "There is no related enetity." }, { "input": "SXRF revealed As accumulation in the center of the caryopsis during its early development and then in the ovular vascular trace.", "output": "There is no related enetity." }, { "input": "* These results indicate that there are different controls on the unloading of inorganic As and DMA; the latter accumulated mainly in the caryopsis before flowering, whereas inorganic As was mainly transported into the caryopsis during grain filling.", "output": "There is no related enetity." }, { "input": "Moreover, nodes appeared to serve as a check - point in As distribution in rice shoots.", "output": "rice." }, { "input": "Reduced predator species richness drives the body gigantism of a frog species on the Zhoushan Archipelago in China.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Shifts in the body size of insular vertebrates have been an interesting theme in ecological and evolutionary studies.", "output": "There is no related enetity." }, { "input": "Four primary factors, including predation pressures, resource availability, inter - species competition and immigrant selection, have been proposed to explain the trend in insular body size.", "output": "There is no related enetity." }, { "input": "Life - history theory predicts that body size, average age, the proportion of old - aged members and the density of insular populations are negatively correlated with predator species richness, and that body size and population density are positively related to resource availability.", "output": "There is no related enetity." }, { "input": "The niche expansion hypothesis argues that a positive relationship is expected to exist between insular body size and prey size, which varies in response to extinction due to small or large competitors.", "output": "There is no related enetity." }, { "input": "The immigrant hypothesis predicts that insular body size is positively correlated with distance to the mainland.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We tested these hypotheses by using populations of rice frogs Rana limnocharis on 20 islands in the Zhoushan Archipelago and two sites of nearby mainland China.", "output": "Rana limnocharis." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "The body size ( snout - vent length ) of rice frogs on half of the islands was larger before and after the variable of age was controlled for; rice frog density and prey availability was higher and prey size was larger on most of the islands as compared to the two mainland sites.", "output": "There is no related enetity." }, { "input": "On the islands, the body size and other features [ e. g. average age, the proportion of old - aged frogs ( ages 3 and 4 ) and density ] of the rice frogs were negatively associated with predator species richness; female body size and other features were positively associated with prey availability.", "output": "There is no related enetity." }, { "input": "The inference of multivariate linear models based on corrected Akaike Information Criterion ( AIC ( c ) ) showed that the relative importance of predator species richness on body size and each of the other features was larger than that of prey availability, prey size and distance to the mainland.", "output": "There is no related enetity." }, { "input": "In addition, the parameters for predator species richness were all negative.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "The results provided strong support for the life - history theory of predation pressures, but weak evidence for the life - history theory of prey availability, the niche expansion or the immigrant hypothesis.", "output": "There is no related enetity." }, { "input": "The reduced predator species richness was a dominant factor contributing to the body gigantism of rice frogs on the islands.", "output": "There is no related enetity." }, { "input": "Contrasted demographic responses facing future climate change in Southern Ocean seabirds.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Recent climate change has affected a wide range of species, but predicting population responses to projected climate change using population dynamics theory and models remains challenging, and very few attempts have been made.", "output": "There is no related enetity." }, { "input": "The Southern Ocean sea surface temperature and sea ice extent are projected to warm and shrink as concentrations of atmospheric greenhouse gases increase, and several top predator species are affected by fluctuations in these oceanographic variables.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We compared and projected the population responses of three seabird species living in sub - tropical, sub - Antarctic and Antarctic biomes to predicted climate change over the next 50 years.", "output": "There is no related enetity." }, { "input": "Using stochastic population models we combined long - term demographic datasets and projections of sea surface temperature and sea ice extent for three different IPCC emission scenarios ( from most to least severe: A1B, A2, B1 ) from general circulation models of Earth ' s climate.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We found that climate mostly affected the probability to breed successfully, and in one case adult survival.", "output": "There is no related enetity." }, { "input": "Interestingly, frequent nonlinear relationships in demographic responses to climate were detected.", "output": "There is no related enetity." }, { "input": "Models forced by future predicted climatic change provided contrasted population responses depending on the species considered.", "output": "There is no related enetity." }, { "input": "The northernmost distributed species was predicted to be little affected by a future warming of the Southern Ocean, whereas steep declines were projected for the more southerly distributed species due to sea surface temperature warming and decrease in sea ice extent.", "output": "There is no related enetity." }, { "input": "For the most southerly distributed species, the A1B and B1 emission scenarios were respectively the most and less damaging.", "output": "There is no related enetity." }, { "input": "For the two other species, population responses were similar for all emission scenarios.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "This is among the first attempts to study the demographic responses for several populations with contrasted environmental conditions, which illustrates that investigating the effects of climate change on core population dynamics is feasible for different populations using a common methodological framework.", "output": "There is no related enetity." }, { "input": "Our approach was limited to single populations and have neglected population settlement in new favourable habitats or changes in inter - specific relations as a potential response to future climate change.", "output": "There is no related enetity." }, { "input": "Predictions may be enhanced by merging demographic population models and climatic envelope models.", "output": "There is no related enetity." }, { "input": "The role of abscisic acid and water stress in root herbivore - induced leaf resistance.", "output": "There is no related enetity." }, { "input": "* Herbivore - induced systemic resistance occurs in many plants and is commonly assumed to be adaptive.", "output": "There is no related enetity." }, { "input": "The mechanisms triggered by leaf - herbivores that lead to systemic resistance are largely understood, but it remains unknown how and why root herbivory also increases resistance in leaves.", "output": "There is no related enetity." }, { "input": "* To resolve this, we investigated the mechanism by which the root herbivore Diabrotica virgifera induces resistance against lepidopteran herbivores in the leaves of Zea mays.", "output": "Diabrotica virgifera, Zea mays." }, { "input": "* Diabrotica virgifera infested plants suffered less aboveground herbivory in the field and showed reduced growth of Spodoptera littoralis caterpillars in the laboratory.", "output": "Diabrotica virgifera, Spodoptera littoralis." }, { "input": "Root herbivory did not lead to a jasmonate - dependent response in the leaves, but specifically triggered water loss and abscisic acid ( ABA ) accumulation.", "output": "There is no related enetity." }, { "input": "The induction of ABA by itself was partly responsible for the induction of leaf defenses, but not for the resistance against S. littoralis.", "output": "S . littoralis." }, { "input": "Root - herbivore induced hydraulic changes in the leaves, however, were crucial for the increase in insect resistance.", "output": "There is no related enetity." }, { "input": "* We conclude that the induced leaf resistance after root feeding is the result of hydraulic changes, which reduce the quality of the leaves for chewing herbivores.", "output": "There is no related enetity." }, { "input": "This finding calls into question whether root - herbivore induced leaf - resistance is an evolved response.", "output": "There is no related enetity." }, { "input": "Do quantitative vessel and pit characters account for ion - mediated changes in the hydraulic conductance of angiosperm xylem?", "output": "There is no related enetity." }, { "input": "* The hydraulic conductance of angiosperm xylem has been suggested to vary with changes in sap solute concentrations because of intervessel pit properties.", "output": "There is no related enetity." }, { "input": "* The magnitude of the ' ionic effect ' was linked with vessel and pit dimensions in 20 angiosperm species covering 13 families including six Lauraceae species.", "output": "There is no related enetity." }, { "input": "* A positive correlation was found between ionic effect and vessel grouping parameters, especially the portion of vessel walls in contact with neighbouring vessels.", "output": "There is no related enetity." }, { "input": "Species with intervessel contact fraction ( F ( C ) ) values & lt; 0. 1 showed an ionic effect between 2 % and 17 %, while species with F ( C ) values > 0. 1 exhibited a response between 10 % and 32 %.", "output": "There is no related enetity." }, { "input": "The ionic effect increased linearly with the mean fraction of the total vessel wall area occupied by intervessel pits as well as with the intervessel contact length.", "output": "There is no related enetity." }, { "input": "However, no significant correlation occurred between the ionic effect and total intervessel pit membrane area per vessel, vessel diameter, vessel length, vessel wall area, and intervessel pit membrane thickness.", "output": "There is no related enetity." }, { "input": "* Quantitative vessel and pit characters are suggested to contribute to interspecific variation of the ionic effect, whereas chemical properties of intervessel pit membranes are likely to play an additional role.", "output": "There is no related enetity." }, { "input": "Identification and characterization of genes responsible for biosynthesis of kojic acid, an industrially important compound from Aspergillus oryzae.", "output": "Aspergillus oryzae." }, { "input": "Kojic acid is produced in large amounts by Aspergillus oryzae as a secondary metabolite and is widely used in the cosmetic industry.", "output": "Aspergillus oryzae." }, { "input": "Glucose can be converted to kojic acid, perhaps by only a few steps, but no genes for the conversion have thus far been revealed.", "output": "There is no related enetity." }, { "input": "Using a DNA microarray, gene expression profiles under three pairs of conditions significantly affecting kojic acid production were compared.", "output": "There is no related enetity." }, { "input": "All genes were ranked using an index parameter reflecting both high amounts of transcription and a high induction ratio under producing conditions.", "output": "There is no related enetity." }, { "input": "After disruption of nine candidate genes selected from the top of the list, two genes of unknown function were found to be responsible for kojic acid biosynthesis, one having an oxidoreductase motif and the other a transporter motif.", "output": "There is no related enetity." }, { "input": "These two genes are closely associated in the genome, showing typical characteristics of genes involved in secondary metabolism.", "output": "There is no related enetity." }, { "input": "Identification of the structural proteins of VP1 and VP2 of a novel mud crab dicistrovirus.", "output": "mud crab dicistrovirus." }, { "input": "Mud crab dicistrovirus ( MCDV ), a newly identified single - stranded positive RNA virus, is an important pathogen that causes serious economic losses to mud crab aquaculture.", "output": "Mud crab dicistrovirus, MCDV, mud crab." }, { "input": "In this study, MCDV was purified, and three structural proteins of MCDV were separated by SDS - PAGE.", "output": "MCDV, MCDV." }, { "input": "The N - terminal 15 amino acids were sequenced and aligned with the main structural proteins of other dicistrovirus.", "output": "There is no related enetity." }, { "input": "The three structural proteins were named VP1, VP2 and VP3.", "output": "There is no related enetity." }, { "input": "Monoclonal antibodies ( MAbs ) against the two main structural proteins, VP1 and VP2, were prepared, and the two structural proteins were then identified using these MAbs.", "output": "There is no related enetity." }, { "input": "The results of Western blot analyses demonstrated that five MAbs recognised VP1 and two recognised VP2.", "output": "There is no related enetity." }, { "input": "The results of immunogold transmission electron microscopy ( IEM ) revealed that the epitopes of the two structural proteins recognised by the MAbs were located at the outer surface of the virions, which suggested that the two structural proteins are MCDV capsid proteins.", "output": "MCDV." }, { "input": "The identification of the two structural proteins of MCDV is useful for studying their functions, as well as the mechanism of infection and the pathogenesis of MCDV.", "output": "MCDV, MCDV." }, { "input": "SGT1 contributes to coronatine signaling and Pseudomonas syringae pv. tomato disease symptom development in tomato and Arabidopsis.", "output": "Pseudomonas syringae pv . tomato, tomato." }, { "input": "* Pseudomonas syringae pv. tomato DC3000 ( Pst DC3000 ) causes an economically important bacterial speck disease on tomato and produces symptoms with necrotic lesions surrounded by chlorosis.", "output": "Pseudomonas syringae pv . tomato DC3000, Pst DC3000, tomato." }, { "input": "The chlorosis is mainly attributed to a jasmonic acid ( JA ) - isoleucine analogue, coronatine ( COR ), produced by Pst DC3000.", "output": "Pst DC3000." }, { "input": "However, the molecular processes underlying lesion development and COR - induced chlorosis are poorly understood.", "output": "There is no related enetity." }, { "input": "* In this study, we took advantage of a chlorotic phenotype elicited by COR on Nicotiana benthamiana leaves and virus - induced gene silencing ( VIGS ) as a rapid reverse genetic screening tool and identified a role for SGT1 ( suppressor of G2 allele of skp1 ) in COR - induced chlorosis.", "output": "Nicotiana benthamiana." }, { "input": "* Silencing of SGT1 in tomato resulted in reduction of disease - associated symptoms ( cell death and chlorosis ), suggesting a molecular connection between COR - induced chlorosis and cell death.", "output": "tomato." }, { "input": "In Arabidopsis, AtSGT1b but not AtSGT1a was required for COR responses, including root growth inhibition and Pst DC3000 symptom ( water soaked lesion ) development.", "output": "Pst DC3000." }, { "input": "Notably, overexpression of AtSGT1b did not alter Pst DC3000 symptoms or sensitivity to COR.", "output": "Pst DC3000." }, { "input": "* Taken together, our results demonstrate that SGT1 / SGT1b is required for COR - induced chlorosis and subsequent necrotic disease development in tomato and Arabidopsis.", "output": "tomato." }, { "input": "SGT1 is therefore a component of the COR / JA - mediated signal transduction pathway.", "output": "There is no related enetity." }, { "input": "Growth - mediated stress escape: convergence of signal transduction pathways activated upon exposure to two different environmental stresses.", "output": "There is no related enetity." }, { "input": "* Plants can escape from specific environmental stresses through active growth strategies.", "output": "There is no related enetity." }, { "input": "Here, we compared two such stress - escape syndromes to investigate whether plants use conserved signal transduction pathways to escape from different stresses.", "output": "There is no related enetity." }, { "input": "* Full submergence is a threat to terrestrial plants as it cuts off their access to oxygen and CO ( 2 ).", "output": "There is no related enetity." }, { "input": "Proximate neighbors, in contrast, take away resources such as light.", "output": "There is no related enetity." }, { "input": "Both submergence and shade can be escaped through rapid shoot elongation.", "output": "There is no related enetity." }, { "input": "We analysed the precise kinetics and physiological control of petiole elongation responses to shade and submergence in the flood - tolerant species Rumex palustris.", "output": "Rumex palustris." }, { "input": "* We found that petiole elongation induced by submergence and that induced by shade occurred with similar kinetics, both involving cell expansion.", "output": "There is no related enetity." }, { "input": "These responses were induced by two different signals, elevated ethylene and a reduced red: far - red light ratio ( R: FR ), respectively.", "output": "There is no related enetity." }, { "input": "A downstream target for ethylene was abscisic acid, but low R: FR appeared to act independently of this hormone.", "output": "There is no related enetity." }, { "input": "Gibberellin, however, appeared to be essential to both ethylene - and low R: FR - induced petiole elongation.", "output": "There is no related enetity." }, { "input": "* We propose that gibberellin and expansins, a family of cell wall - loosening proteins, represent elements of a conserved growth machinery that is activated by stress - specific signaling events to regulate escape from stress.", "output": "There is no related enetity." }, { "input": "PsOr1, a potential target for RNA interference - based pest management.", "output": "There is no related enetity." }, { "input": "Insect pests cause billions of dollars in agricultural losses, and attempts to kill them have resulted in growing threats from insecticide resistance, dietary pesticide pollution and environmental destruction.", "output": "There is no related enetity." }, { "input": "New approaches to control refractory insect pests are therefore needed.", "output": "There is no related enetity." }, { "input": "The host - plant preferences of insect pests rely on olfaction and are mediated via a seven transmembrane - domain odorant receptor ( Or ) family.", "output": "There is no related enetity." }, { "input": "The present study reports the cloning and characterization of PsOr1, the first candidate member of the Or gene family from Phyllotreta striolata, a devastating beetle pest that causes damage worldwide.", "output": "Phyllotreta striolata." }, { "input": "PsOr1 is remarkably well conserved with respect to other insect orthologues, including DmOr83b from Drosophila melanogaster.", "output": "Drosophila melanogaster." }, { "input": "These insect orthologues form an essential non - conventional Or sub - family and may play an important and generalized role in insect olfaction.", "output": "There is no related enetity." }, { "input": "We designed double - stranded ( ds ) RNA directly against the PsOr1 gene and exploited RNA interference ( RNAi ) to control P. striolata.", "output": "P . striolata." }, { "input": "The chemotactic behavioural measurements showed that adult beetles were unable to sense the attractant or repellent odour stimulus after microinjection of dsRNA against PsOr1.", "output": "There is no related enetity." }, { "input": "Reverse Transcription ( RT ) - PCR analysis showed specific down - regulation of mRNA transcript levels for this gene.", "output": "There is no related enetity." }, { "input": "Furthermore, host - plant preference experiments confirmed that silencing PsOr1 by RNAi treatment impaired the host - plant preferences of P. striolata for cruciferous vegetables.", "output": "P . striolata." }, { "input": "These results demonstrate that this insect control approach of using RNAi to target PsOr1 and its orthologues might be effective in blocking host - plant - seeking behaviours in diverse insect pests.", "output": "There is no related enetity." }, { "input": "The results also support the theory that this unique receptor type plays an essential general role in insect olfaction.", "output": "There is no related enetity." }, { "input": "Expression of diverse midgut serine proteinases in the sericigenous Lepidoptera Antheraea assamensis ( Helfer ) is influenced by choice of host plant species.", "output": "Antheraea assamensis." }, { "input": "Antheraea assamensis is reared on various species of the Lauraceae family from north - east India for its distinctive cocoon silk.", "output": "Antheraea assamensis." }, { "input": "We demonstrate differential expression of digestive trypsin and chymotrypsins in larvae feeding on a primary host, Persea bombycina Kosterm., in comparison to larvae feeding on Litsea monopetala Roxb. using in vitro proteolytic assays, zymogram analyses with proteinase inhibitors, restriction digestion of RNA - PCR amplicons and quantitative real - time PCR ( RT - PCR ).", "output": "Persea bombycina, Litsea monopetala." }, { "input": "Eight novel members of the serine proteinase gene family were identified, including an intron - spliced trypsin ( AaPb4 ) and seven putative chymotrypsins ( AaPb2, AaPb4, AaPb12, AaLm4, AaLm6, AaLm19 and AaLm29 ).", "output": "There is no related enetity." }, { "input": "Midgut transcript levels of the putative trypsin were higher in larvae fed P. bombycina whereas levels of transcripts encoding putative chymotrypsins were higher in larvae reared on L. monopetala.", "output": "P . bombycina, L . monopetala." }, { "input": "Complex, differential expression of sequence divergent midgut serine proteinases may reflect the ability of lepidopteran larvae to feed on different species of host plants.", "output": "There is no related enetity." }, { "input": "Possible implications of host plant choice on the digestive physiology of A. assamensis are discussed.", "output": "A . assamensis." }, { "input": "Functional test of the influence of Wolbachia genes on cytoplasmic incompatibility expression in Drosophila melanogaster.", "output": "Drosophila melanogaster." }, { "input": "Wolbachia are inherited intracellular bacteria that infect a broad range of invertebrate hosts.", "output": "There is no related enetity." }, { "input": "They commonly manipulate host reproduction in a variety of ways and thereby favour their invasion into host populations.", "output": "There is no related enetity." }, { "input": "While the biology of Wolbachia has been extensively studied at the ecological and phenotypic level, little is known about the molecular mechanisms underlying the interaction between Wolbachia and their hosts.", "output": "There is no related enetity." }, { "input": "Recent comparative genomics studies of Wolbachia strains have revealed putative candidate genes involved in the expression of cytoplasmic incompatibility ( CI ) in insects.", "output": "There is no related enetity." }, { "input": "However the functional testing of these genes is hindered by the lack of available genetic tools in Wolbachia.", "output": "There is no related enetity." }, { "input": "To circumvent this problem we generated transgenic Drosophila lines expressing various Wolbachia CI candidate genes under the control of the GAL4 / UAS system in order to evaluate their possible role in Wolbachia - related phenotypes in Drosophila.", "output": "There is no related enetity." }, { "input": "The expression of a number of these genes in Drosophila melanogaster failed to mimic or alter CI phenotypes across a range of Wolbachia backgrounds or in the absence of Wolbachia.", "output": "Drosophila melanogaster." }, { "input": "Differential transcription of two highly divergent gut - expressed Bm86 antigen gene homologues in the tick Rhipicephalus appendiculatus ( Acari: Ixodida ).", "output": "Rhipicephalus appendiculatus." }, { "input": "The transcriptional control of gene expression is not well documented in the Arthropoda.", "output": "There is no related enetity." }, { "input": "We describe transcriptional analysis of two exceptionally divergent homologues ( Ra86 ) of the Bm86 gut antigen from Rhipicephalus appendiculatus.", "output": "Rhipicephalus appendiculatus." }, { "input": "Bm86 forms the basis of a commercial vaccine for the control of Rhipicephalus ( Boophilus ) microplus.", "output": "Rhipicephalus ( Boophilus ) microplus." }, { "input": "The R. appendiculatus Ra86 proteins contain 654 and 693 amino acids, with only 80 % amino acid sequence identity.", "output": "R . appendiculatus." }, { "input": "Reverse - transcription PCR of gut cDNA showed transcription of only one genotype in individual female ticks.", "output": "There is no related enetity." }, { "input": "PCR amplification of 3 ' untranslated sequences from genomic DNA indicated that both variants could be encoded within a single genome.", "output": "There is no related enetity." }, { "input": "When both variants were present, one of the two Ra86 genotypes was transcriptionally dominant.", "output": "There is no related enetity." }, { "input": "Detection and quantitation of infectious human adenoviruses and JC polyomaviruses in water by immunofluorescence assay.", "output": "human adenoviruses, JC polyomaviruses." }, { "input": "Human adenoviruses ( HAdV ) and JC polyomaviruses ( JCPyV ) have been proposed as markers of fecal / urine contamination of human origin.", "output": "There is no related enetity." }, { "input": "An indirect immunofluorescence assay has been developed to quantify infectious human adenoviruses types 2 and 41 and JC polyomaviruses strain Mad - 4 in water samples.", "output": "human adenoviruses, JC polyomaviruses." }, { "input": "The immunofluorescence assay was compared with other quantitative techniques used commonly such as plaque assay, tissue culture infectious dose - 50 and quantitative PCR ( qPCR ).", "output": "There is no related enetity." }, { "input": "The immunofluorescence assays showed to be specific for the detection of infectious viruses, obtaining negative results when UV or heat - inactivated viruses were analyzed.", "output": "There is no related enetity." }, { "input": "The assays required less time and showed higher sensitivity for the detection of infectious viral particles than other cell culture techniques ( 1 log ( 10 ) more ) evaluated.", "output": "There is no related enetity." }, { "input": "River water samples spiked previously with human adenoviruses and raw sewage samples were also analyzed using the proposed immunofluorescence assay as well as by qPCR.", "output": "human." }, { "input": "The results show quantitations with 2 log ( 10 ) reduction in the numbers of infectious viruses compared with the number of genome copies detected by qPCR.", "output": "There is no related enetity." }, { "input": "The immunofluorescence assay developed is fast, sensitive, specific, and a standardizable technique for the quantitation and detection of infectious viruses in water samples.", "output": "There is no related enetity." }, { "input": "Expression of the C - terminal ORF2 protein of duck astrovirus for application in a serological test.", "output": "duck astrovirus." }, { "input": "Duck astrovirus ( DAstV ) is an important pathogen causing duck viral hepatitis ( DVH ), a highly contagious and fatal disease in young ducklings.", "output": "Duck astrovirus, DAstV." }, { "input": "To provide an antigen for a diagnostic serum test, the C - terminus of DAstV ORF2 protein was expressed in Escherichia coli.", "output": "Escherichia coli." }, { "input": "Four positive and 30 negative sera were used to validate the purified ORF2 protein by developing an indirect enzyme - linked immunosorbent assay ( ELISA ).", "output": "There is no related enetity." }, { "input": "No cross - reactions were found against other duck pathogens, including duck hepatitis A virus, duck plague herpesvirus, duck reovirus, Newcastle disease virus, and Riemerella anatipestifer 12 / 19 ( 63. 2 % ) and 26 / 51 ( 51 % ) sera samples from two flocks of ducks that survived DAstV infections in commercial duck farms were positive for DAstV by this method, respectively.", "output": "duck hepatitis A virus, duck plague herpesvirus, duck reovirus, Newcastle disease virus, Riemerella anatipestifer 12 / 19, 26 / 51, DAstV, DAstV." }, { "input": "Interestingly, DAstV - specific antibodies were also detected in 12 ( 28. 6 % ) of 42 sera samples from a different flock without DVH, indicating a wide distribution of subclinical infections caused by DAstV.", "output": "DAstV, DAstV." }, { "input": "A fundamental, eco - hydrological basis for niche segregation in plant communities.", "output": "There is no related enetity." }, { "input": "* Ecologists still puzzle over how plant species manage to coexist with one another while competing for the same essential resources.", "output": "There is no related enetity." }, { "input": "The classic answer for animal communities is that species occupy different niches, but how plants do this is more difficult to determine.", "output": "There is no related enetity." }, { "input": "We previously found niche segregation along fine - scale hydrological gradients in European wet meadows and proposed that the mechanism might be a general one, especially in communities that experience seasonal saturation.", "output": "There is no related enetity." }, { "input": "* We quantified the hydrological niches of 96 species from eight fynbos communities in the biodiversity hotspot of the Cape Floristic Region, South Africa and 99 species from 18 lowland wet meadow communities in the UK.", "output": "There is no related enetity." }, { "input": "Niche overlap was computed for all combinations of species.", "output": "There is no related enetity." }, { "input": "* Despite the extreme functional and phylogenetic differences between the fynbos and wet meadow communities, an identical trade - off ( i. e. specialization of species towards tolerance of aeration and / or drying stress ) was found to cause segregation along fine - scale hydrological gradients.", "output": "There is no related enetity." }, { "input": "* This study not only confirms the predicted generality of hydrological niche segregation, but also emphasizes its importance for structuring plant communities.", "output": "There is no related enetity." }, { "input": "Eco - hydrological niche segregation will have implications for conservation in habitats that face changing hydrology caused by water abstraction and climate change.", "output": "There is no related enetity." }, { "input": "Role of lupeol synthase in Lotus japonicus nodule formation.", "output": "Lotus japonicus." }, { "input": "* Triterpenes are plant secondary metabolites, derived from the cyclization of 2, 3 - oxidosqualene by oxidosqualene cyclases ( OSCs ).", "output": "There is no related enetity." }, { "input": "Here, we investigated the role of lupeol synthase, encoded by OSC3, and its product, lupeol, in developing roots and nodules of the model legume Lotus japonicus.", "output": "Lotus japonicus." }, { "input": "* The expression patterns of OSC3 in different developmental stages of uninfected roots and in roots infected with Mesorhizobium loti were determined.", "output": "Mesorhizobium loti." }, { "input": "The tissue specificity of OSC3 expression was analysed by in situ hybridization.", "output": "There is no related enetity." }, { "input": "Functional analysis, in which transgenic L. japonicus roots silenced for OSC3 were generated, was performed.", "output": "L . japonicus." }, { "input": "The absence of lupeol in the silenced plant lines was determined by GC - MS.", "output": "There is no related enetity." }, { "input": "* The expression of ENOD40, a marker gene for nodule primordia initiation, was increased significantly in the OSC3 - silenced plant lines, suggesting that lupeol influences nodule formation.", "output": "There is no related enetity." }, { "input": "Silenced plants also showed a more rapid nodulation phenotype, consistent with this.", "output": "There is no related enetity." }, { "input": "Exogenous application of lupeol to M. loti - infected wild - type plants provided further evidence for a negative regulatory effect of lupeol on the expression of ENOD40.", "output": "M . loti." }, { "input": "* The synthesis of lupeol in L. japonicus roots and nodules can be solely attributed to OSC3.", "output": "L . japonicus." }, { "input": "Taken together, our data suggest a role for lupeol biosynthesis in nodule formation through the regulation of ENOD40 gene expression.", "output": "There is no related enetity." }, { "input": "Drug interactions in childhood cancer.", "output": "There is no related enetity." }, { "input": "Children with cancer are increasingly benefiting from new treatment strategies and advances in supportive care, as shown by improvements in both survival and quality - of - life.", "output": "There is no related enetity." }, { "input": "However, the continuous emergence of new cancer drugs and supportive - care drugs has increased the possibility of harmful drug interactions; health - care providers need to be very cautious when combining drugs.", "output": "There is no related enetity." }, { "input": "We discuss the most common interactions between chemotherapeutic drugs and supportive - care drugs - such as anticonvulsants, antiemetics, uric - acid - lowering compounds, acid suppressants, antimicrobials, and pain - management medications in paediatric patients.", "output": "There is no related enetity." }, { "input": "We also review the interactions between chemotherapy drugs and food and herbal supplements, and provide recommendations to avoid unwanted and potentially fatal interactions in children with cancer.", "output": "There is no related enetity." }, { "input": "Because of the constant release of new drugs, health - care providers need to check the most recent references before making recommendations about drug interactions.", "output": "There is no related enetity." }, { "input": "Mutational analysis of the transmembrane helix 2 - HAMP domain connection in the Escherichia coli aspartate chemoreceptor tar.", "output": "Escherichia coli." }, { "input": "Transmembrane helix 2 ( TM2 ) of the Tar chemoreceptor undergoes an inward piston - like displacement of 1 to 3 A upon binding aspartate.", "output": "There is no related enetity." }, { "input": "This signal is transmitted to the kinase - control module via the HAMP domain.", "output": "There is no related enetity." }, { "input": "Within Tar, the HAMP domain forms a parallel four - helix bundle consisting of a dimer of two amphipathic helices connected by a flexible linker.", "output": "There is no related enetity." }, { "input": "In the nuclear magnetic resonance structure of an archaeal HAMP domain, residues corresponding to the MLLT sequence between Arg - 214 at the end of TM2 and Pro - 219 of Tar are an N - terminal helical extension of AS1.", "output": "There is no related enetity." }, { "input": "We modified this region to test whether it behaves as a continuous helical connection between TM2 and HAMP.", "output": "There is no related enetity." }, { "input": "First, one to four Gly residues were inserted between Thr - 218 and Pro - 219.", "output": "There is no related enetity." }, { "input": "Second, the MLLT sequence was replaced with one to nine Gly residues.", "output": "There is no related enetity." }, { "input": "Third, the sequence was shortened or extended with residues compatible with helix formation.", "output": "There is no related enetity." }, { "input": "Cells expressing receptors in which the MLLT sequence was shortened to MLL or in which the MLLT sequence was replaced by four Gly residues performed good aspartate chemotaxis.", "output": "There is no related enetity." }, { "input": "Other mutant receptors supported diminished aspartate taxis.", "output": "There is no related enetity." }, { "input": "Most mutant receptors had biased signal outputs and / or abnormal patterns of adaptive methylation.", "output": "There is no related enetity." }, { "input": "We interpret these results to indicate that a strong, permanent helical connection between TM2 and the HAMP domain is not necessary for normal transmembrane signaling.", "output": "There is no related enetity." }, { "input": "Dissection of the phytohormonal regulation of trichome formation and biosynthesis of the antimalarial compound artemisinin in Artemisia annua plants.", "output": "Artemisia annua plants." }, { "input": "* Biosynthesis of the sesquiterpene lactone and potent antimalarial drug artemisinin occurs in glandular trichomes of Artemisia annua plants and is subjected to a strict network of developmental and other regulatory cues.", "output": "Artemisia annua plants." }, { "input": "* The effects of three hormones, jasmonate, gibberellin and cytokinin, were studied at the structural and molecular levels in two different A. annua chemotypes by microscopic analysis of gland development, and by targeted metabolite and transcript profiling.", "output": "A . annua." }, { "input": "Furthermore, a genome - wide cDNA - amplified fragment length polymorphism ( AFLP ) - based transcriptome profiling was carried out of jasmonate - elicited leaves at different developmental stages.", "output": "There is no related enetity." }, { "input": "* Although cytokinin and gibberellin positively affected at least one aspect of gland formation, these two hormones did not stimulate artemisinin biosynthesis.", "output": "There is no related enetity." }, { "input": "Only jasmonate simultaneously promoted gland formation and coordinated transcriptional activation of biosynthetic gene expression, which ultimately led to increased sesquiterpenoid accumulation with chemotype - dependent effects on the distinct pathway branches.", "output": "There is no related enetity." }, { "input": "Transcriptome profiling revealed a trichome - specific fatty acyl - coenzyme A reductase, trichome - specific fatty acyl - CoA reductase 1 ( TFAR1 ), the expression of which correlates with trichome development and sesquiterpenoid biosynthesis.", "output": "There is no related enetity." }, { "input": "* TFAR1 is potentially involved in cuticular wax formation during glandular trichome expansion in leaves and flowers of A. annua plants.", "output": "A . annua plants." }, { "input": "Analysis of phytohormone - modulated transcriptional regulons provides clues to dissect the concerted regulation of metabolism and development of plant trichomes.", "output": "There is no related enetity." }, { "input": "Climate effects on population fluctuations of the white - throated dipper Cinclus cinclus.", "output": "white - throated dipper, Cinclus cinclus." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Climate change may have profound consequences for many organisms.", "output": "There is no related enetity." }, { "input": "We have studied fluctuations in a population of the white - throated dipper Cinclus cinclus during 31 years ( 1978 - 2008 ) in a river system in southern Norway in relation to both large - scale and local weather conditions occurring during the non - breeding season.", "output": "white - throated dipper, Cinclus cinclus." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Multiple regression and partial least squares regression were used to model the growth rate of the population, accounting for population size in the previous year.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Population growth was influenced by North Atlantic Oscillation ( NAO ), mean winter temperature, precipitation and timing of ice formation on the main lake in the river system in autumn.", "output": "There is no related enetity." }, { "input": "These variables explained 84 % of the variation in population growth over the 31 - year study period.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Local winter conditions played a prominent role in explaining the population fluctuations, which is plausible because the dipper depends on open water for foraging.", "output": "There is no related enetity." }, { "input": "In the study area, winters can be harsh and rivers and lakes may freeze and severely affect the subsequent population size of the dipper in spring.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "The breeding population of the dipper does not seem yet to have reached a level where all possible territories in the area have been occupied, even after mild winters, and the estimated carrying capacity is also decidedly lower ( 66 breeding pairs ) than the number of available territories.", "output": "There is no related enetity." }, { "input": "If the trend of milder winters continues, the population might increase in the future.", "output": "There is no related enetity." }, { "input": "However, strong climate variation is expected to continue in the future, and hence periods of rapid growth of the dipper population will probably be followed by severe declines.", "output": "There is no related enetity." }, { "input": "Interference from long - tailed finches constrains reproduction in the endangered Gouldian finch.", "output": "long - tailed finches, Gouldian finch." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Interspecific interference competition for nest - sites among cavity - nesting birds can have important effects on reproductive fitness and the distribution of competing species.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We observed interference at nest - sites in free - living populations of the endangered Gouldian finch ( Erythrura gouldiae ) and sympatric long - tailed finch ( Poephila acuticauda ), and also experimentally tested the relative strength and effect of interference at nest - sites in captive populations.", "output": "Gouldian finch, Erythrura gouldiae, long - tailed finch, Poephila acuticauda." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Levels of competitive interference at nest - sites in the wild were high for Gouldian, but not long - tailed finches, and interference frequency was inversely related to Gouldian finch reproductive success.", "output": "Gouldian, long - tailed finches, Gouldian finch." }, { "input": "High levels of interference conferred reduced fledging success but did not affect offspring condition.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Captive experiments corroborated the field data, also demonstrating fitness costs of interspecific competition, and that long - tailed finches dominated resources under standardized conditions.", "output": "long - tailed finches." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Such asymmetrical competition dynamics are likely to constrain reproduction in Gouldian finch populations, potentially affecting recruitment and hindering the recovery of remaining populations of this endangered species.", "output": "Gouldian finch." }, { "input": "Predation is associated with variation in colour pattern, but not body shape or colour reflectance, in a rainbowfish ( Melanotaenia australis ).", "output": "rainbowfish, Melanotaenia australis." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "In freshwater fishes, inter - population variation in male phenotype is often associated with differences in predation intensity, but these effects can be difficult to disentangle from environmental influences.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "The western rainbowfish Melanotaenia australis exhibits marked sexual dimorphism - females are plain with a slender body, while males have striking coloration and are deeper in the body.", "output": "western rainbowfish, Melanotaenia australis." }, { "input": "Male traits differ in expression among populations, but this has not been described or explored in the literature.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "This paper describes a study designed to test for geographic structuring of male phenotype in M. australis and to determine whether between - population variation in male phenotype is attributable to variation in predation regime, after accounting for environment.", "output": "M . australis." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "We collected data describing habitat, and the size, activity and abundance of predators at sites containing M. australis populations.", "output": "M . australis." }, { "input": "We then used photography, spectrometry and geometric morphometrics to describe colour pattern, spectral reflectance and body shape in males from these populations.", "output": "There is no related enetity." }, { "input": "Finally, we used permutation - based multivariate statistics to partition variance in these traits according to environment and predation regime.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Downstream environments posed higher predation risk to M. australis.", "output": "M . australis." }, { "input": "Furthermore, males from these sites consistently exhibited larger cheek spots and fewer coloured lateral stripes than those from upstream sites.", "output": "There is no related enetity." }, { "input": "Variation in predation regime accounted for a significant proportion of the total variance in these traits ( 30 * 9 % ), after controlling for the effects of environment.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "Variation in predation regime did not explain variation in reflectance or shape.", "output": "There is no related enetity." }, { "input": "Environmental variation, however, explained a significant portion of the total variance in reflectance ( 74 * 9 % ), and there was a strong trend towards it explaining a portion of the total variance in body shape ( 34 * 9 % ).", "output": "There is no related enetity." }, { "input": "7.", "output": "There is no related enetity." }, { "input": "We conclude that natural selection by predators may be an important determinant of the evolution of colour pattern variation in M. australis, but not of that of body shape or colour reflectance.", "output": "M . australis." }, { "input": "8.", "output": "There is no related enetity." }, { "input": "Further study of M. australis will complement existing models, which show complex relationships between predation regime, environment and phenotype.", "output": "M . australis." }, { "input": "Understanding these relationships is prerequisite to predicting the evolution of phenotypic variation in natural systems.", "output": "There is no related enetity." }, { "input": "Adult predation risk drives shifts in parental care strategies: a long - term study.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Grouping provides antipredatory benefits, and therefore aggregation tendencies increase under heightened predation risk.", "output": "There is no related enetity." }, { "input": "In socially breeding groups, however, conflicts over reproductive shares or safety tend to disintegrate groups.", "output": "There is no related enetity." }, { "input": "Group formation thereby involves a balance between the antipredatory benefits of aggregation and the destabilizing effect of reproductive conflict.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We study the grouping behaviour of a facultatively social precocial sea duck with uniparental female care, the eider ( Somateria mollissima Linnaeus ).", "output": "Somateria mollissima." }, { "input": "Females tend their young solitarily or in groups of 2 - 5 females.", "output": "There is no related enetity." }, { "input": "Here, we focus on the effect predation on adults has on group - formation decisions of brood - caring females.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "By modifying an existing bidding game over care, we model the effects of predation risk on the width of the window of selfishness, which delimits the reproductive sharing allowing cooperation within brood - rearing coalitions, and generate predictions about the relative frequencies of solitary versus cooperative parental care modes.", "output": "There is no related enetity." }, { "input": "Furthermore, we model the dilution effect as a function of female group size and predation risk.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "The window of selfishness widens with increasing predation risk, and the dilution of predation risk increases with both female group size and increasing predation risk, yielding the following predictions: ( i ) cooperative brood care becomes more prevalent and, conversely, solitary brood care less prevalent under heightened predation risk and ( ii ) group sizes increase concomitantly.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "We tested these predictions using 13 years of data on female grouping decisions and annual predation rates, while controlling for the potentially confounding effect of female body condition.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "Our data supported both predictions, where heightened predation risk of nesting females, but not changes in their condition, increased the relative frequency of cooperative brood care.", "output": "There is no related enetity." }, { "input": "Increased female nesting mortality also resulted in larger groups of cooperative females.", "output": "There is no related enetity." }, { "input": "7.", "output": "There is no related enetity." }, { "input": "The predation risk of incubating females has long - term implications for later parental care decisions.", "output": "There is no related enetity." }, { "input": "We discuss the potential consequences of predation - induced shifts in group size on per capita fitness and population - wide productivity.", "output": "There is no related enetity." }, { "input": "Evidence for functional divergence in arbuscular mycorrhizal fungi from contrasting climatic origins.", "output": "There is no related enetity." }, { "input": "A considerable amount of phenotypic, genetic and symbiotic functional variability has been documented in arbuscular mycorrhizal fungi ( AMF ).", "output": "There is no related enetity." }, { "input": "However, little is known about whether distinct AMF ecotypes have evolved within their geographic range.", "output": "There is no related enetity." }, { "input": "We tested the hypothesis that AMF growing at temperatures closer to those prevalent within their origin would benefit their host and grow more than isolates distant from their native conditions.", "output": "There is no related enetity." }, { "input": "For each of six AMF species, we chose pairs of isolates that originated from distant areas with contrasting climates.", "output": "There is no related enetity." }, { "input": "Each isolate was grown in association with two grass species of different thermal optima at two temperature settings.", "output": "There is no related enetity." }, { "input": "Thus, we also tested whether AMF from different climatic origins were dependent on the thermal adaptation of the host plant species or to temperature per se.", "output": "There is no related enetity." }, { "input": "Although fungal growth was not directly affected by temperature, we found that AMF isolates originating from contrasting climates consistently and differentially altered plant growth.", "output": "There is no related enetity." }, { "input": "Our results suggest that AMF from contrasting climates have altered symbiotic function, thus linking an abiotic factor to ecotypic differentiation of putatively important symbionts.", "output": "There is no related enetity." }, { "input": "A new, vapour - phase mechanism for stomatal responses to humidity and temperature.", "output": "There is no related enetity." }, { "input": "A new mechanism for stomatal responses to humidity and temperature is proposed.", "output": "There is no related enetity." }, { "input": "Unlike previously - proposed mechanisms, which rely on liquid water transport to create water potential gradients within the leaf, the new mechanism assumes that water transport to the guard cells is primarily through the vapour phase.", "output": "There is no related enetity." }, { "input": "Under steady - state conditions, guard cells are assumed to be in near - equilibrium with the water vapour in the air near the bottom of the stomatal pore.", "output": "There is no related enetity." }, { "input": "As the water potential of this air varies with changing air humidity and leaf temperature, the resultant changes in guard cell water potential produce stomatal movements.", "output": "There is no related enetity." }, { "input": "A simple, closed - form, mathematical model based on this idea is derived.", "output": "There is no related enetity." }, { "input": "The new model is parameterized for a previously published set of data and is shown to fit the data as well as or better than existing models.", "output": "There is no related enetity." }, { "input": "The model contains mathematical elements that are consistent with previously - proposed mechanistic models based on liquid flow as well as empirical models based on relative humidity.", "output": "There is no related enetity." }, { "input": "As such, it provides a mechanistic explanation for the realm of validity for each of these approaches.", "output": "There is no related enetity." }, { "input": "Cadmium uptake and sequestration kinetics in individual leaf cell protoplasts of the Cd / Zn hyperaccumulator Thlaspi caerulescens.", "output": "Thlaspi caerulescens." }, { "input": "Hyperaccumulators store accumulated metals in the vacuoles of large leaf epidermal cells ( storage cells ).", "output": "There is no related enetity." }, { "input": "For investigating cadmium uptake, we incubated protoplasts obtained from leaves of Thlaspi caerulescens ( Ganges ecotype ) with a Cd - specific fluorescent dye.", "output": "Thlaspi caerulescens ( Ganges ecotype )." }, { "input": "A fluorescence kinetic microscope was used for selectively measuring Cd - uptake and photosynthesis in different cell types, so that physical separation of cell types was not necessary.", "output": "There is no related enetity." }, { "input": "Few minutes after its addition, cadmium accumulated in the cytoplasm before its transport into the vacuole.", "output": "There is no related enetity." }, { "input": "This demonstrated that vacuolar sequestration is the rate - limiting step in cadmium uptake into protoplasts of all leaf cell types.", "output": "There is no related enetity." }, { "input": "During accumulation in the cytoplasm, Cd - rich vesicle - like structures were observed.", "output": "There is no related enetity." }, { "input": "Cd uptake rates into epidermal storage cells were higher than into standard - sized epidermal cells and mesophyll cells.", "output": "There is no related enetity." }, { "input": "This shows that the preferential heavy metal accumulation in epidermal storage cells, previously observed for several metals in intact leaves of various hyperaccumulator species, is due to differences in active metal transport and not differences in passive mechanisms like transpiration stream transport or cell wall adhesion.", "output": "There is no related enetity." }, { "input": "Combining this with previous studies, it seems likely that the transport steps over the plasma and tonoplast membranes of leaf epidermal storage cells are driving forces behind the hyperaccumulation phenotype.", "output": "There is no related enetity." }, { "input": "Factors required for the high CO2 specificity of the anaerobically induced maize GapC4 promoter in transgenic tobacco.", "output": "maize, tobacco." }, { "input": "Flooding, a natural cause of anaerobiosis, is often accompanied by high CO ( 2 ) concentrations in the flood water.", "output": "There is no related enetity." }, { "input": "Plants need to respond to these environmental conditions.", "output": "There is no related enetity." }, { "input": "Strong anaerobic reporter gene activity in tobacco ( Nicotiana tabacum ) controlled by the glycolytic glyceraldehyde - 3 - phosphate dehydrogenase ( GapC4 ) promoter from maize ( Zea mays ) depends on the presence of CO ( 2 ) and light.", "output": "tobacco, Nicotiana tabacum, maize, Zea mays." }, { "input": "To identify factors required for CO ( 2 ) regulated gene expression, promoter deletions fused to the Beta - glucuronidase reporter gene were studied in transgenic tobacco.", "output": "tobacco." }, { "input": "Deletion of a 40 bp fragment directly upstream of the TATA box leads to increased anaerobic reporter gene activity both, in the presence and absence of CO ( 2 ).", "output": "There is no related enetity." }, { "input": "This deletion does not affect light specific anaerobic expression.", "output": "There is no related enetity." }, { "input": "A positive correlation between increasing CO ( 2 ) concentrations and gene activity is observed.", "output": "There is no related enetity." }, { "input": "Electrophoretic mobility shift experiments indicate that tobacco nuclear extracts harbour proteins that bind to part of the 40 bp fragment.", "output": "tobacco." }, { "input": "Database assisted as well as experimental analysis reveal a role for AP2 / EREBP transcription factors for conferring the high CO ( 2 ) specificity to the GapC4 promoter in tobacco leaves.", "output": "tobacco." }, { "input": "This work highlights the importance for plants to respond to high environmental CO ( 2 ) concentrations under anaerobic conditions.", "output": "There is no related enetity." }, { "input": "Arabidopsis thaliana populations show clinal variation in a climatic gradient associated with altitude.", "output": "Arabidopsis thaliana." }, { "input": "* Understanding the adaptive basis of life history variation is a central goal in evolutionary ecology.", "output": "There is no related enetity." }, { "input": "The use of model species enables the combination of molecular mechanistic knowledge with ecological and evolutionary questions, but the study of life history variation in natural environments is required to merge these disciplines.", "output": "There is no related enetity." }, { "input": "* Here, we tested for clinal variation in life history and associated traits along an environmental and altitudinal gradient in the model species Arabidopsis thaliana.", "output": "Arabidopsis thaliana." }, { "input": "Seventeen natural populations of A. thaliana were geo - referenced in north - eastern Spain on a gradient in which precipitation increases but maximum spring temperature and minimum winter temperature decrease with altitude.", "output": "A . thaliana." }, { "input": "* One hundred and eighty - nine genotypes from the 17 populations were grown under uniform controlled conditions.", "output": "There is no related enetity." }, { "input": "Variations in traits related to biomass allocation, fecundity, phenology and vegetative growth were tested for relationships with the altitude and climatic variables associated with the home sites.", "output": "There is no related enetity." }, { "input": "Above - ground mass, number of rosette leaves at bolting, developmental time and seed weight increased with the home site ' s altitude.", "output": "There is no related enetity." }, { "input": "Root allocation, vegetative growth during winter and number of seeds decreased with altitude.", "output": "There is no related enetity." }, { "input": "* We suggest that the differences among home sites provide clues to the variation in adaptive strategies associated with the climatic gradient.", "output": "There is no related enetity." }, { "input": "We compared these results with adaptations and clinal relationships reported for other species and with molecular mechanisms described in Arabidopsis.", "output": "Arabidopsis." }, { "input": "Recovery of ectomycorrhiza after ' nitrogen saturation ' of a conifer forest.", "output": "There is no related enetity." }, { "input": "Trees reduce their carbon ( C ) allocation to roots and mycorrhizal fungi in response to high nitrogen ( N ) additions, which should reduce the N retention capacity of forests.", "output": "There is no related enetity." }, { "input": "The time needed for recovery of mycorrhizas after termination of N loading remains unknown.", "output": "There is no related enetity." }, { "input": "Here, we report the long - term impact of N loading and the recovery of ectomycorrhiza after high N loading on a Pinus sylvestris forest.", "output": "Pinus sylvestris." }, { "input": "We analysed the N % and abundance of the stable isotope ( 15 ) N in tree needles and soil, soil microbial fatty acid biomarkers and fungal DNA.", "output": "There is no related enetity." }, { "input": "Needles in N - loaded plots became enriched in ( 15 ) N, reflecting decreased N retention by mycorrhizal fungi and isotopic discrimination against ( 15 ) N during loss of N.", "output": "There is no related enetity." }, { "input": "Meanwhile, needles in N - limited ( control ) plots became depleted in ( 15 ) N, reflecting high retention of ( 15 ) N by mycorrhizal fungi.", "output": "There is no related enetity." }, { "input": "N loading was terminated after 20yr.", "output": "There is no related enetity." }, { "input": "The delta ( 15 ) N and N % of the needles decreased 6yr after N loading had been terminated, and approached values in control plots after 15yr.", "output": "There is no related enetity." }, { "input": "This decrease, and the larger contributions compared with N - loaded plots of a fungal fatty acid biomarker and ectomycorrhizal sequences, suggest recovery of ectomycorrhiza.", "output": "There is no related enetity." }, { "input": "High N loading rapidly decreased the functional role of ectomycorrhiza in the forest N cycle, but significant recovery occurred within 6 - 15yr after termination of N loading.", "output": "There is no related enetity." }, { "input": "Structural and hydraulic correlates of heterophylly in Ginkgo biloba.", "output": "Ginkgo biloba." }, { "input": "This study investigates the functional significance of heterophylly in Ginkgo biloba, where leaves borne on short shoots are ontogenetically distinct from those on long shoots.", "output": "Ginkgo biloba." }, { "input": "Short shoots are compact, with minimal internodal elongation; their leaves are supplied with water through mature branches.", "output": "There is no related enetity." }, { "input": "Long shoots extend the canopy and have significant internodal elongation; their expanding leaves receive water from a shoot that is itself maturing.", "output": "There is no related enetity." }, { "input": "Morphology, stomatal traits, hydraulic architecture, Huber values, water transport efficiency, in situ gas exchange and laboratory - based steady - state hydraulic conductance were examined for each leaf type.", "output": "There is no related enetity." }, { "input": "Both structure and physiology differed markedly between the two leaf types.", "output": "There is no related enetity." }, { "input": "Short - shoot leaves were thinner and had higher vein density, lower stomatal pore index, smaller bundle sheath extensions and lower hydraulic conductance than long - shoot leaves.", "output": "There is no related enetity." }, { "input": "Long shoots had lower xylem area: leaf area ratios than short shoots during leaf expansion, but this ratio was reversed at shoot maturity.", "output": "There is no related enetity." }, { "input": "Long - shoot leaves had higher rates of photosynthesis, stomatal conductance and transpiration than short - shoot leaves.", "output": "There is no related enetity." }, { "input": "We propose that structural differences between the two G. biloba leaf types reflect greater hydraulic limitation of long - shoot leaves during expansion.", "output": "G . biloba." }, { "input": "In turn, differences in physiological performance of short - and long - shoot leaves correspond to their distinct ontogeny and architecture.", "output": "There is no related enetity." }, { "input": "Symbiotic Chlorella vulgaris of the ciliate Paramecium bursaria plays an important role in maintaining perialgal vacuole membrane functions.", "output": "Chlorella vulgaris, Paramecium bursaria." }, { "input": "Treatment of symbiotic alga - bearing Paramecium bursaria cells with a protein synthesis inhibitor, cycloheximide, induces synchronous swelling of all perialgal vacuoles at about 24h after treatment under a constant light condition.", "output": "Paramecium bursaria." }, { "input": "Subsequently, the vacuoles detach from the host cell cortex.", "output": "There is no related enetity." }, { "input": "The algae in the vacuoles are digested by the host ' s lysosomal fusion to the vacuoles.", "output": "There is no related enetity." }, { "input": "To elucidate the timing of algal degeneration, P. bursaria cells were treated with cycloheximide under a constant light condition.", "output": "P . bursaria." }, { "input": "Then the cells were observed using transmission electron microscopy.", "output": "There is no related enetity." }, { "input": "Results show that algal chloroplasts and nuclei degenerated within 9h after treatment, but before the synchronous swelling of the perialgal vacuole and appearance of acid phosphatase activity in the perialgal vacuole by lysosomal fusion.", "output": "There is no related enetity." }, { "input": "Treatment with cycloheximide under a constant dark condition and treatment with chloramphenicol under a constant light condition induced neither synchronous swelling of the vacuoles nor digestion of the algae inside the vacuoles.", "output": "There is no related enetity." }, { "input": "These results demonstrate that algal proteins synthesized during photosynthesis are necessary to maintain chloroplastic and nuclear structures, and that inhibition of protein synthesis induces rapid lysis of these organelles, after which synchronous swelling of the perialgal vacuole and fusion occur with the host lysosomes.", "output": "There is no related enetity." }, { "input": "Rapid and sensitive detection of infectious hypodermal and hematopoietic necrosis virus by loop - mediated isothermal amplification combined with a lateral flow dipstick.", "output": "infectious hypodermal and hematopoietic necrosis virus." }, { "input": "Infectious hypodermal and hematopoietic necrosis virus ( IHHNV ) is an important shrimp pathogen that causes mortality in Penaeus stylirostris and stunting ( called runt deformity syndrome or RDS ) in Penaeus vannamei.", "output": "Infectious hypodermal and hematopoietic necrosis virus, IHHNV, Penaeus stylirostris, Penaeus vannamei." }, { "input": "Loop - mediated isothermal amplification ( LAMP ) allows rapid amplification of nucleic acids under isothermal conditions.", "output": "There is no related enetity." }, { "input": "It can be combined with a chromatographic lateral flow dipstick ( LFD ) for highly specific, rapid and simple visual detection of IHHNV - specific amplicons.", "output": "IHHNV." }, { "input": "Using this protocol, a 30 - min amplification followed by 5 min hybridization with an FITC - labeled DNA probe and 5 min LFD resulted in visualization of DNA amplicons trapped at the LFD test line.", "output": "There is no related enetity." }, { "input": "Thus, 10 min for rapid DNA extraction followed by LAMP combined with LFD detection resulted in a total assay time of approximately 50 min.", "output": "There is no related enetity." }, { "input": "Detection sensitivity was comparable to other methods used commonly for nested PCR detection of IHHNV but had the additional advantages of reduced assay time, confirmation of amplicon identity by hybridization and elimination of electrophoresis with carcinogenic ethidium bromide.", "output": "IHHNV." }, { "input": "The FvMK1 mitogen - activated protein kinase gene regulates conidiation, pathogenesis, and fumonisin production in Fusarium verticillioides.", "output": "Fusarium verticillioides." }, { "input": "Fusarium verticillioides is one of the most important fungal pathogens to cause destructive diseases of maize worldwide.", "output": "Fusarium verticillioides, maize." }, { "input": "Fumonisins produced by the fungus are harmful to human and animal health.", "output": "human." }, { "input": "To date, our understanding of the molecular mechanisms associated with pathogenicity and fumonisin biosynthesis in F. verticillioides is limited.", "output": "F . verticillioides." }, { "input": "Because MAP kinase pathways have been implicated in regulating diverse processes important for plant infection in phytopathogenic fungi, in this study we identified and functionally characterized the FvMK1 gene in F. verticillioides.", "output": "F . verticillioides." }, { "input": "FvMK1 is orthologous to FMK1 in F. oxysporum and GPMK1 in F. graminearum.", "output": "F . oxysporum, F . graminearum." }, { "input": "The Fvmk1 deletion mutant was reduced in vegetative growth and production of microconidia.", "output": "There is no related enetity." }, { "input": "However, it was normal in sexual reproduction and increased in the production of macroconidia.", "output": "There is no related enetity." }, { "input": "In infection assays with developing corn kernels, the Fvmk1 mutant was non - pathogenic and failed to colonize through wounding sites.", "output": "corn." }, { "input": "It also failed to cause stalk rot symptoms beyond the inoculation sites on corn stalks, indicating that FvMK1 is essential for plant infection.", "output": "corn." }, { "input": "Furthermore, the Fvmk1 mutant was significantly reduced in fumonisin production and expression levels of FUM1 and FUM8, two genes involved in fumonisin biosynthesis.", "output": "There is no related enetity." }, { "input": "The defects of the Fvmk1 mutant were fully complemented by re - introducing the wild type FvMK1 allele.", "output": "There is no related enetity." }, { "input": "These results demonstrate that FvMK1 plays critical roles in the regulation of vegetative growth, asexual reproduction, fumonisin biosynthesis, and pathogenicity.", "output": "There is no related enetity." }, { "input": "Phylogeny and historical biogeography of true morels ( Morchella ) reveals an early Cretaceous origin and high continental endemism and provincialism in the Holarctic.", "output": "morels." }, { "input": "True morels ( Morchella, Ascomycota ) are arguably the most highly - prized of the estimated 1. 5 million fungi that inhabit our planet.", "output": "morels." }, { "input": "Field guides treat these epicurean macrofungi as belonging to a few species with cosmopolitan distributions, but this hypothesis has not been tested.", "output": "There is no related enetity." }, { "input": "Prompted by the results of a growing number of molecular studies, which have shown many microbes exhibit strong biogeographic structure and cryptic speciation, we constructed a 4 - gene dataset for 177 members of the Morchellaceae to elucidate their origin, evolutionary diversification and historical biogeography.", "output": "There is no related enetity." }, { "input": "Diversification time estimates place the origin of the Morchellaceae in the middle Triassic 243. 63 ( 95 % highest posterior density [ HPD ] interval: 169. 35 - 319. 89 ) million years ago ( Mya ) and the divergence of Morchella from its closest relatives in the early Cretaceous 129. 61 ( 95 % HPD interval: 90. 26 - 173. 16 ) Mya, both within western North America.", "output": "There is no related enetity." }, { "input": "Phylogenetic analyses identified three lineages within Morchella: a basal monotypic lineage represented by Morchella rufobrunnea, and two sister clades comprising the black morels ( Elata Clade, 26 species ) and yellow morels ( Esculenta Clade, 16 species ).", "output": "Morchella rufobrunnea, black morels, yellow morels." }, { "input": "Morchella possesses a Laurasian distribution with 37 / 41 species restricted to the Holarctic.", "output": "There is no related enetity." }, { "input": "All 33 Holarctic species represented by multiple collections exhibited continental endemism.", "output": "There is no related enetity." }, { "input": "Moreover, 16 / 18 North American and 13 / 15 Eurasian species appeared to exhibit provincialism.", "output": "There is no related enetity." }, { "input": "Although morel fruit bodies produce thousands of explosively discharged spores that are well suited to aerial dispersal, our results suggest that they are poorly adapted at invading novel niches.", "output": "There is no related enetity." }, { "input": "Morels also appear to have retained the ancestral fruit body plan, which has remained remarkably static since the Cretaceous.", "output": "Morels." }, { "input": "A genomic map enriched for markers linked to Avr1 in Cronartium quercuum f. sp. fusiforme.", "output": "Cronartium quercuum f . sp . fusiforme." }, { "input": "A novel approach is presented to map avirulence gene Avr1 in the basidiomycete Cronartium quercuum f. sp. fusiforme, the causal agent of fusiform rust disease in pines.", "output": "Cronartium quercuum f . sp . fusiforme." }, { "input": "DNA markers tightly linked to resistance gene Fr1 in loblolly pine tree 10 - 5 were used to classify 10 - 5 seedling progeny as either resistant or susceptible.", "output": "loblolly pine." }, { "input": "A single dikaryotic isolate ( P2 ) heterozygous at the corresponding Avr1 gene was developed by crossing Fr1 avirulent isolate SC20 - 21 with Fr1 virulent isolate NC2 - 40.", "output": "There is no related enetity." }, { "input": "Bulk basidiospore inoculum derived from isolate P2 was used to challenge the pine progeny.", "output": "There is no related enetity." }, { "input": "The ability to unambiguously marker classify 10 - 5 progeny as resistant ( selecting for virulence ) or susceptible ( non - selecting ) permitted the genetic mapping of the corresponding Avr1 gene by bulked segregant analysis.", "output": "There is no related enetity." }, { "input": "Using this approach, 14 genetic markers significantly linked to Avr1 were identified and placed within the context of a genome - wide linkage map produced for isolate P2 using samples from susceptible seedlings.", "output": "There is no related enetity." }, { "input": "Universal primers for rapid detection of hytrosaviruses.", "output": "There is no related enetity." }, { "input": "Hytrosaviridae is a proposed virus family encompassing viruses that cause salivary gland hypertrophy ( SGH ) syndrome in infected insects and reduce the fertility in their dipteran insect hosts.", "output": "There is no related enetity." }, { "input": "They contain a large, double stranded DNA genome of 120 - 190 kbp.", "output": "There is no related enetity." }, { "input": "To date, these viruses have been detected only in adult Diptera.", "output": "There is no related enetity." }, { "input": "These include hytrosaviruses detected in various tsetse fly species ( Glossina spp. ), the narcissus bulb fly Merodon equestris and the house fly Musca domestica.", "output": "narcissus bulb fly, Merodon equestris, house fly, Musca domestica." }, { "input": "The limited number of hytrosaviruses reported to date may be a reflection of the frequent absence of external symptoms in infected adult flies and the fact that the virus does not cause rapid mortality.", "output": "There is no related enetity." }, { "input": "Based on the complete genome sequence of Glossinia pallidipes ( GpSGHV ) and Musca domestica ( MdSGHV ) salivary gland hypertrophy viruses, a PCR based methodology was developed to detect the viruses in these species.", "output": "Glossinia pallidipes, Musca domestica." }, { "input": "To be able to detect hytrosaviruses in other Diptera, five degenerate primer pairs were designed and tested on GpSGHV and MdSGHV DNA using gradient PCR with annealing temperatures from 37 to 61 ^ 0C.", "output": "There is no related enetity." }, { "input": "Two pairs of primers were selected from p74, two pairs from PIF - 1 and one pair from ODV - e66 homologous proteins.", "output": "There is no related enetity." }, { "input": "Four primer pairs generated a virus specific PCR product on both MdSGHV and GpSGHV at all tested annealing temperatures, while the ODV - e66 based primers did not generate a virus specific product with annealing temperatures higher that 47 ^ 0C.", "output": "There is no related enetity." }, { "input": "No non - specific PCR product was found when using genomic DNA of infected flies as template DNA.", "output": "There is no related enetity." }, { "input": "These results offer new sets of primers that could be used to detect hytrosaviruses in other insects.", "output": "There is no related enetity." }, { "input": "Simultaneous virus - specific detection of the two cassava brown streak - associated viruses by RT - PCR reveals wide distribution in East Africa, mixed infections, and infections in Manihot glaziovii.", "output": "cassava, Manihot glaziovii." }, { "input": "The expanding cassava brown streak disease ( CBSD ) epidemic in East Africa is caused by two ipomoviruses ( genus Ipomovirus; Potyviridae ), namely, Cassava brown streak virus ( CBSV ), and Ugandan cassava brown streak virus ( UCBSV ) that was described recently.", "output": "cassava, Cassava brown streak virus, CBSV, Ugandan cassava brown streak virus, UCBSV." }, { "input": "A reverse transcription polymerase chain reaction ( RT - PCR ) based diagnostic method was developed in this study for simultaneous virus - specific detection of the two viruses.", "output": "There is no related enetity." }, { "input": "Results showed that CBSV and UCBSV are distributed widely in the highlands ( > 1000 m above the sea level ) of the Lake Victoria zone in Uganda and Tanzania and also in the Indian Ocean costal lowlands of Tanzania.", "output": "CBSV, UCBSV." }, { "input": "Isolates of UCBSV from the Lake Victoria zone were placed to two phylogenetic clusters in accordance with their origin in Uganda or Tanzania, respectively.", "output": "UCBSV." }, { "input": "Mixed infections with CBSV and UCBSV were detected in many cassava plants in the areas surveyed.", "output": "CBSV, UCBSV, cassava." }, { "input": "CBSV was also detected in the perennial species Manihot glaziovii ( DNA - barcoded in this study ) in Tanzania, which revealed the first virus reservoir other than cassava.", "output": "CBSV, Manihot glaziovii, cassava." }, { "input": "The method for detection of CBSV and UCBSV described in this study has important applications for plant quarantine, resistance breeding of cassava, and studies on epidemiology and control of CBSD in East Africa.", "output": "CBSV, UCBSV, cassava." }, { "input": "Development of a blocking ELISA for detection of serum neutralizing antibodies against porcine circovirus type 2.", "output": "porcine circovirus type 2." }, { "input": "A monoclonal antibody ( Mab ) - based blocking ELISA was developed for the detection of serum neutralizing antibodies to porcine circovirus type 2 ( PCV2 ).", "output": "porcine circovirus type 2 ( PCV2 )." }, { "input": "The Mab with neutralizing activity, which was produced by immunizing a recombinant capsid protein of PCV2 expressed in insect cells, was used as the detector antibody.", "output": "There is no related enetity." }, { "input": "The assay was evaluated in comparison with a serum neutralization assay, and its sensitivity and specificity were determined to be 98. 8 % and 88. 5 %, respectively.", "output": "There is no related enetity." }, { "input": "A significant positive correlation was found between results of the blocking ELISA and the serum neutralization assay ( r = 0. 9381 ).", "output": "There is no related enetity." }, { "input": "The assay was verified by testing experimental and commercial pig sera.", "output": "pig." }, { "input": "A longitudinal antibody profile showed that serum neutralizing antibodies were detected 2 weeks after vaccination and that the detection rate reached 100 % at 4 weeks.", "output": "There is no related enetity." }, { "input": "The serum neutralizing antibody profile showed a decrease from the age of 4 to 13 weeks, and seroconversion after 13 weeks in pigs from a commercial pig farm.", "output": "pigs, pig." }, { "input": "Additionally, the positive detection rate in 703 sera collected from nine commercial pig farms was 73 %.", "output": "pig." }, { "input": "This report demonstrates that the assay is a simple, specific, sensitive and convenient method for epidemiological surveys and evaluations of serum neutralizing antibodies against PCV2.", "output": "There is no related enetity." }, { "input": "Oramoeba fumarolia gen. nov., sp. nov., a new marine heterolobosean amoeboflagellate growing at 54 ^ 0C.", "output": "Oramoeba fumarolia." }, { "input": "An amoeba strain was isolated from marine sediment taken from the beach near a fumarole in Italy.", "output": "There is no related enetity." }, { "input": "The trophozoites of this new marine species transforms into flagellates with variable numbers of flagella, from 2 to 10.", "output": "There is no related enetity." }, { "input": "The strain forms round to oval cysts.", "output": "There is no related enetity." }, { "input": "This thermophilic amoeboflagellate grows at temperatures up to 54 ^ 0C.", "output": "There is no related enetity." }, { "input": "Molecular phylogenetic analysis of the small subunit ribosomal DNA ( SSU rDNA ) places the amoeboflagellate in the Heterolobosea.", "output": "There is no related enetity." }, { "input": "The closest relatives are Stachyamoeba sp. ATCC50324, a strain isolated from an ocean sample, and Vrihiamoeba italica, a recent isolate from a rice field.", "output": "Stachyamoeba sp . ATCC50324, Vrihiamoeba italica, rice." }, { "input": "Like some other heterolobosean species, this new isolate has a group I intron in the SSU rDNA.", "output": "There is no related enetity." }, { "input": "Because of the unique place in the molecular phylogenetic tree, and because there is no species found in the literature with similar morphological and physiological characteristics, this isolate is considered to be a new genus and a new species, Oramoeba fumarolia gen. nov., sp. nov.", "output": "Oramoeba fumarolia." }, { "input": "Monoclonal antibody - based triple antibody sandwich - enzyme - linked immunosorbent assay and immunocapture reverse transcription - polymerase chain reaction for Odontoglossum ringspot virus detection.", "output": "Odontoglossum ringspot virus." }, { "input": "Odontoglossum ringspot virus ( ORSV ) infects numerous commercially important orchids and causes significant losses worldwide.", "output": "Odontoglossum ringspot virus, ORSV." }, { "input": "The coat protein ( CP ) gene of ORSV was cloned and expressed in Escherichia coli by using the pET - 32a expression vector, and the expression of recombinant protein was confirmed by Western blotting using anti - ORSV antibodies.", "output": "ORSV, Escherichia coli, ORSV." }, { "input": "The recombinant protein was purified using Ni - NTA agarose, and the purified protein was used as an immunogen to produce monoclonal antibodies ( MAbs ) and polyclonal antibodies ( PAbs ).", "output": "There is no related enetity." }, { "input": "Five murine MAbs against ORSV CP were obtained.", "output": "ORSV." }, { "input": "Among them, two MAbs ( 6B4 and 1D1 ) also reacted with TMV CP.", "output": "There is no related enetity." }, { "input": "The triple antibody sandwich enzyme - linked immunosorbent assay ( TAS - ELISA ) and immunocapture reverse transcription - polymerase chain reaction ( IC - RT - PCR ) methods using the MAb ( 8A5 ) were then developed for sensitive, specific, and rapid detection of ORSV.", "output": "ORSV." }, { "input": "TAS - ELISA and IC - RT - PCR could detect ORSV in the infected leaf saps with dilutions of 1: 10, 240 and 1: 81, 920 ( w / v, g mL ( - 1 ) ), respectively.", "output": "ORSV." }, { "input": "TAS - ELISA and IC - RT - PCR detections indicated that ORSV was prevalent in orchids in the Zhejiang Province of China.", "output": "ORSV." }, { "input": "Detection and discrimination of members of the family Luteoviridae by real - time PCR and SYBR ( R ) GreenER ( TM ) melting curve analysis.", "output": "There is no related enetity." }, { "input": "This study investigated the suitability of a two step real - time RT - PCR melting curve analysis as a tool for the detection and discrimination of nine species in the plant virus family Luteoviridae, being Soybean dwarf virus [ SbDV ], Bean leafroll virus [ BLRV ], Beet chlorosis virus [ BChV ], Beet mild yellowing virus [ BMYV ], Beet western yellows virus [ BWYV ], Cereal yellow dwarf virus - RPV [ CYDV - RPV ], Cucurbit aphid - borne yellows virus [ CABYV ], Potato leafroll virus [ PLRV ] and Turnip yellows virus [ TuYV ].", "output": "Soybean dwarf virus, SbDV, Bean leafroll virus, BLRV, Beet chlorosis virus, BChV, Beet mild yellowing virus, BMYV, Beet western yellows virus, BWYV, Cereal yellow dwarf virus - RPV, CYDV - RPV, Cucurbit aphid - borne yellows virus, CABYV, Potato leafroll virus, PLRV, Turnip yellows virus, TuYV." }, { "input": "Melting temperature and shape of the melting peak were analysed for 68 bp and 148 bp coat protein gene amplicons using SYBR ( R ) GreenER ( TM ) fluorescent dye.", "output": "There is no related enetity." }, { "input": "Specific melting peaks with unique melting temperature were observed for the various species of the family Luteoviridae using the 68 bp amplicon, but not with the 148 bp amplicon.", "output": "There is no related enetity." }, { "input": "Due to the high variability of sequences for some members of this family, different melting temperatures were also observed between different isolates of the species CYDV - RPV and TuYV.", "output": "CYDV - RPV, TuYV." }, { "input": "Nevertheless, discrimination between species was achieved for SbDV, BLRV, BChV, BMYV, CABYV and either PLRV or BWYV.", "output": "SbDV, BLRV, BChV, BMYV, CABYV, PLRV, BWYV." }, { "input": "Melting curve analysis, in this study, is a faster and more discriminatory alternative to gel electrophoresis of end - point PCR products for the detection of Luteoviridae infection.", "output": "There is no related enetity." }, { "input": "Detection and differentiation of tick - borne encephalitis virus subtypes by a reverse transcription quantitative real - time PCR and pyrosequencing.", "output": "tick - borne encephalitis virus." }, { "input": "Tick - borne encephalitis ( TBE ) virus causes one of the most important flaviviral infections of the human central nervous system in Europe and Asia.", "output": "Tick - borne encephalitis ( TBE ) virus, human." }, { "input": "In recent years the rate of TBE infection has been raising and the virus has been spreading to new areas.", "output": "TBE." }, { "input": "Currently, the diagnosis of TBE is based on detection of specific antibodies in patients ' sera which appear as late as about 2 weeks post - infection.", "output": "TBE." }, { "input": "For a timely diagnosis of TBE virus infections and epidemiological studies, a TBE virus - specific reverse transcription quantitative real - time PCR ( RT - qPCR ) followed by pyrosequencing was developed.", "output": "TBE virus, TBE virus." }, { "input": "The assay is based on one degenerated primer pair detecting all three human - pathogenic TBE virus subtypes with a detection limit of 10 copies.", "output": "human, TBE virus." }, { "input": "Even though primers and probe are highly degenerated, the assay is specific for TBE virus species and detects all subtypes with a comparable sensitivity.", "output": "TBE virus." }, { "input": "Furthermore, TBE virus RT - qPCR could be carried out as one - step or two - step assay.", "output": "TBE virus." }, { "input": "RT - qPCR can be followed by pyrosequencing which allows a rapid subtyping of TBE viruses.", "output": "TBE viruses." }, { "input": "For detection purposes an internal control to monitor RNA extraction, cDNA synthesis and amplification is included.", "output": "There is no related enetity." }, { "input": "In summary, the method is sensitive, highly specific and easy - to - handle tool for the detection and differentiation of TBE virus in the early phase of illness or in TBE host animal species and ticks.", "output": "TBE virus, TBE." }, { "input": "Adaptation of a Madin - Darby canine kidney cell line to suspension growth in serum - free media and comparison of its ability to produce avian influenza virus to Vero and BHK21 cell lines.", "output": "canine." }, { "input": "Madin - Darby canine kidney ( MDCK ) cells are currently considered for influenza vaccine manufacturing.", "output": "canine." }, { "input": "A drawback of these cells is their anchorage dependent growth, which greatly complicates process scale - up.", "output": "There is no related enetity." }, { "input": "In this paper a novel MDCK cell line ( MDCK - SFS ) is described that grows efficiently in suspension and retained high expression levels of both alpha - 2, 6 and alpha - 2, 3 sialic acid receptors, which bind preferably to human and avian influenza viruses, respectively.", "output": "There is no related enetity." }, { "input": "The production of avian influenza virus by BHK21, Vero and MDCK - SFS cell lines was compared.", "output": "There is no related enetity." }, { "input": "Although BHK21 cells consisted of two populations, one of which lacks the alpha - 2, 3 receptor, they supported the replication of two influenza strains to high titres.", "output": "There is no related enetity." }, { "input": "However, BHK21 cells are generally not applicable for influenza production since they supported the replication of six further strains poorly.", "output": "There is no related enetity." }, { "input": "MDCK - SFS cells yielded the highest infectious virus titres and virus genome equivalent concentration for five of the eight influenza strains analyzed and the highest hemagglutination activity for all eight virus strains.", "output": "There is no related enetity." }, { "input": "Taken together with their suitability for suspension growth this makes the MDCK - SFS cell line potentially useful for large scale influenza virus production.", "output": "There is no related enetity." }, { "input": "Cyanobacterial endosymbionts in the benthic dinoflagellate Sinophysis canaliculata ( Dinophysiales, Dinophyceae ).", "output": "There is no related enetity." }, { "input": "Photosynthetic dinoflagellates possess a great diversity of plastids that have been acquired through successful serial endosymbiosis.", "output": "There is no related enetity." }, { "input": "The peridinin - containing plastid in dinoflagellates is canonical, but many other types are known within this group.", "output": "There is no related enetity." }, { "input": "Within the Dinophysiales, several species of Dinophysis contain plastids, derived from cryptophytes or haptophytes.", "output": "There is no related enetity." }, { "input": "In this work, the presence of numerous intracellular cyanobacteria - like microorganisms compartmentalized by a separate membrane is reported for the first time within the benthic dinophysoid dinoflagellate Sinophysis canaliculata Quod et al., a species from a genus morphologically close to Dinophysis.", "output": "There is no related enetity." }, { "input": "Although the contribution of these cyanobacterial endosymbionts to S. canaliculata is still unknown, this finding suggests a possible undergoing primary endosymbiosis in a dinoflagellate.", "output": "There is no related enetity." }, { "input": "Roles of vaccinia virus genes E3L and K3L and host genes PKR and RNase L during intratracheal infection of C57BL / 6 mice.", "output": "vaccinia virus, mice." }, { "input": "The importance of the 2 ' - 5 ' oligoadenylate synthetase ( OAS ) / RNase L and double - stranded RNA ( dsRNA ) - dependent protein kinase ( PKR ) pathways in host interferon induction resulting from virus infection in response to dsRNA has been well documented.", "output": "There is no related enetity." }, { "input": "In poxvirus infections, the interactions between the vaccinia virus ( VV ) genes E3L and K3L, which target RNase L and PKR, respectively, serve to prevent the induction of the dsRNA - dependent induced interferon response in cell culture.", "output": "vaccinia virus, VV." }, { "input": "To determine the importance of these host genes in controlling VV infections, mouse single - gene knockouts of RNase L and PKR and double - knockout mice were studied following intratracheal infection with VV, VVDeltaK3L, or VVDeltaE3L.", "output": "VV, mouse, mice, VV, VVDeltaK3L." }, { "input": "VV caused lethal disease in all mouse strains.", "output": "mouse." }, { "input": "The single - knockout animals were more susceptible than wild - type animals, while the RNase L ( - / - ) PKR ( - / - ) mice were the most susceptible.", "output": "mice." }, { "input": "VVDeltaE3L infections of wild - type mice were asymptomatic, demonstrating that E3L plays a critical role in controlling the host immune response.", "output": "mice." }, { "input": "RNase L ( - / - ) mice showed no disease, whereas 20 % of the PKR ( - / - ) mice succumbed at a dose of 10 ( 8 ) PFU.", "output": "mice, mice." }, { "input": "Lethal disease was routinely observed in RNase L ( - / - ) PKR ( - / - ) mice inoculated with 10 ( 8 ) PFU of VVDeltaE3L, with a distinct pathology.", "output": "mice." }, { "input": "VVDeltaK3L infections exhibited no differences in virulence among any of the mouse constructs, suggesting that PKR is not the exclusive target of K3L.", "output": "mouse." }, { "input": "Surprisingly, VVDeltaK3L did not disseminate to other tissues from the lung.", "output": "There is no related enetity." }, { "input": "Hence, the cause of death in this model is respiratory disease.", "output": "There is no related enetity." }, { "input": "These results also suggest that an unanticipated role of the K3L gene is to facilitate virus dissemination.", "output": "There is no related enetity." }, { "input": "Host plant secondary metabolite profiling shows a complex, strain - dependent response of maize to plant growth - promoting rhizobacteria of the genus Azospirillum.", "output": "maize." }, { "input": "Most Azospirillum plant growth - promoting rhizobacteria ( PGPR ) benefit plant growth through source effects related to free nitrogen fixation and / or phytohormone production, but little is known about their potential effects on plant physiology.", "output": "There is no related enetity." }, { "input": "These effects were assessed by comparing the early impacts of three Azospirillum inoculant strains on secondary metabolite profiles of two different maize ( Zea mays ) cultivars.", "output": "maize, Zea mays." }, { "input": "After 10d of growth in nonsterile soil, maize methanolic extracts were analyzed by reverse - phase high - performance liquid chromatography ( RP - HPLC ) and secondary metabolites identified by liquid chromatography / mass spectrometry ( LC / MS ) and nuclear magnetic resonance ( NMR ).", "output": "maize." }, { "input": "Seed inoculation resulted in increased shoot biomass ( and also root biomass with one strain ) of hybrid PR37Y15 but had no stimulatory effect on hybrid DK315.", "output": "There is no related enetity." }, { "input": "In parallel, Azospirillum inoculation led to major qualitative and quantitative modifications of the contents of secondary metabolites, especially benzoxazinoids, in the maize plants.", "output": "maize." }, { "input": "These modifications depended on the PGPR strainxplant cultivar combination.", "output": "There is no related enetity." }, { "input": "Thus, Azospirillum inoculation resulted in early, strain - dependent modifications in the biosynthetic pathways of benzoxazine derivatives in maize in compatible interactions.", "output": "maize." }, { "input": "This is the first study documenting a PGPR effect on plant secondary metabolite profiles, and suggests the establishment of complex interactions between Azospirillum PGPR and maize.", "output": "There is no related enetity." }, { "input": "A seed high - lysine trait is negatively associated with the TCA cycle and slows down Arabidopsis seed germination.", "output": "There is no related enetity." }, { "input": "* Lysine is a nutritionally important essential amino acid, but significant elevation of its levels in Arabidopsis seeds, by enhancing its synthesis and blocking its catabolism, causes a retardation of germination.", "output": "There is no related enetity." }, { "input": "Here, we hypothesized that this negative effect is associated with changes in primary metabolism and gene expression programs that are essential for early germination.", "output": "There is no related enetity." }, { "input": "* Seeds at different stages of germination sensu stricto of the seed - high - lysine genotype were subjected to detailed analysis of primary metabolism, using GC - MS, as well as microarray analysis and two - dimensional, isoelectric focusing, sodium dodecylsulfate polyacrylamide gel electrophoresis, to detect storage protein mobilization.", "output": "There is no related enetity." }, { "input": "* Our results exposed a major negative effect of the seed - specific increased lysine synthesis and knockout of its catabolism on the levels of a number of TCA cycle metabolites.", "output": "There is no related enetity." }, { "input": "This metabolic alteration also influences significantly the transcriptome, primarily attenuating the boost of specific transcriptional programs that are essential for seedling establishment, such as the onset of photosynthesis, as well as the turnover of specific transcriptional programs associated with seed embryonic traits.", "output": "There is no related enetity." }, { "input": "* Our results indicate that catabolism of the aspartic acid family of amino acids is an important contributor to the energy status of plants, and hence to the onset of autotrophic growth - associated processes during germination.", "output": "There is no related enetity." }, { "input": "Functional characterization of pheromone receptors in the tobacco budworm Heliothis virescens.", "output": "tobacco budworm, Heliothis virescens." }, { "input": "Functional analyses of candidate Heliothis virescens pheromone odorant receptors ( HvORs ) were conducted using heterologous expression in Xenopus oocytes.", "output": "Heliothis virescens." }, { "input": "HvOR6 was found to be highly tuned to Z9 - 14: Ald, while HvOR13, HvOR14 and HvOR16 showed specificity for Z11 - 16: Ald, Z11 - 16: OAc and Z11 - 16: OH, respectively.", "output": "There is no related enetity." }, { "input": "HvOR15, which had been considered a candidate receptor for Z9 - 14: Ald did not respond to any of the pheromone compounds tested, nor to 50 other general odorants.", "output": "There is no related enetity." }, { "input": "Thus, while HvOR15 is specifically expressed in H. virescens male antennae, its role in pheromone reception remains unknown.", "output": "H . virescens." }, { "input": "Based on our results and previous research we can now assign pheromone receptors in H. virescens males to each of the critical H. virescens agonistic pheromone compounds and two antagonistic compounds produced by heterospecific females.", "output": "H . virescens, H . virescens." }, { "input": "Glycinebetaine protects plants against abiotic stress: mechanisms and biotechnological applications.", "output": "There is no related enetity." }, { "input": "Various compatible solutes enable plants to tolerate abiotic stress, and glycinebetaine ( GB ) is one of the most - studied among such solutes.", "output": "There is no related enetity." }, { "input": "Early research on GB focused on the maintenance of cellular osmotic potential in plant cells.", "output": "There is no related enetity." }, { "input": "Subsequent genetically engineered synthesis of GB - biosynthetic enzymes and studies of transgenic plants demonstrated that accumulation of GB increases tolerance of plants to various abiotic stresses at all stages of their life cycle.", "output": "There is no related enetity." }, { "input": "Such GB - accumulating plants exhibit various advantageous traits, such as enlarged fruits and flowers and / or increased seed number under non - stress conditions.", "output": "There is no related enetity." }, { "input": "However, levels of GB in transgenic GB - accumulating plants are relatively low being, generally, in the millimolar range.", "output": "There is no related enetity." }, { "input": "Nonetheless, these low levels of GB confer considerable tolerance to various stresses, without necessarily contributing significantly to cellular osmotic potential.", "output": "There is no related enetity." }, { "input": "Moreover, low levels of GB, applied exogenously or generated by transgenes for GB biosynthesis, can induce the expression of certain stress - responsive genes, including those for enzymes that scavenge reactive oxygen species.", "output": "There is no related enetity." }, { "input": "Thus, transgenic approaches that increase tolerance to abiotic stress have enhanced our understanding of mechanisms that protect plants against such stress.", "output": "There is no related enetity." }, { "input": "Evaluation of an immunoglobulin M - specific capture enzyme - linked immunosorbent assay for rapid diagnosis of dengue infection.", "output": "dengue." }, { "input": "Various assays have been developed to diagnose dengue virus infection, relying on techniques from the fields of serology and molecular biology.", "output": "dengue virus." }, { "input": "Many of these assays have been successful, but there is still an urgent need for accurate, simple and rapid diagnostic assays to diagnose dengue virus infection and to assist in patient management.", "output": "dengue virus." }, { "input": "Using a panel of well - characterized sera and a collection of retrospective samples obtained during the dengue epidemics that occurred in Belem, Brazil, between 2002 and 2009, a modified immunoglobulin M - specific capture enzyme - linked immunosorbent assay ( Rapid - MAC - ELISA ) was evaluated and compared with the & quot; gold standard & quot; MAC - ELISA, in order to assess the specificity, sensitivity, stability, reproducibility and cost - effectiveness of this new assay.", "output": "dengue." }, { "input": "These results demonstrated that the Rapid - MAC - ELISA is comparable to the MAC - ELISA in terms of sensitivity and specificity and is highly reproducible; additionally, it is easily performed, less expensive than other available formats and can be completed within three hours.", "output": "There is no related enetity." }, { "input": "Furthermore, the Rapid - MAC - ELISA can be used for the diagnosis of dengue virus infections in resource - limited areas where dengue is endemic.", "output": "dengue virus, dengue." }, { "input": "Rapid detection of Newcastle disease virus replication in embryonated chicken eggs using quantitative real time polymerase chain reaction.", "output": "Newcastle disease virus, chicken." }, { "input": "Newcastle disease virus ( NDV ), an avian paramyxovirus, is an economically important disease of poultry globally.", "output": "Newcastle disease virus, NDV, poultry." }, { "input": "Rapid methods to detect and differentiate the virus are important to curtail the spread of this virus.", "output": "There is no related enetity." }, { "input": "Nucleic acid based detection methods are routinely employed for diagnosis that suffer from the disadvantage of failure to discriminate viable virus and non - infectious genome.", "output": "There is no related enetity." }, { "input": "However, virus isolation remains the gold standard for diagnosis of field outbreaks.", "output": "There is no related enetity." }, { "input": "The sensitivity of virus isolation was combined with nucleic acid based detection methods so that the time taken for confirmatory diagnosis could be considerably reduced while increasing sensitivity.", "output": "There is no related enetity." }, { "input": "Quantitative real time reverse transcription polymerase chain reaction ( qRT - PCR ) and conventional RT - PCR techniques were compared for the detection of NDV genome replication in 9 - 11 - day - old embryonated chicken eggs ( ECE ) using the nucleoprotein ( NP ) gene of the virus as a target.", "output": "NDV, chicken." }, { "input": "The results suggest that at least two to fourfold increase in cycle threshold ( C ( t ) ) values over the baseline C ( t ) value of samples lacking infectious virus, would indicate live NDV replication.", "output": "NDV." }, { "input": "The limit of detection of NDV replication using qRT - PCR was 1x10 ( 4. 0 ) mean embryo infective doses ( EID ( 50 ) ).", "output": "NDV." }, { "input": "The earliest time point when live virus replication was detectable by qRT - PCR or RT - PCR was 30h post - inoculation in ECE.", "output": "There is no related enetity." }, { "input": "Development of a polyprobe to detect six viroids of pome and stone fruit trees.", "output": "There is no related enetity." }, { "input": "A simple and sensitive dot blot hybridization assay using a digoxigenin - labeled cRNA polyprobe was developed for the simultaneous detection of six viroids that infect pome and stone fruit trees.", "output": "There is no related enetity." }, { "input": "The polyprobe was constructed by cloning sequentially partial sequences of each viroid into a single vector, with run - off transcription driven by the T7 promoter.", "output": "There is no related enetity." }, { "input": "All six viroids were detectable within a dilution range of 5 ( - 3 ) to 5 ( - 4 ) in total nucleic acid extracts from infected trees.", "output": "There is no related enetity." }, { "input": "Individual trees were co - inoculated to create mixed infections and all four pome fruit viroids and both stone fruit viroids could be detected in pear and peach trees, respectively, using the polyprobe.", "output": "peach." }, { "input": "The results of the assays using the polyprobe were comparable to those using single probes.", "output": "There is no related enetity." }, { "input": "The methods were validated by testing geographically diverse isolates of viroids, as well as field samples from several collections in the US.", "output": "There is no related enetity." }, { "input": "The assay offers a rapid, reliable and cost - effective approach to the simultaneous detection of six fruit trees viroids and has the potential for routine use in quarantine, certification, and plant genebank programs where many samples are tested and distributed worldwide.", "output": "There is no related enetity." }, { "input": "Development and validation of a lateral flow immunoassay using colloidal gold for the identification of serotype - specific foot - and - mouth disease virus O, A and Asia 1.", "output": "foot - and - mouth disease virus O, A, Asia 1." }, { "input": "A lateral flow immunoassay ( LFI ) was developed to identify and diagnose foot - and - mouth disease virus ( FMDV ) serotypes O, A and Asia 1.", "output": "foot - and - mouth disease virus, FMDV, O, A, Asia 1." }, { "input": "Antibodies obtained from rabbits and guinea pigs immunized with cell - culture - adapted virus strains ( O / CHA / 99, A / GS / LX / 66, Asia 1 / CHN / 05 ) and suckling - mouse adapted virus strains ( O / AV99 ( L ), A / AV88 ( L ), Asia 1 / YNBS / 58 ) were used as capture antibodies.", "output": "rabbits, O / CHA / 99, A / GS / LX / 66, Asia 1 / CHN / 05, mouse, O / AV99 ( L ), A / AV88 ( L ), Asia 1 / YNBS / 58." }, { "input": "The diagnostic kit included three immunochromatographic strips of types O, A and Asia 1, and the type - specific results were confirmed by color on the test lines of the three strips.", "output": "O, A, Asia 1." }, { "input": "The LFI was evaluated using epithelial and vesicular samples ( n = 396 ) prepared from current and historical field samples ( provide by the National Foot - and - Mouth Disease Reference Laboratory of China at Lanzhou Veterinary Research Institute ).", "output": "There is no related enetity." }, { "input": "Negative samples ( n = 95 ) were collected from healthy animals.", "output": "There is no related enetity." }, { "input": "The diagnostic sensitivity of the LFI for FMDV serotypes O, A and Asia 1 was 88. 3 % compared to 89. 7 % obtained by the reference method of indirect - sandwich ELISA.", "output": "FMDV, O, A, Asia 1." }, { "input": "The sensitivity of the LFI for FMDV type Asia 1 was higher at 92. 1 % compared to 90. 5 % for the ELISA.", "output": "FMDV type Asia 1." }, { "input": "The specificity of the LFI was 97. 1 % compared with 97. 4 %.", "output": "There is no related enetity." }, { "input": "Implementation and validation of a sensitive PCR detection method in the eradication campaign against Aleutian mink disease virus.", "output": "Aleutian mink disease virus." }, { "input": "Aleutian mink disease virus ( AMDV ) is a severe progressive disease causing multiple different clinical syndromes in mink.", "output": "Aleutian mink disease virus ( AMDV ), mink." }, { "input": "In Denmark, the disease is notifiable and under official control.", "output": "There is no related enetity." }, { "input": "The control programme, based on serological screening, has confined successfully AMDV to the northern part of Denmark.", "output": "AMDV." }, { "input": "However, re - infections and new introductions of virus into farms require a confirmatory virological test to verify the positive test results of single animals and ultimately to investigate disease transmission.", "output": "There is no related enetity." }, { "input": "A one step PCR amplifying a 374 - base fragment of the NS1 gene of AMDV was compared to the counter - current immune electrophoresis ( CIE ) routinely used in the serological screening programme.", "output": "AMDV." }, { "input": "Mink organs ( n = 299 ) obtained from 55 recently infected farms and 8 non - infected farms from 2008 to 2010 were tested by PCR, and the results were found to have a high correlation with the serological status of the mink.", "output": "Mink, mink." }, { "input": "The relative diagnostic sensitivity of the PCR was 94. 7 %, and the relative diagnostic specificity was 97. 9 % when read in parallel with the CIE.", "output": "There is no related enetity." }, { "input": "PCR positive samples were sequenced and phylogenetic analysis revealed high similarity within the analysed AMDV strains and to AMDV strains described previously.", "output": "AMDV strains, AMDV strains." }, { "input": "A new method for detection of pandemic influenza virus using High Resolution Melting analysis of the neuraminidase gene.", "output": "pandemic influenza virus." }, { "input": "Diagnostic methods based upon exclusive detection of haemagglutinin do not detect sequence variation in other gene segments of the Influenza A virus.", "output": "Influenza A virus." }, { "input": "A complementary approach is described based upon high - resolution melting curve analysis of the neuraminidase gene, an approach with the potential ability to detect small changes in the neuraminidase sequence without the need for specific probes.", "output": "There is no related enetity." }, { "input": "Physiological and morphological adaptations in relation to water use efficiency in Mediterranean accessions of Solanum lycopersicum.", "output": "Solanum lycopersicum." }, { "input": "The physiological traits underlying the apparent drought resistance of ' Tomatiga de Ramellet ' ( TR ) cultivars, a population of Mediterranean tomato cultivars with delayed fruit deterioration ( DFD ) phenotype and typically grown under non - irrigation conditions, are evaluated.", "output": "tomato." }, { "input": "Eight different tomato accessions were selected and included six TR accessions, one Mediterranean non - TR accession ( NTR ( M ) ) and a processing cultivar ( NTR ( O ) ).", "output": "tomato." }, { "input": "Among the TR accessions two leaf morphology types, normal divided leaves and potato - leaf, were selected.", "output": "potato." }, { "input": "Plants were field grown under well - watered ( WW ) and water - stressed ( WS ) treatments, with 30 and 10 % of soil water capacity, respectively.", "output": "There is no related enetity." }, { "input": "Accessions were clustered according to the leaf type and TR phenotype under WW and WS, respectively.", "output": "There is no related enetity." }, { "input": "Correlation among parameters under the different water treatments suggested that potential improvements in the intrinsic water - use efficiency ( A ( N ) / g ( s ) ) are possible without negative impacts on yield.", "output": "There is no related enetity." }, { "input": "Under WS TR accessions displayed higher A ( N ) / g ( s ), which was not due to differences in Rubisco - related parameters, but correlated with the ratio between the leaf mesophyll and stomatal conductances ( g ( m ) / g ( s ) ).", "output": "There is no related enetity." }, { "input": "The results confirm the existence of differential traits in the response to drought stress in Mediterranean accessions of tomato, and demonstrate that increases in the g ( m ) / g ( s ) ratio would allow improvements in A ( N ) / g ( s ) in horticultural crops.", "output": "tomato." }, { "input": "A new filter that accurately mimics the solar UV - B spectrum using standard UV lamps: the photochemical properties, stabilization and use of the urate anion liquid filter.", "output": "There is no related enetity." }, { "input": "The physiological effects unique to solar ultraviolet ( UV ) - B exposure ( 280 - 315 nm ) are difficult to accurately replicate in the laboratory.", "output": "There is no related enetity." }, { "input": "This study evaluates the effectiveness of the sodium urate anion in a liquid filter that yields a spectrum nearly indistinguishable from the solar UV - B spectrum while filtering the emissions of widely used UV - B lamps.", "output": "There is no related enetity." }, { "input": "The photochemical properties and stability of this filter are examined and weighed against a typical spectrum of ground - level solar UV - B radiation.", "output": "There is no related enetity." }, { "input": "To test the effectiveness of this filter, light - saturated photosynthetic oxygen evolution rates were measured following exposure to UV - B filtered either by this urate filter or the widely used cellulose acetate ( CA ) filter.", "output": "There is no related enetity." }, { "input": "The ubiquitous marine Chlorophyte alga Dunaliella tertiolecta was tested under identical UV - B flux densities coupled with ecologically realistic fluxes of UV - A and visible radiation for 6 and 12 h exposures.", "output": "Dunaliella tertiolecta." }, { "input": "These results indicate that the urate - filtered UV - B radiation yields minor photosynthetic inhibition when compared with exposures lacking in UV - B.", "output": "There is no related enetity." }, { "input": "This is in agreement with published experiments using solar radiation.", "output": "There is no related enetity." }, { "input": "In sharp contrast, radiation filtered by CA filters produced large inhibition of photosynthesis.", "output": "There is no related enetity." }, { "input": "The 13C / 12C isotopic signal of day - respired CO2 in variegated leaves of Pelargonium x hortorum.", "output": "Pelargonium x hortorum." }, { "input": "In leaves, although it is accepted that CO ( 2 ) evolved by dark respiration after illumination is naturally ( 13 ) C - enriched compared to organic matter or substrate sucrose, much uncertainty remains on whether day respiration produces ( 13 ) C - depleted or ( 13 ) C - enriched CO ( 2 ).", "output": "There is no related enetity." }, { "input": "Here, we applied equations described previously for mesocosm CO ( 2 ) exchange to investigate the carbon isotope composition of CO ( 2 ) respired by autotrophic and heterotrophic tissues of Pelargonium x hortorum leaves, taking advantage of leaf variegation.", "output": "Pelargonium x hortorum." }, { "input": "Day - respired CO ( 2 ) was slightly ( 13 ) C - depleted compared to organic matter both under 21 % O ( 2 ) and 2 % O ( 2 ).", "output": "There is no related enetity." }, { "input": "Furthermore, most, if not all CO ( 2 ) molecules evolved in the light came from carbon atoms that had been fixed previously before the experiments, in both variegated and green leaves.", "output": "There is no related enetity." }, { "input": "We conclude that the usual definition of day respiratory fractionation, that assumes carbon fixed by current net photosynthesis is the respiratory substrate, is not valid in Pelargonium leaves under our conditions.", "output": "There is no related enetity." }, { "input": "In variegated leaves, total organic matter was slightly ( 13 ) C - depleted in white areas and so were most primary metabolites.", "output": "There is no related enetity." }, { "input": "This small isotopic difference between white and green areas probably came from the small contribution of photosynthetic CO ( 2 ) refixation and the specific nitrogen metabolism in white leaf areas.", "output": "There is no related enetity." }, { "input": "Auxin depletion in barley plants under high - temperature conditions represses DNA proliferation in organelles and nuclei via transcriptional alterations.", "output": "barley." }, { "input": "Many plant species are susceptible to high - temperature ( HT ) injury during reproductive development.", "output": "There is no related enetity." }, { "input": "We recently demonstrated that HT represses the expression of YUCCA auxin biosynthesis genes and reduces endogenous auxin in the developing anthers of barley and Arabidopsis.", "output": "barley." }, { "input": "Here, we show that DNA proliferation in mitochondria, chloroplasts and nuclei of developing panicles is inhibited with increasing temperatures in barley.", "output": "barley." }, { "input": "Following DNA proliferation suppression, terminal abnormalities were observed in the organelles of anther wall cells, including mitochondrial swelling and overdevelopment of chloroplasts.", "output": "There is no related enetity." }, { "input": "Comprehensive transcriptome analyses using both reproductive organs and vegetative tissues showed high and positive pairwise correlations between the expression profiles of auxin - induced genes, DNA replication - related genes and mitochondrial - related genes.", "output": "There is no related enetity." }, { "input": "In contrast, the expression profiles of auxin - repressed protein genes and photosynthesis - / chloroplast - related genes were negatively correlated with those of the previously mentioned genes.", "output": "There is no related enetity." }, { "input": "Under HT conditions, the former was repressed and the latter was up - regulated in the developing panicles.", "output": "There is no related enetity." }, { "input": "Furthermore, application of exogenous auxin promoted the expression of DNA replication - related genes under HT conditions, inducing anther cell proliferation.", "output": "There is no related enetity." }, { "input": "These suggest that compromised auxin biosynthesis / IAA level under HT condition results in nuclear and organellar DNA proliferation arrest due to co - transcriptional alterations.", "output": "There is no related enetity." }, { "input": "Minimum hydraulic safety leads to maximum water - use efficiency in a forage grass.", "output": "There is no related enetity." }, { "input": "Understanding how water - use regulation relates to biomass accumulation is imperative for improving crop production in water - limited environments.", "output": "There is no related enetity." }, { "input": "Here, we examine how the vulnerability of xylem to water stress - induced cavitation and the coordination between water transport capacity and assimilation ( A ) influences diurnal water - use efficiency ( WUE ) and dry - matter production in Lolium perenne L.", "output": "Lolium perenne." }, { "input": "- a commercial forage grass.", "output": "There is no related enetity." }, { "input": "Plants were exposed to a range of water stresses, causing up to 90 % leaf death, by withholding water and then rewatering to observe the recovery process.", "output": "There is no related enetity." }, { "input": "Leaf hydraulic conductance ( K ( leaf ) ) declined to 50 % of maximum at a leaf water potential ( psi ( leaf ) ) of - 1 MPa, whereas complete stomatal closure occurred well after this point, at - 2. 35 MPa, providing no protection against hydraulic dysfunction.", "output": "There is no related enetity." }, { "input": "Instantaneous A remained maximal until & gt; 70 % of hydraulic conductivity had been lost.", "output": "There is no related enetity." }, { "input": "Post - stress rewatering showed that 95 % loss of K ( leaf ) could be incurred before the recovery of gas exchange exceeded 1 d, with a rapid transition to leaf death after this point.", "output": "There is no related enetity." }, { "input": "Plants exposed to sustained soil water deficits through restricted nightly watering regimes did not suffer cumulative losses in K ( leaf ); instead, psi ( leaf ) and gas exchange recovered diurnally.", "output": "There is no related enetity." }, { "input": "The effect was improved WUE during the day and optimal psi ( leaf ) during the night for the maintenance of growth.", "output": "There is no related enetity." }, { "input": "Novel mutations reveal two important regions in Aspergillus nidulans transcriptional activator MetR.", "output": "Aspergillus nidulans." }, { "input": "Expression of the sulfur assimilation pathway in Aspergillus nidulans is under control of sulfur metabolite repression, which is composed of scon genes encoding subunits of ubiquitin ligase and the metR gene coding for a transcriptional activator.", "output": "Aspergillus nidulans." }, { "input": "In this paper we report three dominant suppressors of methionine requirement isolated from a metB3 diploid strain.", "output": "There is no related enetity." }, { "input": "All three mutations lead to the substitution of phenylalanine 48 by serine or leucine in the conserved N - terminal region of the MetR protein.", "output": "There is no related enetity." }, { "input": "Strains carrying the dominant suppressor mutations exhibit increased activities of homocysteine synthase and sulfur assimilation enzymes as well as elevated levels of the corresponding transcripts.", "output": "There is no related enetity." }, { "input": "These changes are observed even under conditions of methionine repression, which suggests that the mutated MetR protein may be resistant to inactivation or degradation mediated by sulfur metabolite repression.", "output": "There is no related enetity." }, { "input": "We also found that a mutant impaired in sulfite reductase activity, known until now as sG8, has a frameshift which changes 41 C - terminal amino acids.", "output": "There is no related enetity." }, { "input": "Therefore, it is now designated metR18.", "output": "There is no related enetity." }, { "input": "This mutant has elevated levels of MetR - regulated transcripts and of activities of sulfur assimilation enzymes ( except sulfite reductase ), which can be repressed to the wild type level by exogenous methionine.", "output": "There is no related enetity." }, { "input": "Thus, metR18 and the three dominant suppressors represent new types of mutations affecting different parts of the A. nidulans MetR protein.", "output": "A . nidulans." }, { "input": "Paralogous cyp51 genes in Fusarium graminearum mediate differential sensitivity to sterol demethylation inhibitors.", "output": "Fusarium graminearum." }, { "input": "Analysis of the genome sequence of Fusarium graminearum revealed three paralogous cyp51 genes ( designated cyp51A, - B, and - C ) encoding 14 - alpha demethylases in this fungus.", "output": "Fusarium graminearum." }, { "input": "Targeted gene disruption showed that the cyp51A, - B or - C disruption mutants were morphologically indistinguishable from the parent isolate on potato dextrose agar medium, which indicates that none of these genes is essential for mycelial growth.", "output": "potato." }, { "input": "The sensitivity of cyp51A deletion mutants to seven sterol demethylation inhibitor ( DMI ) fungicides increased significantly compared to the parent strain, while sensitivity of cyp51C deletion mutants increased to some but not all DMIs.", "output": "There is no related enetity." }, { "input": "No change in DMI sensitivity was observed for cyp51B deletion mutants.", "output": "There is no related enetity." }, { "input": "The parental phenotypes of cyp51A and cyp51C deletion mutants were completely restored by genetic complementation with the wild - type cyp51A and cyp51C genes, respectively.", "output": "There is no related enetity." }, { "input": "The sensitivity of F. graminearum isolates increased significantly when subjected in vitro to a mixture of DMI fungicides triadimefon and tebuconazole as compared to the individual components.", "output": "F . graminearum." }, { "input": "These results indicate that different DMI fungicides target different CYP51 proteins in F. graminearum and that a mixture of DMI fungicides can result in synergistic effects.", "output": "F . graminearum." }, { "input": "Our findings have directly implications on chemical management strategies of plant diseases caused by Fusarium species.", "output": "There is no related enetity." }, { "input": "Comparative sequence analysis of wheat and barley powdery mildew fungi reveals gene colinearity, dates divergence and indicates host - pathogen co - evolution.", "output": "wheat, barley." }, { "input": "The two fungal pathogens Blumeria graminis f. sp. tritici ( B. g. tritici ) and hordei ( B. g. hordei ) cause powdery mildew specifically in wheat or barley.", "output": "Blumeria graminis f . sp . tritici, B . g . tritici, hordei, B . g . hordei, wheat, barley." }, { "input": "They have the same life cycle, but their growth is restricted to the respective host.", "output": "There is no related enetity." }, { "input": "Here, we compared the sequences of two loci in both cereal mildews to determine their divergence time and their relationship with the evolution of their hosts.", "output": "There is no related enetity." }, { "input": "We sequenced a total of 273. 3kb derived from B. g. tritici BAC sequences and compared them with the orthologous regions in the B. g. hordei genome.", "output": "B . g . tritici, B . g . hordei." }, { "input": "Protein - coding genes were colinear and well conserved.", "output": "There is no related enetity." }, { "input": "In contrast, the intergenic regions showed very low conservation mostly due to different integration patterns of transposable elements.", "output": "There is no related enetity." }, { "input": "To estimate the divergence time of B. g. tritici and B. g. hordei, we used conserved intergenic sequences including orthologous transposable elements.", "output": "B . g . tritici, B . g . hordei." }, { "input": "This revealed that B. g. tritici and B. g. hordei have diverged about 10 million years ago ( MYA ), two million years after wheat and barley ( 12 MYA ).", "output": "B . g . tritici, B . g . hordei, wheat, barley." }, { "input": "These data suggest that B. g. tritici and B. g. hordei have co - evolved with their hosts during most of their evolutionary history after host divergence, possibly after a short phase of host expansion when the same pathogen could still grow on the two diverged hosts.", "output": "B . g . tritici, B . g . hordei." }, { "input": "Can we predict carbon stocks in tropical ecosystems from tree diversity?", "output": "There is no related enetity." }, { "input": "Comparing species and functional diversity in a plantation and a natural forest.", "output": "There is no related enetity." }, { "input": "* Linking tree diversity to carbon storage can provide further motivation to conserve tropical forests and to design carbon - enriched plantations.", "output": "There is no related enetity." }, { "input": "Here, we examine the role of tree diversity and functional traits in determining carbon storage in a mixed - species plantation and in a natural tropical forest in Panama.", "output": "There is no related enetity." }, { "input": "* We used species richness, functional trait diversity, species dominance and functional trait dominance to predict tree carbon storage across these two forests.", "output": "There is no related enetity." }, { "input": "Then we compared the species ranking based on wood density, maximum diameter, maximum height, and leaf mass per area ( LMA ) between sites to reveal how these values changed between different forests.", "output": "There is no related enetity." }, { "input": "* Increased species richness, a higher proportion of nitrogen fixers and species with low LMA increased carbon storage in the mixed - species plantation, while a higher proportion of large trees and species with high LMA increased tree carbon storage in the natural forest.", "output": "There is no related enetity." }, { "input": "Furthermore, we found that tree species varied greatly in their absolute and relative values between study sites.", "output": "There is no related enetity." }, { "input": "* Different results in different forests mean that we cannot easily predict carbon storage capacity in natural forests using data from experimental plantations.", "output": "There is no related enetity." }, { "input": "Managers should be cautious when applying functional traits measured in natural populations in the design of carbon - enriched plantations.", "output": "There is no related enetity." }, { "input": "Profile of the mosaic element BTMR1 in the genome of the bumble bee Bombus terrestris ( Hymenoptera: Apidae ).", "output": "Bombus terrestris." }, { "input": "Co - evolution involving a mariner transposon, Botmar1 and the other repeats contained in the Bombus terrestris genome was investigated.", "output": "Bombus terrestris." }, { "input": "We found that the 5 ' - region of Botmar1 forms one of the components of a mosaic element, known as B. terrestris mosaic repeat 1 ( BTMR1 ), which is also composed of inner segments originating from two different retrotransposons and a pseudogene corresponding to an RNA methyltransferase cDNA.", "output": "B . terrestris." }, { "input": "The fact that BTMR1 is interspersed within chromosomes and the differences in its abundance in different species indicate that it is very probably a mobile element.", "output": "There is no related enetity." }, { "input": "Nevertheless, the absences of direct or inverted repeats at its ends and of target site duplication indicate that its mobility is not ensured by a cardinal transposable element, but putatively by a Crypton - like element.", "output": "There is no related enetity." }, { "input": "The RNA - Seq approach to studying the expression of mosquito mitochondrial genes.", "output": "There is no related enetity." }, { "input": "In this study, we used extensive expressed sequence tag evidence obtained through 454 and Solexa next - generation sequencing to explore mtDNA transcription in male and female first instar larvae of Aedes aegypti and adults of Aedes aegypti, Anopheles gambiae, and Anopheles quadrimaculatus.", "output": "Aedes aegypti, Aedes aegypti, Anopheles gambiae, Anopheles quadrimaculatus." }, { "input": "Relative abundances of individual transcripts differed considerably within each sample, consistent with the differential stability of messenger RNA species.", "output": "There is no related enetity." }, { "input": "Large differences were also observed between species and between larval and adult stages; however, the male and female larval samples were remarkably similar.", "output": "There is no related enetity." }, { "input": "Quantitative PCR analysis of selected genes, cox1, l - rRNA and nd5, in larvae and adults of Ae. aegypti and in An. gambiae adults was consistent with the RNA - Seq - based quantification of expression.", "output": "Ae . aegypti, An . gambiae." }, { "input": "Finally, the absence of a conserved mtDNA region involved in transcriptional control in other dipterans suggests that mosquitoes have evolved a distinct mechanism of regulation of gene expression in the mitochondrion.", "output": "There is no related enetity." }, { "input": "Isolation and characterization of MAT genes in the symbiotic ascomycete Tuber melanosporum.", "output": "Tuber melanosporum." }, { "input": "* The genome of Tuber melanosporum has recently been sequenced.", "output": "Tuber melanosporum." }, { "input": "Here, we used this information to identify genes involved in the reproductive processes of this edible fungus.", "output": "There is no related enetity." }, { "input": "The sequenced strain ( Mel28 ) possesses only one of the two master genes required for mating, that is, the gene that codes for the high mobility group ( HMG ) transcription factor ( MAT1 - 2 - 1 ), whereas it lacks the gene that codes for the protein containing the alpha - box - domain ( MAT1 - 1 - 1 ), suggesting that this fungus is heterothallic.", "output": "There is no related enetity." }, { "input": "* A PCR - based approach was initially employed to screen truffles for the presence of the MAT1 - 2 - 1 gene and amplify the conserved regions flanking the mating type ( MAT ) locus.", "output": "There is no related enetity." }, { "input": "The MAT1 - 1 - 1 gene was finally identified using primers designed from the conserved regions of strains that lack the MAT1 - 2 - 1 gene.", "output": "There is no related enetity." }, { "input": "* Mating type - specific primer pairs were developed to screen asci and gleba from truffles of different origins and to genotype single ascospores within the asci.", "output": "There is no related enetity." }, { "input": "These analyses provided definitive evidence that T. melanosporum is a heterothallic species with a MAT locus that is organized similarly to those of ancient fungal lineages.", "output": "T . melanosporum." }, { "input": "* A greater understanding of the reproductive mechanisms that exist in Tuber spp. allows for optimization of truffle plantation management strategies.", "output": "There is no related enetity." }, { "input": "Updated hypothesis on the evolution of oligotrichid ciliates ( Ciliophora, Spirotricha, Oligotrichida ) based on somatic ciliary patterns and ontogenetic data.", "output": "There is no related enetity." }, { "input": "The two recently established genera Apostrombidium Xu et al., 2009 and Varistrombidium Xu et al., 2009 and the analysis of ontogenetic data in Strombidium constrictum, S. montagnesi, S. wilberti, Omegastrombidium elegans, and Paratontonia gracillima necessitated a revision of the hypothesis about the somatic ciliary pattern evolution in oligotrichid ciliates.", "output": "Omegastrombidium elegans." }, { "input": "As a consequence, the species - rich genus Strombidium was split, establishing two genera for species with a horizontal girdle kinety posterior to the oral primordium: Opisthostrombidium nov. gen. with the extrusome attachment sites along the anterior margin of the girdle kinety and posterior to the oral primordium and Foissneridium nov. gen. with the extrusome attachment sites distinctly apart from the girdle kinety and anterior to the oral primordium.", "output": "There is no related enetity." }, { "input": "The ontogenetic data revealed that the Omega - shaped girdle kinety pattern evolved convergently from the Pseudotontonia pattern with its horizontal girdle kinety in the tailed genus Paratontonia and from the Novistrombidium pattern with its dextrally spiralled girdle kinety in the tailless genus Omegastrombidium.", "output": "There is no related enetity." }, { "input": "The somatic ciliary pattern of the latter genus probably gave rise to the patterns of Apostrombidium and Varistrombidium.", "output": "There is no related enetity." }, { "input": "Neutralizing antibody - resistant hepatitis C virus cell - to - cell transmission.", "output": "hepatitis C virus." }, { "input": "Hepatitis C virus ( HCV ) can initiate infection by cell - free particle and cell - cell contact - dependent transmission.", "output": "HCV." }, { "input": "In this study we use a novel infectious coculture system to examine these alternative modes of infection.", "output": "There is no related enetity." }, { "input": "Cell - to - cell transmission is relatively resistant to anti - HCV glycoprotein monoclonal antibodies and polyclonal immunoglobulin isolated from infected individuals, providing an effective strategy for escaping host humoral immune responses.", "output": "anti - HCV." }, { "input": "Chimeric viruses expressing the structural proteins representing the seven major HCV genotypes demonstrate neutralizing antibody - resistant cell - to - cell transmission.", "output": "HCV." }, { "input": "HCV entry is a multistep process involving numerous receptors.", "output": "HCV." }, { "input": "In this study we demonstrate that, in contrast to earlier reports, CD81 and the tight - junction components claudin - 1 and occludin are all essential for both cell - free and cell - to - cell viral transmission.", "output": "There is no related enetity." }, { "input": "However, scavenger receptor BI ( SR - BI ) has a more prominent role in cell - to - cell transmission of the virus, with SR - BI - specific antibodies and small - molecule inhibitors showing preferential inhibition of this infection route.", "output": "There is no related enetity." }, { "input": "These observations highlight the importance of targeting host cell receptors, in particular SR - BI, to control viral infection and spread in the liver.", "output": "There is no related enetity." }, { "input": "Chikungunya virus induces IPS - 1 - dependent innate immune activation and protein kinase R - independent translational shutoff.", "output": "Chikungunya virus." }, { "input": "Chikungunya virus ( CHIKV ) is an arthritogenic mosquito - transmitted alphavirus that is undergoing reemergence in areas around the Indian Ocean.", "output": "Chikungunya virus, CHIKV." }, { "input": "Despite the current and potential danger posed by this virus, we know surprisingly little about the induction and evasion of CHIKV - associated antiviral immune responses.", "output": "CHIKV." }, { "input": "With this in mind we investigated innate immune reactions to CHIKV in human fibroblasts, a demonstrable in vivo target of virus replication and spread.", "output": "CHIKV, human." }, { "input": "We show that CHIKV infection leads to activation of the transcription factor interferon regulatory factor 3 ( IRF3 ) and subsequent transcription of IRF3 - dependent antiviral genes, including beta interferon ( IFN - Beta ).", "output": "CHIKV." }, { "input": "IRF3 activation occurs by way of a virus - induced innate immune signaling pathway that includes the adaptor molecule interferon promoter stimulator 1 ( IPS - 1 ).", "output": "There is no related enetity." }, { "input": "Despite strong transcriptional upregulation of these genes, however, translation of the corresponding proteins is not observed.", "output": "There is no related enetity." }, { "input": "We further demonstrate that translation of cellular ( but not viral ) genes is blocked during infection and that although CHIKV is found to trigger inactivation of the translational molecule eukaryotic initiation factor subunit 2alpha by way of the double - stranded RNA sensor protein kinase R, this response is not required for the block to protein synthesis.", "output": "CHIKV." }, { "input": "Furthermore, overall diminution of cellular RNA synthesis is also observed in the presence of CHIKV and transcription of IRF3 - dependent antiviral genes appears specifically blocked late in infection.", "output": "CHIKV." }, { "input": "We hypothesize that the observed absence of IFN - Beta and antiviral proteins during infection results from an evasion mechanism exhibited by CHIKV that is dependent on widespread shutoff of cellular protein synthesis and a targeted block to late synthesis of antiviral mRNA transcripts.", "output": "CHIKV." }, { "input": "Blood myeloid dendritic cells from HIV - 1 - infected individuals display a proapoptotic profile characterized by decreased Bcl - 2 levels and by caspase - 3 + frequencies that are associated with levels of plasma viremia and T cell activation in an exploratory study.", "output": "HIV - 1." }, { "input": "Reduced frequencies of myeloid and plasmacytoid dendritic cell ( DC ) subsets ( mDCs and pDCs, respectively ) have been observed in the peripheral blood of HIV - 1 - infected individuals throughout the course of disease.", "output": "HIV - 1." }, { "input": "Accumulation of DCs in lymph nodes ( LNs ) may partly account for the decreased numbers observed in blood, but increased DC death may also be a contributing factor.", "output": "There is no related enetity." }, { "input": "We used multiparameter flow cytometry to evaluate pro - and antiapoptotic markers in blood mDCs and pDCs from untreated HIV - 1 - infected donors, from a subset of infected donors before and after receiving antiretroviral therapy ( ART ), and from uninfected control donors.", "output": "HIV - 1." }, { "input": "Blood mDCs, but not pDCs, from untreated HIV - 1 - infected donors expressed lower levels of antiapoptotic Bcl - 2 than DCs from uninfected donors.", "output": "HIV - 1." }, { "input": "A subset of HIV - 1 - infected donors had elevated frequencies of proapoptotic caspase - 3 ( + ) blood mDCs, and positive correlations were observed between caspase - 3 ( + ) mDC frequencies and plasma viral load and CD8 ( + ) T - cell activation levels.", "output": "HIV - 1." }, { "input": "Caspase - 3 ( + ) mDC frequencies, but not mDC Bcl - 2 expression, were reduced with viral suppression on ART.", "output": "There is no related enetity." }, { "input": "Apoptosis markers on DCs in blood and LN samples from a cohort of untreated, HIV - 1 - infected donors with chronic disease were also evaluated.", "output": "HIV - 1." }, { "input": "LN mDCs displayed higher levels of Bcl - 2 and lower caspase - 3 ( + ) frequencies than did matched blood mDCs.", "output": "There is no related enetity." }, { "input": "Conversely, LN pDCs expressed lower Bcl - 2 levels than their blood counterparts.", "output": "There is no related enetity." }, { "input": "In summary, blood mDCs from untreated HIV - 1 - infected subjects displayed a proapoptotic profile that was partially reversed with viral suppression, suggesting that DC death may be a factor contributing to blood DC depletion in the setting of chronic, untreated HIV disease.", "output": "HIV - 1, HIV." }, { "input": "Identification of binary interactions between human cytomegalovirus virion proteins.", "output": "human cytomegalovirus." }, { "input": "Human cytomegalovirus ( HCMV ) virions are composed of a DNA - containing nucleocapsid surrounded by a tegument layer and host - derived lipid envelope studded with virally encoded glycoproteins.", "output": "Human cytomegalovirus, HCMV." }, { "input": "These complex virions are estimated to be composed of more than 50 viral proteins.", "output": "There is no related enetity." }, { "input": "Assembly of HCMV virions is poorly understood, especially with respect to acquisition of the tegument; however, it is thought to involve the stepwise addition of virion components through protein - protein interactions.", "output": "HCMV." }, { "input": "We sought to identify interactions among HCMV virion proteins using yeast two - hybrid analysis.", "output": "HCMV, yeast." }, { "input": "Using 33 known capsid and tegument proteins, we tested 1, 089 pairwise combinations for binary interaction in the two - hybrid assay.", "output": "There is no related enetity." }, { "input": "We identified 24 interactions among HCMV virion proteins, including 13 novel interactions among tegument proteins and one novel interaction between capsid proteins.", "output": "HCMV." }, { "input": "Several of these novel interactions were confirmed by coimmunoprecipitation of protein complexes from transfected cells.", "output": "There is no related enetity." }, { "input": "In addition, we demonstrate three of these interactions in the context of HCMV infection.", "output": "HCMV." }, { "input": "This study reveals several new protein - protein interactions among HCMV tegument proteins, some of which are likely important for HCMV replication and pathogenesis.", "output": "HCMV, HCMV." }, { "input": "Modifications in the polymerase genes of a swine - like triple - reassortant influenza virus to generate live attenuated vaccines against 2009 pandemic H1N1 viruses.", "output": "swine, influenza virus, H1N1 viruses." }, { "input": "On 11 June 2009, the World Health Organization ( WHO ) declared that the outbreaks caused by novel swine - origin influenza A ( H1N1 ) virus had reached pandemic proportions.", "output": "swine - origin influenza A ( H1N1 ) virus." }, { "input": "The pandemic H1N1 ( H1N1pdm ) virus is the predominant influenza virus strain in the human population.", "output": "influenza virus, human." }, { "input": "It has also crossed the species barriers and infected turkeys and swine in several countries.", "output": "swine." }, { "input": "Thus, the development of a vaccine that is effective in multiple animal species is urgently needed.", "output": "There is no related enetity." }, { "input": "We have previously demonstrated that the introduction of temperature - sensitive mutations into the PB2 and PB1 genes of an avian H9N2 virus, combined with the insertion of a hemagglutinin ( HA ) tag in PB1, resulted in an attenuated ( att ) vaccine backbone for both chickens and mice.", "output": "H9N2 virus, chickens." }, { "input": "Because the new pandemic strain is a triple - reassortant ( TR ) virus, we chose to introduce the double attenuating modifications into a swine - like TR virus isolate, A / turkey / OH / 313053 / 04 ( H3N2 ) ( ty / 04 ), with the goal of producing live attenuated influenza vaccines ( LAIV ).", "output": "swine, A / turkey / OH / 313053 / 04 ( H3N2 )." }, { "input": "This genetically modified backbone had impaired polymerase activity and restricted virus growth at elevated temperatures.", "output": "There is no related enetity." }, { "input": "In vivo characterization of two H1N1 vaccine candidates generated using the ty / 04 att backbone demonstrated that this vaccine is highly attenuated in mice, as indicated by the absence of signs of disease, limited replication, and minimum histopathological alterations in the respiratory tract.", "output": "H1N1." }, { "input": "A single immunization with the ty / 04 att - based vaccines conferred complete protection against a lethal H1N1pdm virus infection in mice.", "output": "There is no related enetity." }, { "input": "More importantly, vaccination of pigs with a ty / 04 att - H1N1 vaccine candidate resulted in sterilizing immunity upon an aggressive intratracheal challenge with the 2009 H1N1 pandemic virus.", "output": "There is no related enetity." }, { "input": "Our studies highlight the safety of the ty / 04 att vaccine platform and its potential as a master donor strain for the generation of live attenuated vaccines for humans and livestock.", "output": "humans." }, { "input": "Novel F141L pre - S2 mutation in hepatitis B virus increases the risk of hepatocellular carcinoma in patients with chronic genotype C infections.", "output": "hepatitis B virus." }, { "input": "Several lines of evidence have suggested that some naturally occurring mutations of hepatitis B virus ( HBV ) play a critical role in hepatocellular carcinoma ( HCC ).", "output": "hepatitis B virus, HBV." }, { "input": "Here, we describe a novel HCC - related pre - S2 mutation, F141L.", "output": "There is no related enetity." }, { "input": "To prove the relationship between the F141L mutation and HCC, molecular epidemiology studies using MboII PCR restriction analysis ( PRA ) were performed, and the molecular mechanism was investigated through construction of a stable hepatocyte cell line expressing the large surface HB protein ( LHB ) with the F141L mutation ( F141L - LHB ).", "output": "There is no related enetity." }, { "input": "Application of MboII PRA to samples from 241 Korean patients with chronic liver diseases of different clinical stages confirmed that F141L mutants were significantly related to HCC, even in comparison to liver cirrhosis ( HCC, 26. 3 % of patients, or 26 / 99; liver cirrhosis, 3. 8 % of patients, or 2 / 52; P = 0. 001 ).", "output": "There is no related enetity." }, { "input": "By studying stable cell lines, we found that F141L - LHBs could induce cell cycle progression by downregulating the p53 and p21 pathways and upregulating CDK4 and cyclin A.", "output": "There is no related enetity." }, { "input": "Furthermore, we found that in a colony - forming assay, the colony - forming rates in cell lines expressing F141L - LHBs were about twice as high as those of the wild type.", "output": "There is no related enetity." }, { "input": "In conclusion, our results suggest that F141L - LHBs may contribute importantly to the pathogenesis of HCC by inducing cell proliferation and transformation.", "output": "There is no related enetity." }, { "input": "So, the F141L mutation examined in this study could serve as a diagnostic marker for the prognosis of HCC.", "output": "There is no related enetity." }, { "input": "Poliovirus - mediated disruption of cytoplasmic processing bodies.", "output": "Poliovirus." }, { "input": "Metazoan cells form cytoplasmic mRNA granules such as stress granules ( SG ) and processing bodies ( P bodies ) that are proposed to be sites of aggregated, translationally silenced mRNAs and mRNA degradation.", "output": "There is no related enetity." }, { "input": "Poliovirus ( PV ) is a plus - strand RNA virus containing a genome that is a functional mRNA; thus, we investigated if PV antagonizes the processes that lead to formation of these structures.", "output": "Poliovirus, PV, PV." }, { "input": "We have previously shown that PV infection inhibits the ability of cells to form stress granules by cleaving RasGAP - SH3 - binding protein ( G3BP ).", "output": "PV." }, { "input": "Here, we show that P bodies are also disrupted during PV infection in cells by 4 h postinfection.", "output": "PV." }, { "input": "The disruption of P bodies is more rapid and more complete than disruption of stress granules.", "output": "There is no related enetity." }, { "input": "The kinetics of P body disruption correlated with production of viral proteinases and required substantial viral gene product expression.", "output": "There is no related enetity." }, { "input": "The organizing mechanism that forms P body foci in cells is unknown; however, potential scaffolding, aggregating, or other regulatory proteins found in P bodies were investigated for degradation.", "output": "There is no related enetity." }, { "input": "Two factors involved in 5 ' - end mRNA decapping and degradation, Xrn1 and Dcp1a, and the 3 ' deadenylase complex component Pan3 underwent accelerated degradation during infection, and Dcp1a may be a direct substrate of PV 3C proteinase.", "output": "PV." }, { "input": "Several other key factors proposed to be essential for P body formation, GW182, Edc3, and Edc4, were unaffected by poliovirus infection.", "output": "poliovirus." }, { "input": "Since deadenylation has been reported to be required for P body formation, viral inhibition of deadenylation, through Pan3 degradation, is a potential mechanism of P body disruption.", "output": "There is no related enetity." }, { "input": "The magnitude of local immunity in the lungs of mice induced by live attenuated influenza vaccines is determined by local viral replication and induction of cytokines.", "output": "mice." }, { "input": "While live attenuated influenza vaccines ( LAIVs ) have been shown to be efficacious and have been licensed for human use, the surface glycoproteins hemagglutinin ( HA ) and neuraminidase ( NA ) have to be updated for optimal protective efficacy.", "output": "human." }, { "input": "Little is known about the effect of different HA and NA proteins on the immunogenicity of LAIVs developed using the same backbone.", "output": "There is no related enetity." }, { "input": "A panel of LAIVs that share the internal protein genes, with unique HA and NA gene segments from different influenza subtypes, was rescued by reverse genetics, and a comparative study of immune responses induced by these vaccines was conducted in mice.", "output": "mice." }, { "input": "The results suggest that the magnitude of lung immunity, including pulmonary IgA antibody and memory CD8 ( + ) T lymphocytes, induced by the vaccines depends on the replication efficiency of the LAIVs, as well as the induction of cytokines / chemokines in the lungs.", "output": "There is no related enetity." }, { "input": "However, these factors are not important in determining systemic immunity such as serum antibody titers and memory CD8 ( + ) T cells in the spleen.", "output": "There is no related enetity." }, { "input": "A qualitative analysis of immune responses induced by a single dose of an H5N1 LAIV revealed that the vaccine induced robust systemic and mucosal immunity in mice.", "output": "H5N1, mice." }, { "input": "In addition, antibodies and memory lymphocytes established in the lungs following vaccination were required for protection against lethal challenge with homologous and heterologous H5N1 viruses.", "output": "H5N1 viruses." }, { "input": "Our results highlight the different requirements for inducing systemic and lung immunity that can be explored for the development of pulmonary immunity for protection against respiratory pathogens.", "output": "There is no related enetity." }, { "input": "Multiple innate immune pathways contribute to the immunogenicity of recombinant adenovirus vaccine vectors.", "output": "There is no related enetity." }, { "input": "The innate immune pathways that contribute to the potent immunogenicity of recombinant adenovirus ( rAd ) vaccine vectors remain largely undefined.", "output": "There is no related enetity." }, { "input": "Previous studies assessing innate immunity triggered by vaccine vectors have largely focused on in vitro studies involving antigen - presenting cells and on early in vivo inflammatory responses.", "output": "There is no related enetity." }, { "input": "Here, we systematically explore the Toll - like receptor ( TLR ) signaling requirements for the generation of cellular immune responses by intramuscular immunization with common and alternative serotype rAd vectors in mice.", "output": "There is no related enetity." }, { "input": "Antigen - specific CD8 ( + ) T - lymphocyte responses elicited by these rAd vectors were significantly diminished in MyD88 ( - / - ) mice but not in TRIF ( - / - ) or TLR3 ( - / - ) mice, suggesting the importance of MyD88 - dependent TLR signaling.", "output": "There is no related enetity." }, { "input": "However, the absence of each individual TLR resulted in minimal to no effect on vaccine - elicited cellular immune responses.", "output": "There is no related enetity." }, { "input": "Moreover, responses were not diminished in IL - 1R ( - / - ) or IL - 18R ( - / - ) mice.", "output": "There is no related enetity." }, { "input": "These data suggest that rAd vectors engage multiple MyD88 - dependent signaling pathways, none of which are individually critical; rather, they are integrated to contribute to the potent immunogenicity of rAd vectors.", "output": "There is no related enetity." }, { "input": "Stimulation of multiple innate immune mechanisms may prove a generalizable property of potent vaccines, and this strategy could be harnessed in the development of next - generation vaccine vectors and adjuvants.", "output": "There is no related enetity." }, { "input": "Marek ' s disease virus type 1 microRNA miR - M3 suppresses cisplatin - induced apoptosis by targeting Smad2 of the transforming growth factor beta signal pathway.", "output": "Marek ' s disease virus type 1." }, { "input": "Viruses cause about 15 % of the cancers that are still the leading causes of human mortality.", "output": "human." }, { "input": "The discovery of viral oncogenes has enhanced our understanding of viral oncogenesis.", "output": "There is no related enetity." }, { "input": "However, the underlying molecular mechanisms of virus - induced cancers are complex and require further investigation.", "output": "There is no related enetity." }, { "input": "The present study has attempted to investigate the effects of the microRNAs ( miRNAs ) encoded by Marek ' s disease virus 1 ( MDV1 ), a chicken herpesvirus causing acute T - cell lymphomas and solid visceral tumors in chickens, on anti - cancer drug - induced apoptosis and identify the targets of the miRNAs.", "output": "Marek ' s disease virus 1, MDV1, chicken, chickens." }, { "input": "The results showed that of the total 14 miRNAs encoded by MDV1, MDV1 - miR - M3 significantly promoted cell survival under treatment with cisplatin, a widely used chemotherapy drug.", "output": "MDV1, MDV1." }, { "input": "MDV1 - miR - M3 suppressed cisplatin - induced apoptosis by directly downregulating expression at the protein but not the mRNA level of Smad2, a critical component in the transforming growth factor Beta signal pathway.", "output": "MDV1." }, { "input": "Our data suggest that latent / oncogenic viruses may encode miRNAs to directly target cellular factors involved in antiviral processes including apoptosis, thus proactively creating a cellular environment beneficial to viral latency and oncogenesis.", "output": "There is no related enetity." }, { "input": "Furthermore, the knowledge of the apoptosis resistance conferred by viral miRNAs has great practical implications for improving the efficacy of chemotherapies for treating cancers, especially those induced by oncogenic viruses.", "output": "There is no related enetity." }, { "input": "Macaque long - term nonprogressors resist superinfection with multiple CD8 + T cell escape variants of simian immunodeficiency virus.", "output": "simian immunodeficiency virus." }, { "input": "Human immunodeficiency virus ( HIV ) - positive individuals can be superinfected with different virus strains.", "output": "Human immunodeficiency virus, HIV." }, { "input": "Individuals who control an initial HIV infection are therefore still at risk for subsequent infection with divergent viruses, but the barriers to such superinfection remain unclear.", "output": "HIV." }, { "input": "Here we tested long - term nonprogressors ' ( LTNPs ' ) susceptibility to superinfection using Indian rhesus macaques that express the major histocompatibility complex class I ( MHC - I ) allele Mamu - B 17, which is associated with control of the pathogenic AIDS virus SIVmac239.", "output": "Indian rhesus macaques, virus SIVmac239." }, { "input": "The Mamu - B 17 - restricted CD8 ( + ) T cell repertoire is focused almost entirely on 5 epitopes.", "output": "There is no related enetity." }, { "input": "We engineered a series of SIVmac239 variants bearing mutations in 3, 4, or all 5 of these epitopes and used them to serially challenge 2 Mamu - B 17 - positive LTNPs.", "output": "There is no related enetity." }, { "input": "None of the escape variants caused breakthrough replication in LTNPs, although they readily infected Mamu - B 17 - negative naive macaques.", "output": "There is no related enetity." }, { "input": "In vitro competing coculture assays and examination of viral evolution in hosts lacking Mamu - B 17 suggested that the mutant viruses had negligible defects in replicative fitness.", "output": "There is no related enetity." }, { "input": "Both LTNPs maintained robust immune responses, including simian immunodeficiency virus ( SIV ) - specific CD8 ( + ) and CD4 ( + ) T cells and neutralizing antibodies.", "output": "simian immunodeficiency virus, SIV." }, { "input": "Our results suggest that escape mutations in epitopes bound by & quot; protective & quot; MHC - I molecules may not be sufficient to establish superinfection in LTNPs.", "output": "There is no related enetity." }, { "input": "Induction of type I interferon secretion through recombinant Newcastle disease virus expressing measles virus hemagglutinin stimulates antibody secretion in the presence of maternal antibodies.", "output": "Newcastle disease virus, measles virus." }, { "input": "Measles virus ( MV ) vaccine effectively protects seronegative individuals against infection.", "output": "Measles virus, MV." }, { "input": "However, inhibition of vaccine - induced seroconversion by maternal antibodies after vaccination remains a problem, as it leaves infants susceptible to MV infection.", "output": "MV." }, { "input": "In cotton rats, passive transfer of MV - specific IgG mimics maternal antibodies and inhibits vaccine - induced seroconversion.", "output": "MV." }, { "input": "Here, we report that immunization in the presence of passively transferred IgG inhibits the secretion of neutralizing antibodies but not the generation of MV - specific B cells.", "output": "MV." }, { "input": "This finding suggested that MV - specific B cells require an additional stimulus to mature into antibody - secreting plasma cells.", "output": "MV." }, { "input": "In order to provide such a stimulus, we generated a recombinant Newcastle disease virus ( NDV ) expressing the MV hemagglutinin ( NDV - H ).", "output": "Newcastle disease virus, NDV, MV, NDV - H." }, { "input": "In contrast to MV, NDV - H induced high levels of type I interferon in plasmacytoid dendritic cells and in lung tissue.", "output": "MV, NDV - H." }, { "input": "In cotton rats immunized with NDV - H, neutralizing antibodies were also generated in the presence of passively transferred antibodies.", "output": "NDV - H." }, { "input": "In the latter case, however, the level and kinetics of antibody generation were reduced.", "output": "There is no related enetity." }, { "input": "In vitro, alpha interferon stimulated the activation of MV - specific B cells from MV - immune spleen cells.", "output": "MV, MV." }, { "input": "NDV infection ( which induces alpha interferon ) had the same effect, and stimulation could be abrogated by antibodies neutralizing alpha interferon, but not interleukin 6 ( IL - 6 ).", "output": "NDV." }, { "input": "In vivo, coapplication of UV - inactivated MV with NDV led to increased MV - specific antibody production in the presence and absence of passively transferred antibodies.", "output": "MV, NDV, MV." }, { "input": "These data indicate that MV - specific B cells are being generated after immunization in the presence of maternal antibodies and that the provision of alpha interferon as an additional signal leads to antibody secretion.", "output": "MV." }, { "input": "Human pluripotent stem cells produce natural killer cells that mediate anti - HIV - 1 activity by utilizing diverse cellular mechanisms.", "output": "Human, HIV - 1." }, { "input": "Cell - based therapies against HIV / AIDS have been gaining increased interest.", "output": "There is no related enetity." }, { "input": "Natural killer ( NK ) cells are a key component of the innate immune system with the ability to kill diverse tumor cells and virus - infected cells.", "output": "There is no related enetity." }, { "input": "While NK cells have been shown to play an important role in the control of HIV - 1 replication, their functional activities are often compromised in HIV - 1 - infected individuals.", "output": "HIV - 1, HIV - 1." }, { "input": "We have previously demonstrated the derivation of NK cells from human embryonic stem cells ( hESCs ) with the ability to potently kill multiple types of tumor cells both in vitro and in vivo.", "output": "human." }, { "input": "We now demonstrate the derivation of functional NK cells from human induced pluripotent stem cells ( iPSCs ).", "output": "There is no related enetity." }, { "input": "More importantly, both hESC - and iPSC - derived NK cells are able to inhibit HIV - 1 NL4 - 3 infection of CEM - GFP cells.", "output": "HIV - 1." }, { "input": "Additional studies using HIV - 1 - infected human primary CD4 ( + ) T cells illustrated that hESC - and iPSC - derived NK cells suppress HIV - 1 infection by at least three distinct cellular mechanisms: killing of infected targets through direct lysis, antibody - dependent cellular cytotoxicity, and production of chemokines and cytokines.", "output": "HIV - 1, HIV - 1." }, { "input": "Our results establish the potential to utilize hESC - and iPSC - derived NK cells to better understand anti - HIV - 1 immunity and provide a novel cellular immunotherapeutic approach to treat HIV / AIDS.", "output": "HIV - 1." }, { "input": "Yeast - elicited cross - reactive antibodies to HIV Env glycans efficiently neutralize virions expressing exclusively high - mannose N - linked glycans.", "output": "Yeast, HIV." }, { "input": "The HIV envelope ( Env ) protein uses a dense coat of glycans to mask conserved domains and evade host humoral immune responses.", "output": "There is no related enetity." }, { "input": "The broadly neutralizing antibody 2G12, which binds a specific cluster of high - mannose glycans on HIV Env, shows that the glycan shield can also serve as a target for neutralizing antibodies.", "output": "There is no related enetity." }, { "input": "We have described a triple mutant Saccharomyces cerevisiae strain that expresses high - mannose glycoproteins that bind to 2G12.", "output": "Saccharomyces cerevisiae." }, { "input": "When used to immunize rabbits, this yeast elicits antibodies that bind to gp120 - associated glycans but fail to neutralize virus.", "output": "rabbits, yeast." }, { "input": "Here we sought to determine the reason for these discordant results.", "output": "There is no related enetity." }, { "input": "Affinity purification of sera over columns conjugated with three 2G12 - reactive yeast glycoproteins showed that these proteins could adsorb 80 % of the antibodies that bind to gp120 glycans.", "output": "yeast." }, { "input": "Despite binding to monomeric gp120, these mannose - specific antibodies failed to bind cell surface - expressed trimeric Env.", "output": "There is no related enetity." }, { "input": "However, when Env was expressed in the presence of the mannosidase inhibitor kifunensine to force retention of high - mannose glycans at all sites, the purified antibodies gained the abilities to bind trimeric Env and to strongly and broadly neutralize viruses produced under these conditions.", "output": "There is no related enetity." }, { "input": "Combined, these data show that the triple mutant yeast strain elicits antibodies that bind to high - mannose glycans presented on the HIV envelope, but only when they are displayed in a manner not found on native Env trimers.", "output": "yeast." }, { "input": "This implies that the underlying structure of the protein scaffold used to present the high - mannose glycans may be critical to allow elicitation of antibodies that recognize trimeric Env and neutralize virus.", "output": "There is no related enetity." }, { "input": "Role of RNase MRP in viral RNA degradation and RNA recombination.", "output": "There is no related enetity." }, { "input": "RNA degradation, together with RNA synthesis, controls the steady - state level of viral RNAs in infected cells.", "output": "There is no related enetity." }, { "input": "The endoribonucleolytic cleavage of viral RNA is important not only for viral RNA degradation but for RNA recombination as well, due to the participation of some RNA degradation products in the RNA recombination process.", "output": "There is no related enetity." }, { "input": "To identify host endoribonucleases involved in degradation of Tomato bushy stunt virus ( TBSV ) in a Saccharomyces cerevisiae model host, we tested eight known endoribonucleases.", "output": "Tomato bushy stunt virus, TBSV, Saccharomyces cerevisiae." }, { "input": "Here we report that downregulation of SNM1, encoding a component of the RNase MRP, and a temperature - sensitive mutation in the NME1 gene, coding for the RNA component of RNase MRP, lead to reduced production of the endoribonucleolytically cleaved TBSV RNA in yeast.", "output": "TBSV, yeast." }, { "input": "We also show that the highly purified yeast RNase MRP cleaves the TBSV RNA in vitro, resulting in TBSV RNA degradation products similar in size to those observed in yeast cells.", "output": "yeast, TBSV, TBSV, yeast." }, { "input": "Knocking down the NME1 homolog in Nicotiana benthamiana also led to decreased production of the cleaved TBSV RNA, suggesting that in plants, RNase MRP is involved in TBSV RNA degradation.", "output": "Nicotiana benthamiana, TBSV, TBSV." }, { "input": "Altogether, this work suggests a role for the host endoribonuclease RNase MRP in viral RNA degradation and recombination.", "output": "There is no related enetity." }, { "input": "Identification and structural characterization of the ALIX - binding late domains of simian immunodeficiency virus SIVmac239 and SIVagmTan - 1.", "output": "simian immunodeficiency virus, SIVagmTan - 1." }, { "input": "Retroviral Gag proteins contain short late - domain motifs that recruit cellular ESCRT pathway proteins to facilitate virus budding.", "output": "Retroviral." }, { "input": "ALIX - binding late domains often contain the core consensus sequence YPX ( n ) L ( where X ( n ) can vary in sequence and length ).", "output": "There is no related enetity." }, { "input": "However, some simian immunodeficiency virus ( SIV ) Gag proteins lack this consensus sequence, yet still bind ALIX.", "output": "simian immunodeficiency virus, SIV." }, { "input": "We mapped divergent, ALIX - binding late domains within the p6 ( Gag ) proteins of SIV ( mac239 ) ( ( 40 ) SREKPYKEVTEDLLHLNSLF ( 59 ) ) and SIV ( agmTan - 1 ) ( ( 24 ) AAGAYDPARKLLEQYAKK ( 41 ) ).", "output": "SIV ( agmTan - 1 )." }, { "input": "Crystal structures revealed that anchoring tyrosines ( in lightface ) and nearby hydrophobic residues ( underlined ) contact the ALIX V domain, revealing how lentiviruses employ a diverse family of late - domain sequences to bind ALIX and promote virus budding.", "output": "There is no related enetity." }, { "input": "Variola and monkeypox viruses utilize conserved mechanisms of virion motility and release that depend on abl and SRC family tyrosine kinases.", "output": "Variola, monkeypox viruses." }, { "input": "Vaccinia virus ( VacV ) enters mammalian cells, replicates extranuclearly, and produces virions that move to the cell surface along microtubules, fuse with the plasma membrane, and move from infected cells toward apposing cells on actin - filled membranous protrusions or actin tails.", "output": "Vaccinia virus, VacV." }, { "input": "To form actin tails, cell - associated enveloped virions ( CEV ) require Abl and Src family tyrosine kinases.", "output": "There is no related enetity." }, { "input": "Furthermore, release of CEV from the cell requires Abl but not Src family tyrosine kinases and is blocked by imatinib mesylate ( STI - 571; Gleevec ), an Abl family kinase inhibitor used to treat chronic myelogenous leukemia in humans.", "output": "humans." }, { "input": "Here we demonstrate that the Poxviridae family members monkeypox virus ( MPX ) and variola virus ( VarV ) use conserved mechanisms for actin motility and extracellular enveloped virion ( EEV ) release.", "output": "monkeypox virus, MPX, variola virus, VarV." }, { "input": "Furthermore, we show that imatinib mesylate is effective in a mouse model of infection with VacV, whether delivered prophylactically or postinfection, and restricts spread of virions from the site of inoculation.", "output": "mouse, VacV." }, { "input": "While inhibitors of both Src and Abl family kinases, such as dasatinib ( BMS - 354825; Sprycel ), are effective in limiting dissemination of VacV, VarV, and MPX in vitro, members of this class of drugs appear to have immunosuppressive effects in vivo that preclude their use as anti - infectives.", "output": "VacV, VarV, MPX." }, { "input": "Together, these data suggest a possible utility for imatinib mesylate in treating smallpox or MPX infections or complications associated with vaccination.", "output": "MPX." }, { "input": "Replicative and transcriptional activities of hepatitis B virus in patients coinfected with hepatitis B and hepatitis delta viruses.", "output": "hepatitis B virus, hepatitis B, hepatitis delta viruses." }, { "input": "Hepatitis B virus ( HBV ) and hepatitis delta virus ( HDV ) interplay was investigated by examining liver and serum samples from 21 coinfected and 22 HBV - monoinfected patients with chronic liver disease.", "output": "Hepatitis B virus, HBV, hepatitis delta virus, HDV, HBV." }, { "input": "Different real - time PCR assays were applied to evaluate intrahepatic amounts of HBV DNA, covalently closed circular DNA ( cccDNA ), pregenomic RNA ( pgRNA ), pre - S / S RNAs, and HDV RNA.", "output": "HBV, HDV." }, { "input": "Besides HBV DNA and HDV RNA levels, HBsAg concentrations in the sera were also determined.", "output": "HBV, HDV." }, { "input": "HDV - coinfected cases showed significantly lower median levels of serum HBV DNA ( - 5 log ), intrahepatic relaxed - circular DNA ( - 2 log ), and cccDNA ( - 2 log ) than those of HBV - monoinfected cases.", "output": "HDV, HBV, HBV." }, { "input": "Interestingly, pgRNA and pre - S / S RNA amounts were significantly lower ( both - 1 log ) in HDV - positive patients, whereas serum HBsAg concentrations were comparable between the two patient groups.", "output": "HDV." }, { "input": "Pre - S / S RNA and HBsAg amounts per cccDNA molecule were higher in HDV - positive patients ( 3 - fold and 1 log, respectively ), showing that HBV replication was reduced, whereas synthesis of envelope proteins was not specifically decreased.", "output": "HDV, HBV." }, { "input": "The ratios of cccDNA to intracellular total HBV DNA showed a larger proportion of cccDNA molecules in HDV - positive cases.", "output": "HBV, HDV." }, { "input": "For these patients, both intrahepatic and serum HDV RNA amounts were associated with cccDNA but not with HBsAg or HBV DNA levels.", "output": "HDV." }, { "input": "Finally, HBV genomes with large deletions in the basal core promoter / precore region were detected in 5 / 21 HDV - positive patients but in no HDV - negative patients and were associated with lower viremia levels.", "output": "HDV, HDV." }, { "input": "These findings provide significant information about the interference exerted by HDV on HBV replication and transcription activities in the human liver.", "output": "HBV, human." }, { "input": "Dynamics of two separate but linked HIV - 1 CRF01 _ AE outbreaks among injection drug users in Stockholm, Sweden, and Helsinki, Finland.", "output": "HIV - 1 CRF01 _ AE." }, { "input": "Detailed phylogenetic analyses were performed to characterize an HIV - 1 outbreak among injection drug users ( IDUs ) in Stockholm, Sweden, in 2006.", "output": "HIV - 1." }, { "input": "This study investigated the source and dynamics of HIV - 1 spread during the outbreak as well as associated demographic and clinical factors.", "output": "HIV - 1." }, { "input": "Seventy Swedish IDUs diagnosed during 2004 to 2007 were studied.", "output": "There is no related enetity." }, { "input": "Demographic, clinical, and laboratory data were collected, and the V3 region of the HIV - 1 envelope gene was sequenced to allow detailed phylogenetic analyses.", "output": "HIV - 1." }, { "input": "The results showed that the Stockholm outbreak was caused by a CRF01 _ AE variant imported from Helsinki, Finland, around 2003, which was quiescent until the outbreak started in 2006.", "output": "CRF01 _ AE." }, { "input": "Local Swedish subtype B variants continued to spread at a lower rate.", "output": "subtype B." }, { "input": "The number of new CRF01 _ AE cases over a rooted phylogenetic tree accurately reflected the transmission dynamics and showed a temporary increase, by a factor of 12, in HIV incidence during the outbreak.", "output": "CRF01 _ AE, HIV." }, { "input": "Virus levels were similar in CRF01 _ AE and subtype B infections, arguing against differences in contagiousness.", "output": "CRF01 _ AE, subtype B." }, { "input": "Similarly, there were no major differences in other baseline characteristics.", "output": "There is no related enetity." }, { "input": "Instead, the outbreak in Stockholm ( and Helsinki ) was best explained by an introduction of HIV into a standing network of previously uninfected IDUs.", "output": "HIV." }, { "input": "The combination of phylogenetics and epidemiological data creates a powerful tool for investigating outbreaks of HIV and other infectious diseases that could improve surveillance and prevention.", "output": "HIV." }, { "input": "Thermally contingent plasticity: temperature alters expression of predator - induced colour and morphology in a Neotropical treefrog tadpole.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Behavioural, morphological and coloration plasticity are common responses of prey to predation risk.", "output": "There is no related enetity." }, { "input": "Theory predicts that prey should respond to the relative magnitude of risk, rather than a single level of response to any risk level.", "output": "There is no related enetity." }, { "input": "In addition to conspecific and predator densities, prey growth and differentiation rates affect the duration of vulnerability to size - and stage - limited predators and therefore the relative value of defences.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We reared tadpoles of the Neotropical treefrog Dendropsophus ebraccatus with or without cues from a predator ( Belostoma sp. ) in ecologically relevant warm or cool temperatures.", "output": "Dendropsophus ebraccatus." }, { "input": "To track phenotypic changes, we measured morphology, tail coloration and developmental stage at three points during the larval period.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Cues from predators interacted with growth conditions causing tadpoles to alter their phenotype, changing only tail colour in response to predators in warm water, but both morphology and colour in cool growth conditions.", "output": "There is no related enetity." }, { "input": "Tadpoles with predators in warm water altered coloration early but converged on the morphology of predator - free controls.", "output": "There is no related enetity." }, { "input": "Water temperature alone had no effect on tadpole phenotype.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "We demonstrate that seemingly small variation in abiotic environmental conditions can alter the expression of phenotypic plasticity, consistent with predictions about how growth rate affects risk.", "output": "There is no related enetity." }, { "input": "Predator - induced tadpole phenotypes depended on temperature, with strong expression only in temperatures that slow development.", "output": "There is no related enetity." }, { "input": "Thermal modulation of plastic responses to predators may be broadly relevant to poikilotherm development.", "output": "There is no related enetity." }, { "input": "It is important to include a range of realistic growth conditions in experiments to more fully understand the ecological and evolutionary significance of plasticity.", "output": "There is no related enetity." }, { "input": "Contrasting covariation of above - and belowground invertebrate species across plant genotypes.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Invertebrate species generally do not respond independently to genotypic variation in plants, giving rise to clusters of species that naturally associate with or avoid certain genotypes.", "output": "There is no related enetity." }, { "input": "This covariation causes coevolution to be diffuse rather than pairwise.", "output": "There is no related enetity." }, { "input": "Studies on this topic, however, have never considered the belowground invertebrate community, leaving a critical gap in our understanding.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We investigated the covariation among naturally colonising above - and belowground invertebrate species across six genetically distinct populations of the dune grass Ammophila arenaria.", "output": "Ammophila arenaria." }, { "input": "After having grown from seed in a common garden, plants were randomised in a single field site to exclude all but broad - sense genetic variation.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Strong positive covariation across genotypes among both above - and belowground invertebrates was detected, while correlations between these two groups were negative.", "output": "There is no related enetity." }, { "input": "This clustering of above - and belowground species matched well with order level taxonomy.", "output": "There is no related enetity." }, { "input": "Host range, trophic level and food type on the other hand did not correspond well with the clusters.", "output": "There is no related enetity." }, { "input": "Within the cluster of aboveground fauna, subsequent groupings were not related to any phylogenetic or ecological characteristic, although correlations within these subgroups were very high.", "output": "There is no related enetity." }, { "input": "We furthermore demonstrated significant differences in multiple invertebrate species occurrence between plant genotypes, in general as well as at the above - and belowground level.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "The observed strong covariation suggests diffuse coevolution between A. arenaria and its associated invertebrate species.", "output": "A . arenaria." }, { "input": "The trade - off between root and shoot invertebrates could however hamper directional selection on resistance to either group.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Our results clearly demonstrate the need for studies of plant - animal interactions to include the belowground fauna, as this might drastically alter our general conception of how plants and their associated animal communities interact and how these interactions shape the process of evolution.", "output": "There is no related enetity." }, { "input": "Density - dependent population dynamics and dispersal in heterogeneous metapopulations.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Metapopulation microcosms were constructed to test the effect of four different types of habitat heterogeneity on the dynamics and dispersal in spatially extended systems; homogeneity, spatial heterogeneity, temporal heterogeneity and spatio - temporal heterogeneity.", "output": "There is no related enetity." }, { "input": "Resources were distributed across discrete habitat patches in bruchid beetle ( Callosobruchus maculatus ) metapopulations, and long - term time series were recorded.", "output": "Callosobruchus maculatus." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Mathematical models were fitted to the long - term time series from the experimental systems using a maximum likelihood approach.", "output": "There is no related enetity." }, { "input": "Models were composed of separate birth, death, emigration and immigration terms all of which incorporated stochasticity drawn from different probability distributions.", "output": "There is no related enetity." }, { "input": "Models with density - dependent and density - independent birth, death and emigration terms were investigated and, in each case, the model that best described the empirical data was identified.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "At the local scale, population sizes differed between patches depending on the type of heterogeneity.", "output": "There is no related enetity." }, { "input": "Larger populations were associated with higher resource availabilities.", "output": "There is no related enetity." }, { "input": "As a result of this, the variation between local population sizes was greatest when there was spatial heterogeneity in which mean resource abundance varied from patch to patch.", "output": "There is no related enetity." }, { "input": "Variation in population sizes within patches was largest when there was temporal heterogeneity.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Density - dependent processes leading to the regulation of local population dynamics in our experimental systems were strongest in homogeneity or temporal heterogeneity treatments.", "output": "There is no related enetity." }, { "input": "Associated with this, we found that these systems were best described using mathematical models with density dependence acting on mortality.", "output": "There is no related enetity." }, { "input": "In contrast, spatial and spatio - temporal time series were adequately described using density - independent population processes.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Experimental metapopulations showed varying degrees of density - dependent dispersal.", "output": "There is no related enetity." }, { "input": "Local net dispersal each week was primarily driven by the local population size and secondarily affected by neighbourhood population density.", "output": "There is no related enetity." }, { "input": "Mathematical population models illustrated the importance of explicit description of density - dependent dispersal in all systems except the homogeneous metapopulations.", "output": "There is no related enetity." }, { "input": "Tuber melanosporum: mating type distribution in a natural plantation and dynamics of strains of different mating types on the roots of nursery - inoculated host plants.", "output": "Tuber melanosporum." }, { "input": "* In light of the recent finding that Tuber melanosporum, the ectomycorrhizal ascomycete that produces the most highly prized black truffles, is a heterothallic species, we monitored the spatial distribution of strains with opposite mating types ( MAT ) in a natural truffle ground and followed strain dynamics in artificially inoculated host plants grown under controlled conditions.", "output": "Tuber melanosporum, black truffles, truffle." }, { "input": "* In a natural truffle ground, ectomycorrhizas ( ECMs ), soil samples and fruit bodies were sampled and genotyped to determine mating types.", "output": "truffle." }, { "input": "Simple sequence repeat ( SSR ) markers were also used to fingerprint ECMs and fruit bodies.", "output": "There is no related enetity." }, { "input": "The ECMs from nursery - inoculated host plants were analysed for mating type at 6 months and 19 months post - inoculation.", "output": "There is no related enetity." }, { "input": "* In open - field conditions, all ECMs from the same sampling site showed an identical mating type and an identical haploid genotype, based on SSR analysis.", "output": "There is no related enetity." }, { "input": "Interestingly, the gleba of fruit bodies always demonstrated the same genotype as the surrounding ECMs.", "output": "There is no related enetity." }, { "input": "Although root tips from nursery - grown plants initially developed ECMs of both mating types, a dominance of ECMs of the same MAT were found after several months.", "output": "There is no related enetity." }, { "input": "* The present study deepens our understanding of the vegetative and sexual propagation modes of T. melanosporum.", "output": "T . melanosporum." }, { "input": "These results are highly relevant for truffle cultivation.", "output": "truffle." }, { "input": "Jasmonate biosynthesis in legume and actinorhizal nodules.", "output": "There is no related enetity." }, { "input": "Jasmonic acid ( JA ) is a plant signalling compound that has been implicated in the regulation of mutualistic symbioses.", "output": "There is no related enetity." }, { "input": "In order to understand the spatial distribution of JA biosynthetic capacity in nodules of two actinorhizal species, Casaurina glauca and Datisca glomerata, and one legume, Medicago truncatula, we determined the localization of allene oxide cyclase ( AOC ) which catalyses a committed step in JA biosynthesis.", "output": "Casaurina glauca, Datisca glomerata, Medicago truncatula." }, { "input": "In all nodule types analysed, AOC was detected exclusively in uninfected cells.", "output": "There is no related enetity." }, { "input": "The levels of JA were compared in the roots and nodules of the three plant species.", "output": "There is no related enetity." }, { "input": "The nodules and noninoculated roots of the two actinorhizal species, and the root systems of M. truncatula, noninoculated or nodulated with wild - type Sinorhizobium meliloti or with mutants unable to fix nitrogen, did not show significant differences in JA levels.", "output": "M . truncatula, Sinorhizobium meliloti." }, { "input": "However, JA levels in all plant organs examined increased significantly on mechanical disturbance.", "output": "There is no related enetity." }, { "input": "To study whether JA played a regulatory role in the nodules of M. truncatula, composite plants containing roots expressing an MtAOC1 - sense or MtAOC1 - RNAi construct were inoculated with S. meliloti.", "output": "M . truncatula, S . meliloti." }, { "input": "Neither an increase nor reduction in AOC levels resulted in altered nodule formation.", "output": "There is no related enetity." }, { "input": "These data suggest that jasmonates are not involved in the development and function of root nodules.", "output": "There is no related enetity." }, { "input": "Distribution and localization of microsatellites in the Perigord black truffle genome and identification of new molecular markers.", "output": "Perigord black truffle." }, { "input": "The level of genetic diversity and genetic structure in the Perigord black truffle ( Tuber melanosporum Vittad. ) has been debated for several years, mainly due to the lack of appropriate genetic markers.", "output": "Perigord black truffle, Tuber melanosporum Vittad .." }, { "input": "Microsatellites or simple sequence repeats ( SSRs ) are important for the genome organisation, phenotypic diversity and are one of the most popular molecular markers.", "output": "There is no related enetity." }, { "input": "In this study, we surveyed the T. melanosporum genome ( 1 ) to characterise its SSR pattern; ( 2 ) to compare it with SSR patterns found in 48 other fungal and three oomycetes genomes and ( 3 ) to identify new polymorphic SSR markers for population genetics.", "output": "T . melanosporum." }, { "input": "The T. melanosporum genome is rich in SSRs with 22, 425 SSRs with mono - nucleotides being the most frequent motifs.", "output": "T . melanosporum." }, { "input": "SSRs were found in all genomic regions although they are more frequent in non - coding regions ( introns and intergenic regions ).", "output": "There is no related enetity." }, { "input": "Sixty out of 135 PCR - amplified mono -, di -, tri -, tetra, penta, and hexa - nucleotides were polymorphic ( 44 % ) within black truffle populations and 27 were randomly selected and analysed on 139 T. melanosporum isolates from France, Italy and Spain.", "output": "black truffle, T . melanosporum." }, { "input": "The number of alleles varied from 2 to 18 and the expected heterozygosity from 0. 124 to 0. 815.", "output": "There is no related enetity." }, { "input": "One hundred and thirty - two different multilocus genotypes out of the 139 T. melanosporum isolates were identified and the genotypic diversity was high ( 0. 999 ).", "output": "T . melanosporum." }, { "input": "Polymorphic SSRs were found in UTR regulatory regions of fruiting bodies and ectomycorrhiza regulated genes, suggesting that they may play a role in phenotypic variation.", "output": "There is no related enetity." }, { "input": "In conclusion, SSRs developed in this study were highly polymorphic and our results showed that T. melanosporum is a species with an important genetic diversity, which is in agreement with its recently uncovered heterothallic mating system.", "output": "T . melanosporum." }, { "input": "Proteotyping to establish the lineage of type A H1N1 and type B human influenza virus.", "output": "type A H1N1, type B human influenza virus." }, { "input": "The ability to establish the lineage of type A H1N1 and type B human influenza virus strains using a new proteotyping approach is demonstrated.", "output": "type A H1N1, type B human influenza virus." }, { "input": "Lineage - specific signature peptides have been determined for the hemagglutinin antigen of type A H1N1 and type B influenza viruses.", "output": "type A H1N1, type B influenza viruses." }, { "input": "The detection of these peptides alone within the high resolution mass spectra of whole antigen digests enables the lineage of the strain to be rapidly and unequivocally assigned.", "output": "There is no related enetity." }, { "input": "This proteotyping approach complements conventional PCR approaches and should aid in the monitoring of the evolution of the influenza virus in both humans and animals.", "output": "influenza virus, humans." }, { "input": "Development of an IgM - capture ELISA for Coxsackievirus A16 infection.", "output": "Coxsackievirus A16." }, { "input": "Diagnosis of Coxsackievirus A16 ( CA16 ) infection in China relies mainly on reverse transcription - polymerase chain reaction ( RT - PCR ) that require expensive equipment and special trained personnel, thus making its wide application in health care settings unlikely.", "output": "Coxsackievirus A16, CA16." }, { "input": "In this study, a novel IgM anti - CA16 assay was developed for the detection of IgM antibodies to CA16 in serum.", "output": "CA16, CA16." }, { "input": "The responses and diagnostic value of IgM for the CA16 infection were assessed by testing 1970 serum samples.", "output": "CA16." }, { "input": "The results showed that sensitivity of IgM test was 84. 6 % ( 259 / 306, 95 % CI: 80. 1 - 88. 5 ), and specificity in control subjects and patients with CA16 HFMD was 99. 2 % ( 1508 / 1520, 95 % CI: 98. 6 - 99. 6 ) and 90. 3 % ( 14 / 144, 95 % CI: 84. 2 - 94. 6 ), respectively.", "output": "CA16." }, { "input": "The IgM positive rate reached 56. 3 % in the sera collected within the first day after onset, increased continuously to 95. 3 % at day 5 to day 7 after onset, and then reached 100 % after more than 8 days.", "output": "There is no related enetity." }, { "input": "The cross - reaction rate in patients infected with other non - CA16 enteroviruses was 9. 7 % ( 14 / 144 ).", "output": "CA16." }, { "input": "These results suggest that the IgM anti - CA16 assay offers a rapid, convenient, and reliable method to detect acute CA16 infections.", "output": "CA16, CA16." }, { "input": "A study of conflict between molecular phylogeny and taxonomy in the Desmidiaceae ( Streptophyta, Viridiplantae ): analyses of 291 rbcL sequences.", "output": "There is no related enetity." }, { "input": "Molecular phylogenetic analyses of 93 new and 198 non - redundant GenBank rbcL sequences of the family Desmidiaceae ( Zygnematophyceae, Streptophyta ) established 22 mostly highly supported clades, in addition to four non - supported lineages and eight single - taxon branches within the family.", "output": "There is no related enetity." }, { "input": "Nine novel clades and single - taxon branches were identified, suggesting that current taxon sampling has not reached saturation in the family.", "output": "There is no related enetity." }, { "input": "The highly polyphyletic nature of most desmid genera corroborated in this study using a large taxon set, calls for re - evaluation of the genus concept in the family Desmidiaceae that traditionally relied on features of cell morphology.", "output": "There is no related enetity." }, { "input": "Molecular phylogenetic data have shown that these morphological characters are highly homoplastic or plesiomorphic and thus cannot be used to delineate genera.", "output": "There is no related enetity." }, { "input": "The dramatic discrepancy between the currently practised systematic treatment of the family and the composition of the clades based on sequence comparisons requires emendation of almost all existing genera and description of a larger number of novel genera.", "output": "There is no related enetity." }, { "input": "The clades identified during this study provide a framework for the future emendation / description of genera in the Desmidiaceae.", "output": "There is no related enetity." }, { "input": "Ste50 adaptor protein governs sexual differentiation of Cryptococcus neoformans via the pheromone - response MAPK signaling pathway.", "output": "Cryptococcus neoformans." }, { "input": "The mitogen - activated protein kinase ( MAPK ) pathways control diverse cellular functions in pathogenic fungi, including sexual differentiation, stress response, and maintenance of cell wall integrity.", "output": "There is no related enetity." }, { "input": "Here we characterized a Cryptococcus neoformans gene, which is homologous to the yeast Ste50 that is known to play an important role in mating pheromone response and stress response as an adaptor protein to the Ste11 MAPK kinase kinase in Saccharomyces cerevisiae.", "output": "Cryptococcus neoformans, Saccharomyces cerevisiae." }, { "input": "The C. neoformans Ste50 was not involved in any of the stress responses or virulence factor production ( capsule and melanin ) that are controlled by the HOG and Ras / cAMP signaling pathways.", "output": "C . neoformans." }, { "input": "However, Ste50 was required for mating in both serotype A and serotype D C. neoformans strains.", "output": "serotype A, serotype D C . neoformans." }, { "input": "The ste50Delta mutant was completely defective in cell - cell fusion and mating pheromone production.", "output": "There is no related enetity." }, { "input": "Double mutation of the STE50 gene blocked increased production of pheromone and the hyper - filamentation phenotype of cells deleted of the CRG1 gene, which encodes the RGS protein that negatively regulates pheromone responsive G - protein signaling via the MAPK pathway.", "output": "There is no related enetity." }, { "input": "Regardless of the presence of the basidiomycota - specific SH3 domains of Ste50 that are known to be required for full virulence of Ustilago maydis, Ste50 was dispensable for virulence of C. neoformans in a murine model of cryptococcosis.", "output": "Ustilago maydis, C . neoformans." }, { "input": "In conclusion, the Ste50 adaptor protein controls sexual differentiation of C. neoformans via the pheromone - responsive MAPK pathway but is not required for virulence.", "output": "C . neoformans." }, { "input": "Nucleotide parasitism by Simkania negevensis ( Chlamydiae ).", "output": "Simkania negevensis." }, { "input": "Intracellular bacteria live in an environment rich in most essential metabolites but need special mechanisms to access these substrates.", "output": "There is no related enetity." }, { "input": "Nucleotide transport proteins ( NTTs ) catalyze the import of ATP and other nucleotides from the eukaryotic host into the bacterial cell and render de novo synthesis of these compounds dispensable.", "output": "There is no related enetity." }, { "input": "The draft genome sequence of Simkania negevensis strain Z, a chlamydial organism considered a newly emerging pathogen, revealed four genes encoding putative nucleotide transport proteins ( SnNTT1 to SnNTT4 ), all of which are transcribed during growth of S. negevensis in Acanthamoeba host cells, as confirmed by reverse transcription - PCR.", "output": "Simkania negevensis strain Z, S . negevensis." }, { "input": "Using heterologous expression in Escherichia coli, we could show that SnNTT1 functions as an ATP / ADP antiporter, SnNTT2 as a guanine nucleotide / ATP / H ( + ) symporter driven by the membrane potential, and SnNTT3 as a nucleotide triphosphate antiporter.", "output": "Escherichia coli." }, { "input": "In addition, SnNTT3 is able to transport dCTP, which has not been shown for a prokaryotic transport protein before.", "output": "There is no related enetity." }, { "input": "No substrate could be identified for SnNTT4.", "output": "There is no related enetity." }, { "input": "Taking these data together, S. negevensis employs a set of nucleotide transport proteins to efficiently tap its host ' s energy and nucleotide pools.", "output": "S . negevensis." }, { "input": "Although similar to other chlamydiae, these transporters show distinct and unique adaptations with respect to substrate specificities and mode of transport.", "output": "There is no related enetity." }, { "input": "Insights into the extracytoplasmic stress response of Xanthomonas campestris pv. campestris: role and regulation of { sigma } E - dependent activity.", "output": "Xanthomonas campestris pv . campestris." }, { "input": "Xanthomonas campestris pv. campestris is an epiphytic bacterium that can become a vascular pathogen responsible for black rot disease of crucifers.", "output": "Xanthomonas campestris pv . campestris." }, { "input": "To adapt gene expression in response to ever - changing habitats, phytopathogenic bacteria have evolved signal transduction regulatory pathways, such as extracytoplasmic function ( ECF ) sigma factors.", "output": "There is no related enetity." }, { "input": "The alternative sigma factor sigma ( E ), encoded by rpoE, is crucial for envelope stress response and plays a role in the pathogenicity of many bacterial species.", "output": "There is no related enetity." }, { "input": "Here, we combine different approaches to investigate the role and mechanism of sigma ( E ) - dependent activation in X. campestris pv. campestris.", "output": "X . campestris pv . campestris." }, { "input": "We show that the rpoE gene is organized as a single transcription unit with the anti - sigma gene rseA and the protease gene mucD and that rpoE transcription is autoregulated.", "output": "There is no related enetity." }, { "input": "rseA and mucD transcription is also controlled by a highly conserved sigma ( E ) - dependent promoter within the sigma ( E ) gene sequence.", "output": "There is no related enetity." }, { "input": "The sigma ( E ) - mediated stress response is required for stationary - phase survival, resistance to cadmium, and adaptation to membrane - perturbing stresses ( elevated temperature and ethanol ).", "output": "There is no related enetity." }, { "input": "Using microarray technology, we started to define the sigma ( E ) regulon of X. campestris pv. campestris.", "output": "X . campestris pv . campestris." }, { "input": "These genes encode proteins belonging to different classes, including periplasmic or membrane proteins, biosynthetic enzymes, classical heat shock proteins, and the heat stress sigma factor sigma ( H ).", "output": "There is no related enetity." }, { "input": "The consensus sequence for the predicted sigma ( E ) - regulated promoter elements is GGAACTN ( 15 - 17 ) GTCNNA.", "output": "There is no related enetity." }, { "input": "Determination of the rpoH transcription start site revealed that rpoH was directly regulated by sigma ( E ) under both normal and heat stress conditions.", "output": "There is no related enetity." }, { "input": "Finally, sigma ( E ) activity is regulated by the putative regulated intramembrane proteolysis ( RIP ) proteases RseP and DegS, as previously described in many other bacteria.", "output": "There is no related enetity." }, { "input": "However, our data suggest that RseP and DegS are not only dedicated to RseA cleavage and that the proteolytic cascade of RseA could involve other proteases.", "output": "There is no related enetity." }, { "input": "Regulation and function of Escherichia coli sugar efflux transporter A ( SetA ) during glucose - phosphate stress.", "output": "Escherichia coli." }, { "input": "Accumulation of certain nonmetabolizable sugar - phosphates ( including alpha - methyl glucoside - 6 - phosphate ) in Escherichia coli is growth inhibitory and elicits the glucose - phosphate stress response.", "output": "There is no related enetity." }, { "input": "The transcription factor SgrR activates transcription of the small RNA SgrS under stress conditions.", "output": "There is no related enetity." }, { "input": "SgrS represses translation of mRNAs encoding sugar transporters.", "output": "There is no related enetity." }, { "input": "The sgrR and sgrS genes are located directly upstream of setA, and this gene organization is conserved in numerous enteric species, prompting the hypothesis that SetA contributes to the glucose - phosphate stress response.", "output": "There is no related enetity." }, { "input": "SetA is a proton motive force - driven efflux pump capable of transporting various sugars and sugar analogs in vitro.", "output": "There is no related enetity." }, { "input": "This study demonstrates that setA expression is induced in response to glucose - phosphate stress, and this requires SgrR.", "output": "There is no related enetity." }, { "input": "Under stress conditions, setA is cotranscribed with sgrS from the sgrS promoter.", "output": "There is no related enetity." }, { "input": "A setA mutant exhibits a growth defect under stress conditions that can be complemented by setA in trans, suggesting that SetA contributes to the optimal cellular recovery from stress.", "output": "There is no related enetity." }, { "input": "Despite previous in vitro evidence that SetA can promote efflux of the stress - causing glucose analog alpha - methyl glucoside, in vivo data in this study indicate that SetA is not the major efflux pump responsible for removal of alpha - methyl glucoside under stress conditions.", "output": "There is no related enetity." }, { "input": "Mapping of the Neisseria meningitidis NadA cell - binding site: relevance of predicted { alpha } - helices in the NH2 - terminal and dimeric coiled - coil regions.", "output": "Neisseria meningitidis." }, { "input": "NadA is a trimeric autotransporter protein of Neisseria meningitidis belonging to the group of oligomeric coiled - coil adhesins.", "output": "Neisseria meningitidis." }, { "input": "It is implicated in the colonization of the human upper respiratory tract by hypervirulent serogroup B N. meningitidis strains and is part of a multiantigen anti - serogroup B vaccine.", "output": "human, N . meningitidis." }, { "input": "Structure prediction indicates that NadA is made by a COOH - terminal membrane anchor ( also necessary for autotranslocation to the bacterial surface ), an intermediate elongated coiled - coil - rich stalk, and an NH ( 2 ) - terminal region involved in cell interaction.", "output": "There is no related enetity." }, { "input": "Electron microscopy analysis and structure prediction suggest that the apical region of NadA forms a compact and globular domain.", "output": "There is no related enetity." }, { "input": "Deletion studies proved that the NH ( 2 ) - terminal sequence ( residues 24 to 87 ) is necessary for cell adhesion.", "output": "There is no related enetity." }, { "input": "In this study, to better define the NadA cell binding site, we exploited ( i ) a panel of NadA mutants lacking sequences along the coiled - coil stalk and ( ii ) several oligoclonal rabbit antibodies, and their relative Fab fragments, directed to linear epitopes distributed along the NadA ectodomain.", "output": "rabbit." }, { "input": "We identified two critical regions for the NadA - cell receptor interaction with Chang cells: the NH ( 2 ) globular head domain and the NH ( 2 ) dimeric intrachain coiled - coil alpha - helices stemming from the stalk.", "output": "There is no related enetity." }, { "input": "This raises the importance of different modules within the predicted NadA structure.", "output": "There is no related enetity." }, { "input": "The identification of linear epitopes involved in receptor binding that are able to induce interfering antibodies reinforces the importance of NadA as a vaccine antigen.", "output": "There is no related enetity." }, { "input": "The Burkholderia cenocepacia LysR - type transcriptional regulator ShvR influences expression of quorum - sensing, protease, type II secretion, and afc genes.", "output": "Burkholderia cenocepacia." }, { "input": "Burkholderia cenocepacia is a significant opportunistic pathogen in individuals with cystic fibrosis.", "output": "Burkholderia cenocepacia." }, { "input": "ShvR, a LysR - type transcriptional regulator, has previously been shown to influence colony morphology, biofilm formation, virulence in plant and animal infection models, and some quorum - sensing - dependent phenotypes.", "output": "There is no related enetity." }, { "input": "In the present study, it was shown that ShvR negatively regulates its own expression, as is typical for LysR - type regulators.", "output": "There is no related enetity." }, { "input": "The production of quorum - sensing signal molecules was detected earlier in growth in the shvR mutant than in the wild type, and ShvR repressed expression of the quorum - sensing regulatory genes cepIR and cciIR.", "output": "There is no related enetity." }, { "input": "Microarray analysis and transcriptional fusions revealed that ShvR regulated over 1, 000 genes, including the zinc metalloproteases zmpA and zmpB.", "output": "There is no related enetity." }, { "input": "The shvR mutant displayed increased gene expression of the type II secretion system and significantly increased protease and lipase activities.", "output": "There is no related enetity." }, { "input": "Both ShvR and CepR influence expression of a 24 - kb genomic region adjacent to shvR that includes the afcA and afcC operons, required for the production of an antifungal agent; however, the reduction in expression was substantially greater in the shvR mutant than in the cepR mutant.", "output": "There is no related enetity." }, { "input": "Only the shvR mutation resulted in reduced antifungal activity against Rhizoctonia solani.", "output": "Rhizoctonia solani." }, { "input": "ShvR, but not CepR, was shown to directly regulate expression of the afcA and afcC promoters.", "output": "There is no related enetity." }, { "input": "In summary, ShvR was determined to have a significant influence on the expression of quorum - sensing, protease, lipase, type II secretion, and afc genes.", "output": "There is no related enetity." }, { "input": "Functional analysis of molybdopterin biosynthesis in mycobacteria identifies a fused molybdopterin synthase in Mycobacterium tuberculosis.", "output": "Mycobacterium tuberculosis." }, { "input": "Most mycobacterial species possess a full complement of genes for the biosynthesis of molybdenum cofactor ( MoCo ).", "output": "There is no related enetity." }, { "input": "However, a distinguishing feature of members of the Mycobacterium tuberculosis complex is their possession of multiple homologs associated with the first two steps of the MoCo biosynthetic pathway.", "output": "There is no related enetity." }, { "input": "A mutant of M. tuberculosis lacking the moaA1 - moaD1 gene cluster and a derivative in which moaD2 was also deleted were significantly impaired for growth in media containing nitrate as a sole nitrogen source, indicating a reduced availability of MoCo to support the assimilatory function of the MoCo - dependent nitrate reductase, NarGHI.", "output": "M . tuberculosis." }, { "input": "However, the double mutant displayed residual respiratory nitrate reductase activity, suggesting that it retains the capacity to produce MoCo.", "output": "There is no related enetity." }, { "input": "The M. tuberculosis moaD and moaE homologs were further analyzed by expressing these genes in mutant strains of M. smegmatis that lacked one or both of the sole molybdopterin ( MPT ) synthase - encoding genes, moaD2 and moaE2, and were unable to grow on nitrate, presumably as a result of the loss of MoCo - dependent nitrate assimilatory activity.", "output": "M . tuberculosis, M . smegmatis." }, { "input": "Expression of M. tuberculosis moaD2 in the M. smegmatis moaD2 mutant and of M. tuberculosis moaE1 or moaE2 in the M. smegmatis moaE2 mutant restored nitrate assimilation, confirming the functionality of these genes in MPT synthesis.", "output": "M . tuberculosis, M . smegmatis, M . tuberculosis, M . smegmatis." }, { "input": "Expression of M. tuberculosis moaX also restored MoCo biosynthesis in M. smegmatis mutants lacking moaD2, moaE2, or both, thus identifying MoaX as a fused MPT synthase.", "output": "M . tuberculosis, M . smegmatis." }, { "input": "By implicating multiple synthase - encoding homologs in MoCo biosynthesis, these results suggest that important cellular functions may be served by their expansion in M. tuberculosis.", "output": "M . tuberculosis." }, { "input": "Plantazolicin, a novel microcin B17 / streptolysin S - like natural product from Bacillus amyloliquefaciens FZB42.", "output": "Bacillus amyloliquefaciens FZB42." }, { "input": "Here we report on a novel thiazole / oxazole - modified microcin ( TOMM ) from Bacillus amyloliquefaciens FZB42, a Gram - positive soil bacterium.", "output": "Bacillus amyloliquefaciens FZB42." }, { "input": "This organism is well known for stimulating plant growth and biosynthesizing complex small molecules that suppress the growth of bacterial and fungal plant pathogens.", "output": "There is no related enetity." }, { "input": "Like microcin B17 and streptolysin S, the TOMM from B. amyloliquefaciens FZB42 undergoes extensive posttranslational modification to become a bioactive natural product.", "output": "B . amyloliquefaciens FZB42." }, { "input": "Our data show that the modified peptide bears a molecular mass of 1, 335 Da and displays antibacterial activity toward closely related Gram - positive bacteria.", "output": "There is no related enetity." }, { "input": "A cluster of 12 genes that covers - 10 kb is essential for the production, modification, export, and self - immunity of this natural product.", "output": "There is no related enetity." }, { "input": "We have named this compound plantazolicin ( PZN ), based on the association of several producing organisms with plants and the incorporation of azole heterocycles, which derive from Cys, Ser, and Thr residues of the precursor peptide.", "output": "There is no related enetity." }, { "input": "Mismatch repair modulation of MutY activity drives Bacillus subtilis stationary - phase mutagenesis.", "output": "Bacillus subtilis." }, { "input": "Stress - promoted mutations that occur in nondividing cells ( adaptive mutations ) have been implicated strongly in causing genetic variability as well as in species survival and evolutionary processes.", "output": "There is no related enetity." }, { "input": "Oxidative stress - induced DNA damage has been associated with generation of adaptive His ( + ) and Met ( + ) but not Leu ( + ) revertants in strain Bacillus subtilis YB955 ( hisC952 metB5 leuC427 ).", "output": "strain Bacillus subtilis YB955 ( hisC952 metB5 leuC427 )." }, { "input": "Here we report that an interplay between MutY and MutSL ( mismatch repair system [ MMR ] ) plays a pivotal role in the production of adaptive Leu ( + ) revertants.", "output": "There is no related enetity." }, { "input": "Essentially, the genetic disruption of MutY dramatically reduced the reversion frequency to the leu allele in this model system.", "output": "There is no related enetity." }, { "input": "Moreover, the increased rate of adaptive Leu ( + ) revertants produced by a MutSL knockout strain was significantly diminished following mutY disruption.", "output": "MutSL knockout strain." }, { "input": "Interestingly, although the expression of mutY took place during growth and stationary phase and was not under the control of RecA, PerR, or sigma ( B ), a null mutation in the mutSL operon increased the expression of mutY several times.", "output": "There is no related enetity." }, { "input": "Thus, in starved cells, saturation of the MMR system may induce the expression of mutY, disturbing the balance between MutY and MMR proteins and aiding in the production of types of mutations detected by reversion to leucine prototrophy.", "output": "There is no related enetity." }, { "input": "In conclusion, our results support the idea that MMR regulation of the mutagenic / antimutagenic properties of MutY promotes stationary - phase mutagenesis in B. subtilis cells.", "output": "B . subtilis." }, { "input": "Mapping interactions between germinants and Clostridium difficile spores.", "output": "Clostridium difficile." }, { "input": "Germination of Clostridium difficile spores is the first required step in establishing C. difficile - associated disease ( CDAD ).", "output": "Clostridium difficile, C . difficile." }, { "input": "Taurocholate ( a bile salt ) and glycine ( an amino acid ) have been shown to be important germinants of C. difficile spores.", "output": "C . difficile." }, { "input": "In the present study, we tested a series of glycine and taurocholate analogs for the ability to induce or inhibit C. difficile spore germination.", "output": "C . difficile." }, { "input": "Testing of glycine analogs revealed that both the carboxy and amino groups are important epitopes for recognition and that the glycine binding site can accommodate compounds with more widely separated termini.", "output": "There is no related enetity." }, { "input": "The C. difficile germination machinery also recognizes other hydrophobic amino acids.", "output": "C . difficile." }, { "input": "In general, linear alkyl side chains are better activators of spore germination than their branched analogs.", "output": "There is no related enetity." }, { "input": "However, L - phenylalanine and L - arginine are also good germinants and are probably recognized by distinct binding sites.", "output": "There is no related enetity." }, { "input": "Testing of taurocholate analogs revealed that the 12 - hydroxyl group of taurocholate is necessary, but not sufficient, to activate spore germination.", "output": "There is no related enetity." }, { "input": "In contrast, the 6 - and 7 - hydroxyl groups are required for inhibition of C. difficile spore germination.", "output": "C . difficile." }, { "input": "Similarly, C. difficile spores are able to detect taurocholate analogs with shorter, but not longer, alkyl amino sulfonic acid side chains.", "output": "C . difficile." }, { "input": "Furthermore, the sulfonic acid group can be partially substituted with other acidic groups.", "output": "There is no related enetity." }, { "input": "Finally, a taurocholate analog with an m - aminobenzenesulfonic acid side chain is a strong inhibitor of C. difficile spore germination.", "output": "C . difficile." }, { "input": "In conclusion, C. difficile spores recognize both amino acids and taurocholate through multiple interactions that are required to bind the germinants and / or activate the germination machinery.", "output": "C . difficile." }, { "input": "In vitro studies of peptidoglycan binding and hydrolysis by the Bacillus anthracis germination - specific lytic enzyme SleB.", "output": "Bacillus anthracis." }, { "input": "The Bacillus anthracis endospore loses resistance properties during germination when its cortex peptidoglycan is degraded by germination - specific lytic enzymes ( GSLEs ).", "output": "Bacillus anthracis." }, { "input": "Although this event normally employs several GSLEs for complete cortex removal, the SleB protein alone can facilitate enough cortex hydrolysis to produce vulnerable spores.", "output": "There is no related enetity." }, { "input": "As a means to better understand its enzymatic function, SleB was overexpressed, purified, and tested in vitro for depolymerization of cortex by measurement of optical density loss and the solubilization of substrate.", "output": "There is no related enetity." }, { "input": "Its ability to bind peptidoglycan was also investigated.", "output": "There is no related enetity." }, { "input": "SleB functions independently as a lytic transglycosylase on both intact and fragmented cortex.", "output": "There is no related enetity." }, { "input": "Most of the muropeptide products that SleB generates are large and are potential substrates for other GSLEs present in the spore.", "output": "There is no related enetity." }, { "input": "Study of a truncated protein revealed that SleB has two domains.", "output": "There is no related enetity." }, { "input": "The N - terminal domain is required for stable peptidoglycan binding, while the C - terminal domain is the region of peptidoglycan hydrolytic activity.", "output": "There is no related enetity." }, { "input": "The C - terminal domain also exhibits dependence on cortex containing muramic - delta - lactam in order to carry out hydrolysis.", "output": "There is no related enetity." }, { "input": "As the conditions and limitations for SleB activity are further elucidated, they will enable the development of treatments that stimulate premature germination of B. anthracis spores, greatly simplifying decontamination measures.", "output": "B . anthracis." }, { "input": "Glucose - dependent activation of Bacillus anthracis toxin gene expression and virulence requires the carbon catabolite protein CcpA.", "output": "Bacillus anthracis." }, { "input": "Sensing environmental conditions is an essential aspect of bacterial physiology and virulence.", "output": "There is no related enetity." }, { "input": "In Bacillus anthracis, the causative agent of anthrax, transcription of the two major virulence factors, toxin and capsule, is triggered by bicarbonate, a major compound in the mammalian body.", "output": "Bacillus anthracis, anthrax." }, { "input": "Here it is shown that glucose is an additional signaling molecule recognized by B. anthracis for toxin synthesis.", "output": "B . anthracis." }, { "input": "The presence of glucose increased the expression of the protective antigen toxin component - encoding gene ( pagA ) by stimulating induction of transcription of the AtxA virulence transcription factor.", "output": "There is no related enetity." }, { "input": "Induction of atxA transcription by glucose required the carbon catabolite protein CcpA via an indirect mechanism.", "output": "There is no related enetity." }, { "input": "CcpA did not bind specifically to any region of the extended atxA promoter.", "output": "There is no related enetity." }, { "input": "The virulence of a B. anthracis strain from which the ccpA gene was deleted was significantly attenuated in a mouse model of infection.", "output": "B . anthracis strain, mouse." }, { "input": "The data demonstrated that glucose is an important host environment - derived signaling molecule and that CcpA is a molecular link between environmental sensing and B. anthracis pathogenesis.", "output": "B . anthracis." }, { "input": "Structural and functional analysis of the type III secretion system from Pseudomonas fluorescens Q8r1 - 96.", "output": "Pseudomonas fluorescens Q8r1 - 96." }, { "input": "Pseudomonas fluorescens Q8r1 - 96 represents a group of rhizosphere strains responsible for the suppressiveness of agricultural soils to take - all disease of wheat.", "output": "Pseudomonas fluorescens Q8r1 - 96." }, { "input": "It produces the antibiotic 2, 4 - diacetylphloroglucinol and aggressively colonizes the roots of cereal crops.", "output": "There is no related enetity." }, { "input": "In this study, we analyzed the genome of Q8r1 - 96 and identified a type III protein secretion system ( T3SS ) gene cluster that has overall organization similar to that of the T3SS gene cluster of the plant pathogen Pseudomonas syringae.", "output": "Q8r1 - 96, Pseudomonas syringae." }, { "input": "We also screened a collection of 30 closely related P. fluorescens strains and detected the T3SS genes in all but one of them.", "output": "P . fluorescens strains." }, { "input": "The Q8r1 - 96 genome contained ropAA and ropM type III effector genes, which are orthologs of the P. syringae effector genes hopAA1 - 1 and hopM1, as well as a novel type III effector gene designated ropB.", "output": "Q8r1 - 96, P . syringae." }, { "input": "These type III effector genes encoded proteins that were secreted in culture and injected into plant cells by both P. syringae and Q8r1 - 96 T3SSs.", "output": "P . syringae, Q8r1 - 96." }, { "input": "The Q8r1 - 96 T3SS was expressed in the rhizosphere, but mutants lacking a functional T3SS were not altered in their rhizosphere competence.", "output": "Q8r1 - 96." }, { "input": "The Q8r1 - 96 type III effectors RopAA, RopB, and RopM were capable of suppressing the hypersensitive response and production of reactive oxygen species, two plant immune responses.", "output": "Q8r1 - 96." }, { "input": "C - terminal domain residues important for secretion and attachment of RgpB in Porphyromonas gingivalis.", "output": "Porphyromonas gingivalis." }, { "input": "Porphyromonas gingivalis, a periodontal pathogen, expresses a group of surface proteins with a common C - terminal domain ( CTD ) that are exported by a novel secretion system to the surface, where they are covalently attached.", "output": "Porphyromonas gingivalis." }, { "input": "Using RgpB as a model CTD protein, we have produced a series of site - directed mutations in the CTD sequence at conserved residues and at residues that may be modified and, hence, surface attached.", "output": "There is no related enetity." }, { "input": "The mutant RgpB proteins were expressed in a P. gingivalis host lacking functional RgpB and RgpA Arg - specific proteases.", "output": "P . gingivalis." }, { "input": "The RgpB mutants produced were Y674F, Y674F Y718F, T675Q S679Q T682Q T684Q, T693Q, F695A, D696A, N698A, G699P, G716P, T724Q, T728Q T730Q, and K732Q and a protein with a deletion of residues 692 to 702 ( Delta692 - 702 ).", "output": "There is no related enetity." }, { "input": "The mutants were characterized for cell - associated Arg - specific protease activity and for cellular distribution using anti - Rgp antibodies and Western blotting of culture fractions.", "output": "There is no related enetity." }, { "input": "All the mutants exhibited cell - associated Arg - specific activity similar to that of the positive control except for the D696A and Delta692 - 702 mutants.", "output": "There is no related enetity." }, { "input": "For all mutants, except D696A and Delta692 - 702, the RgpB proteins were found modified and attached to the cell surface, which was the same profile found in the positive - control strain.", "output": "There is no related enetity." }, { "input": "Only trace amounts of the precursor form of the Delta692 - 702 mutant were detected in the outer membrane, with none detected in the periplasm or culture fluid although cell transcript levels were normal.", "output": "There is no related enetity." }, { "input": "The results suggest that residues 692 to 702 of the CTD, in particular, residue D696, have an important role in the attachment of RgpB at the cell surface and that without attachment secretion does not occur.", "output": "There is no related enetity." }, { "input": "Effects of deficiency and overdose of group 2 sigma factors in triple inactivation strains of Synechocystis sp. strain PCC 6803.", "output": "Synechocystis sp . strain PCC 6803." }, { "input": "Acclimation of cyanobacteria to environmental changes includes major changes in the gene expression patterns partly orchestrated by the replacement of a particular sigma subunit with another in the RNA polymerase holoenzyme.", "output": "There is no related enetity." }, { "input": "The cyanobacterium Synechocystis sp. strain PCC 6803 encodes nine sigma factors, all belonging to the sigma ( 70 ) family.", "output": "Synechocystis sp . strain PCC 6803." }, { "input": "Cyanobacteria typically encode many group 2 sigma factors that closely resemble the principal sigma factor.", "output": "There is no related enetity." }, { "input": "We inactivated three out of the four group 2 sigma factors of Synechocystis simultaneously in all possible combinations and found that all triple inactivation strains grow well under standard conditions.", "output": "There is no related enetity." }, { "input": "Unlike the other strains, the DeltasigBCD strain, which contains SigE as the only functional group 2 sigma factor, did not grow faster under mixotrophic than under autotrophic conditions.", "output": "There is no related enetity." }, { "input": "The SigB and SigD factors were important in low - temperature acclimation, especially under diurnal light rhythm.", "output": "There is no related enetity." }, { "input": "The DeltasigBCD, DeltasigBCE, and DeltasigBDE strains were sensitive to high - light - induced photoinhibition, indicating a central role of the SigB factor in high - light tolerance.", "output": "There is no related enetity." }, { "input": "Furthermore, the DeltasigBCE strain ( SigD is the only functional group 2 sigma factor ) appeared to be locked in the high - fluorescence state ( state 1 ) and grew slowly in blue but not in orange or white light.", "output": "There is no related enetity." }, { "input": "Our results suggest that features of the triple inactivation strains can be categorized as ( i ) direct consequences of the inactivation of a particular sigma factor ( s ) and ( ii ) effects resulting from the higher probability that the remaining group 2 sigma factors associate with the RNA polymerase core.", "output": "There is no related enetity." }, { "input": "A combined method for rescue of modified enteroviruses by mutagenic primers, long PCR and T7 RNA polymerase - driven in vivo transcription.", "output": "There is no related enetity." }, { "input": "The current methods for manipulation of enteroviral RNA genomes and production of modified virus particles include stepwise subcloning procedures and in vitro transcription and RNA transfection steps that are both time - consuming and inefficient.", "output": "There is no related enetity." }, { "input": "Several enteroviral cDNA clones with 5 ' - terminal T7 promoter and coxsackievirus A9 ( CAV9 ) PCR product with the T7 promoter were transfected successfully into target cells expressing T7 RNA polymerase for the rescue of virus particles.", "output": "coxsackievirus A9, CAV9." }, { "input": "This demonstrated the overall feasibility of the in vivo transcription method.", "output": "There is no related enetity." }, { "input": "Furthermore, a rapid method using high - fidelity DNA polymerase, Phusion ( TM ), for amplification and mutagenesis of CAV9 cDNA was generated.", "output": "CAV9." }, { "input": "A long PCR method was employed together with mutagenic primers for direct introduction of a unique restriction enzyme site into the VP1 - 2A junction of the CAV9 cDNA clone during the PCR amplification process.", "output": "CAV9." }, { "input": "Enhanced green fluorescent protein was subcloned to that site, and CAV9 - eGFP cDNA was transfected to the target cells for in vivo transcription and successful rescue of CAV9 - eGFP particles.", "output": "CAV9, CAV9." }, { "input": "The method allowed a straightforward mutagenesis and in vivo production of infectious enteroviral particles, and may be applicable routinely for rapid production of the modified picornaviruses over the use of the traditional subcloning protocols.", "output": "There is no related enetity." }, { "input": "A novel class of miniature inverted repeat transposable elements ( MITEs ) that contain hitchhiking ( GTCY ) ( n ) microsatellites.", "output": "There is no related enetity." }, { "input": "The movement of miniature inverted repeat transposable elements ( MITEs ) modifies genome structure and function.", "output": "There is no related enetity." }, { "input": "We describe the microsatellite - associated interspersed nuclear element 2 ( MINE - 2 ), that integrates at consensus WTTTT target sites, creates dinucleotide TT target site duplications ( TSDs ), and forms predicted MITE - like secondary structures; a 5 ' subterminal inverted repeat ( SIR; AGGGTTCCGTAG ) that is partially complementary to a 5 ' inverted repeat ( IR; ACGAAGCCCT ) and 3 ' - SIRs ( TTACGGAACCCT ).", "output": "There is no related enetity." }, { "input": "A ( GTCY ) ( n ) microsatellite is hitchhiking downstream of conserved 5 ' MINE - 2 secondary structures, causing flanking sequence similarity amongst mobile microsatellite loci.", "output": "There is no related enetity." }, { "input": "Transfection of insect cell lines indicates that MITE - like secondary structures are sufficient to mediate genome integration, and provides insight into the transposition mechanism used by MINE - 2s.", "output": "There is no related enetity." }, { "input": "DNA modifications and genome rearrangements during the development and sex differentiation of the bumble bee Bombus terrestris.", "output": "Bombus terrestris." }, { "input": "Bombus terrestris is a bumble bee that, like most hymenopteran species, exhibits ploidy - specific sex determination controlled by a single sex gene.", "output": "Bombus terrestris." }, { "input": "Depending on their ploidy and the queen pheromone repression, the imagoes differentiate into three castes: males, workers and queens.", "output": "There is no related enetity." }, { "input": "Here, we focus on the differences of genome organization that occur during development and sex differentiation.", "output": "There is no related enetity." }, { "input": "We found that cytosine methylation is a significant epigenetic factor with profiles that can be correlated with both processes.", "output": "There is no related enetity." }, { "input": "We also showed that two kinds of genomic rearrangement occur.", "output": "There is no related enetity." }, { "input": "The first consists of important DNA amplifications that have sequence profiles that differ in the different developmental instars and sexes.", "output": "There is no related enetity." }, { "input": "In the second kind, DNA losses also occur, at least involving the mosaic transposable element B. terrestris mosaic repeat 1 ( BTMR1 ).", "output": "B . terrestris." }, { "input": "A vaccinia virus deletion mutant reveals the presence of additional inhibitors of NF - kappaB.", "output": "vaccinia virus." }, { "input": "The classical nuclear factor kappa B ( NF - kappaB ) signaling pathway is an important regulator of inflammation and innate immunity that is activated by a wide variety of stimuli, including virus infection, tumor necrosis factor alpha ( TNF - alpha ), and interleukin 1Beta ( IL - 1Beta ).", "output": "There is no related enetity." }, { "input": "Poxviruses, including vaccinia virus ( VV ) and ectromelia virus, encode multiple proteins that function in immune evasion.", "output": "vaccinia virus, VV, ectromelia virus." }, { "input": "Recently, a growing number of genes encoded by poxviruses have been shown to target and disrupt the NF - kappaB signaling pathway.", "output": "There is no related enetity." }, { "input": "To determine if additional gene products that interfere with NF - kappaB signaling existed, we used a vaccinia virus deletion mutant, VV811, which is missing 55 open reading frames lacking all known inhibitors of TNF - alpha - induced NF - kappaB activation.", "output": "vaccinia virus." }, { "input": "Immunofluorescence analysis of HeLa cells treated with TNF - alpha and IL - 1Beta revealed that NF - kappaB translocation to the nucleus was inhibited in VV811 - infected cells.", "output": "There is no related enetity." }, { "input": "This was further confirmed through Western blotting of cytoplasmic and nuclear extracts for NF - kappaB.", "output": "There is no related enetity." }, { "input": "Additionally, VV811 infection inhibited TNF - alpha - induced IkappaBalpha degradation.", "output": "There is no related enetity." }, { "input": "In contrast to vaccinia virus strain Copenhagen ( VVCop ) - infected cells, VV811 infection resulted in the dramatic accumulation of phosphorylated IkappaBalpha.", "output": "vaccinia virus strain Copenhagen, VVCop." }, { "input": "Correspondingly, coimmunoprecipitation assays demonstrated that the NF - kappaB - inhibitory IkappaBalpha - p65 - p50 complex was intact in VV811 - infected cells.", "output": "There is no related enetity." }, { "input": "Significantly, cells treated with 1 - Beta - d - arabinofuranosylcytosine, an inhibitor of poxvirus late gene expression, demonstrated that an additional vaccinia virus late gene was involved in the stabilization of IkappaBalpha.", "output": "vaccinia virus." }, { "input": "Overall, this work indicates that unidentified inhibitors of NF - kappaB exist in vaccinia virus.", "output": "vaccinia virus." }, { "input": "The complex inhibition of NF - kappaB by vaccinia virus illustrates the importance of NF - kappaB activation in the antiviral response.", "output": "vaccinia virus." }, { "input": "Template recognition mechanisms by replicase proteins differ between bipartite positive - strand genomic RNAs of a plant virus.", "output": "There is no related enetity." }, { "input": "Recognition of RNA templates by viral replicase proteins is one of the key steps in the replication process of all RNA viruses.", "output": "There is no related enetity." }, { "input": "However, the mechanisms underlying this phenomenon, including primary RNA elements that are recognized by the viral replicase proteins, are not well understood.", "output": "There is no related enetity." }, { "input": "Here, we used aptamer pulldown assays with membrane fractionation and protein - RNA coimmunoprecipitation in a cell - free viral translation / replication system to investigate how viral replicase proteins recognize the bipartite genomic RNAs of the Red clover necrotic mosaic virus ( RCNMV ).", "output": "Red clover necrotic mosaic virus, RCNMV." }, { "input": "RCNMV replicase proteins bound specifically to a Y - shaped RNA element ( YRE ) located in the 3 ' untranslated region ( UTR ) of RNA2, which also interacted with the 480 - kDa replicase complexes that contain viral and host proteins.", "output": "RCNMV." }, { "input": "The replicase - YRE interaction recruited RNA2 to the membrane fraction.", "output": "There is no related enetity." }, { "input": "Conversely, RNA1 fragments failed to interact with the replicase proteins supplied in trans.", "output": "There is no related enetity." }, { "input": "The results of protein - RNA coimmunoprecipitation assays suggest that RNA1 interacts with the replicase proteins coupled with their translation.", "output": "There is no related enetity." }, { "input": "Thus, the initial template recognition mechanisms employed by the replicase differ between RCNMV bipartite genomic RNAs and RNA elements are primary determinants of the differential replication mechanism.", "output": "RCNMV." }, { "input": "Poliovirus RNA is released from the capsid near a twofold symmetry axis.", "output": "Poliovirus." }, { "input": "After recognizing and binding to its host cell, poliovirus ( like other nonenveloped viruses ) faces the challenge of translocating its genome across a cellular membrane and into the cytoplasm.", "output": "poliovirus." }, { "input": "To avoid entanglement with the capsid, the RNA must exit via a single site on the virion surface.", "output": "There is no related enetity." }, { "input": "However, the mechanism by which a single site is selected ( from among 60 equivalents ) is unknown; and until now, even its location on the virion surface has been controversial.", "output": "There is no related enetity." }, { "input": "To help to elucidate the mechanism of infection, we have used single - particle cryo - electron microscopy and tomography to reconstruct conformationally altered intermediates that are formed by the poliovirion at various stages of the poliovirus infection process.", "output": "poliovirus." }, { "input": "Recently, we reported icosahedrally symmetric structures for two forms of the end - state 80S empty capsid particle.", "output": "There is no related enetity." }, { "input": "Surprisingly, RNA was frequently visible near the capsid; and in a subset of the virions, RNA was seen on both the inside and outside of the capsid, caught in the act of exiting.", "output": "There is no related enetity." }, { "input": "To visualize RNA exiting, we have now determined asymmetric reconstructions from that subset, using both single - particle cryo - electron microscopy and cryo - electron tomographic methods, producing independent reconstructions at - 50 - A resolution.", "output": "There is no related enetity." }, { "input": "Contrary to predictions in the literature, the footprint of RNA on the capsid surface is located close to a viral 2 - fold axis, covering a slot - shaped area of reduced density that is present in both of the symmetrized 80S reconstructions and which extends by about 20 A away from the 2 - fold axis toward each neighboring 5 - fold axis.", "output": "There is no related enetity." }, { "input": "Differential regulation of human papillomavirus type 8 by interferon regulatory factors 3 and 7.", "output": "human papillomavirus type 8." }, { "input": "The genus Beta human papillomavirus ( HPV ) type 8 is associated with nonmelanoma skin cancer in patients with epidermodysplasia verruciformis, and evidence for its protumorigenic potential in the general population increases.", "output": "Beta human papillomavirus ( HPV ) type 8." }, { "input": "To date, strategies to suppress genus Beta HPV infections are limited.", "output": "genus Beta HPV." }, { "input": "Interferon regulatory factors IRF - 3 and IRF - 7 play key roles in the activation of the innate immune response to viral infections.", "output": "There is no related enetity." }, { "input": "In this study, we show for the first time that both IRF - 3 and IRF - 7 regulate transcription of a papillomavirus, but with opposing effects.", "output": "There is no related enetity." }, { "input": "IRF - 7, expressed in the suprabasal layers of human epidermis, increased HPV8 late promoter activity via direct binding to viral DNA.", "output": "human, HPV8." }, { "input": "UV - B light - induced activation of the HPV8 promoter involved IRF - 7 as a downstream effector.", "output": "HPV8." }, { "input": "In contrast, IRF - 3, expressed in all layers of human epidermis, induced strong HPV8 suppression in primary keratinocytes.", "output": "human, HPV8." }, { "input": "IRF - 3 - mediated suppression prevailed over IRF - 7 - induced HPV8 transcription.", "output": "HPV8." }, { "input": "Unlike the E6 oncoprotein of the mucosal high - risk HPV16, the HPV8 E6 protein did not bind to IRF - 3 and only weakly antagonized its activity.", "output": "HPV16, HPV8." }, { "input": "Strong antiviral activity was also observed, when keratinocytes were treated with potent IRF - 3 activators, poly ( I: C ) or RNA bearing 5 ' phosphates.", "output": "There is no related enetity." }, { "input": "In conclusion, we show that IRF - 3 activation induces a state of cell - autonomous immunity against HPV in primary human keratinocytes.", "output": "human." }, { "input": "Our study suggests that local application of IRF - 3 - activating compounds might constitute an attractive novel therapeutic strategy against HPV8 - associated diseases, particularly in epidermodysplasia verruciformis patients.", "output": "HPV8." }, { "input": "Cytomegalovirus microRNA expression is tissue specific and is associated with persistence.", "output": "There is no related enetity." }, { "input": "MicroRNAs ( miRNAs ) are a class of small noncoding RNAs involved in posttranscriptional regulation.", "output": "There is no related enetity." }, { "input": "miRNAs are utilized in organisms ranging from plants to higher mammals, and data have shown that DNA viruses also use this method for host and viral gene regulation.", "output": "There is no related enetity." }, { "input": "Here, we report the sequencing of the small RNAs in rat cytomegalovirus ( RCMV ) - infected fibroblasts and persistently infected salivary glands.", "output": "rat cytomegalovirus, RCMV." }, { "input": "We identified 24 unique miRNAs that mapped to hairpin structures found within the viral genome.", "output": "There is no related enetity." }, { "input": "While most miRNAs were detected in both samples, four were detected exclusively in the infected fibroblasts and two were specific for the infected salivary glands.", "output": "There is no related enetity." }, { "input": "The RCMV miRNAs are distributed across the viral genome on both the positive and negative strands, with clusters of miRNAs at a number of locations, including near viral genes r1 and r111.", "output": "RCMV." }, { "input": "The RCMV miRNAs have a genomic positional orientation similar to that of the miRNAs described for mouse cytomegalovirus, but they do not share any substantial sequence conservation.", "output": "RCMV, mouse cytomegalovirus." }, { "input": "Similar to other reported miRNAs, the RCMV miRNAs had considerable variation at their 3 ' and 5 ' ends.", "output": "RCMV." }, { "input": "Interestingly, we found a number of specific examples of differential isoform usage between the fibroblast and salivary gland samples.", "output": "There is no related enetity." }, { "input": "We determined by real - time PCR that expression of the RCMV miRNA miR - r111. 1 - 2 is highly expressed in the salivary glands and that miR - R87 - 1 is expressed in most tissues during the acute infection phase.", "output": "RCMV." }, { "input": "Our study identified the miRNAs expressed by RCMV in vitro and in vivo and demonstrated that expression is tissue specific and associated with a stage of viral infection.", "output": "RCMV." }, { "input": "Adenovirus membrane penetration activates the NLRP3 inflammasome.", "output": "Adenovirus." }, { "input": "Adenovirus type 5 ( Ad5 ) infection of macrophages results in rapid secretion of interleukin - 1Beta ( IL - 1Beta ) and is dependent on the inflammasome components NLRP3 and ASC and the catalytic activity of caspase - 1.", "output": "Adenovirus type 5, Ad5." }, { "input": "Using lentivirus - expressed short hairpin RNA ( shRNA ) and competitive inhibitors, we show that Ad - induced IL - 1Beta release is dependent upon Toll - like receptor 9 ( TLR9 ) sensing of the Ad5 double - stranded DNA ( dsDNA ) genome in human cell lines and primary monocyte - derived macrophages but not in mouse macrophages.", "output": "Ad5, human, mouse." }, { "input": "Additionally, a temperature - sensitive mutant of Ad5 unable to penetrate endosomal membranes, ts1, is unable to induce IL - 1Beta release in TLR2 - primed THP - 1 cells, suggesting that penetration of endosomal membranes is required for IL - 1Beta release.", "output": "Ad5." }, { "input": "Disruption of lysosomal membranes and the release of cathepsin B into the cytoplasm are required for Ad - induced NLRP3 activation.", "output": "Ad." }, { "input": "Ad5 cell entry also induces reactive oxygen species ( ROS ) production, and inhibitors of ROS prevent Ad - induced IL - 1Beta release.", "output": "Ad5, Ad." }, { "input": "Ad5 activation of NLRP3 also induces necrotic cell death, resulting in the release of the proinflammatory molecule HMGB1.", "output": "Ad5." }, { "input": "This work further defines the mechanisms of virally induced inflammasome activation.", "output": "There is no related enetity." }, { "input": "Function of the small hydrophobic protein of J paramyxovirus.", "output": "There is no related enetity." }, { "input": "At 18, 954 nucleotides, the J paramyxovirus ( JPV ) genome is one of the largest in the family Paramyxoviridae, consisting of eight genes in the order 3 ' - N - P / V / C - M - F - SH - TM - G - L - 5 '.", "output": "There is no related enetity." }, { "input": "To study the function of novel paramyxovirus genes in JPV, a plasmid containing a full - length cDNA clone of the genome of JPV was constructed.", "output": "There is no related enetity." }, { "input": "In this study, the function of the small hydrophobic ( SH ) protein of JPV was examined by generating a recombinant JPV lacking the coding sequence of the SH protein ( rJPVDeltaSH ).", "output": "There is no related enetity." }, { "input": "rJPVDeltaSH was viable and had no growth defect in tissue culture cells.", "output": "There is no related enetity." }, { "input": "However, more tumor necrosis factor alpha ( TNF - alpha ) was produced during rJPVDeltaSH infection, suggesting that SH plays a role in inhibiting TNF - alpha production.", "output": "There is no related enetity." }, { "input": "rJPVDeltaSH induced more apoptosis in tissue culture cells than rJPV.", "output": "There is no related enetity." }, { "input": "Virus - induced apoptosis was inhibited by neutralizing antibody against TNF - alpha, suggesting that TNF - alpha contributes to JPV - induced apoptosis in vitro.", "output": "There is no related enetity." }, { "input": "The expression of JPV SH protein inhibited TNF - alpha - induced NF - kappaB activation in a reporter gene assay, suggesting that JPV SH protein can inhibit TNF - alpha signaling in vitro.", "output": "There is no related enetity." }, { "input": "Furthermore, infection of mice with rJPVDeltaSH induced more TNF - alpha expression, indicating that SH plays a role in blocking TNF - alpha expression in vivo.", "output": "mice." }, { "input": "Successful vaccination strategies that protect aged mice from lethal challenge from influenza virus and heterologous severe acute respiratory syndrome coronavirus.", "output": "mice, severe acute respiratory syndrome coronavirus." }, { "input": "Newly emerging viruses often circulate as a heterogeneous swarm in wild animal reservoirs prior to their emergence in humans, and their antigenic identities are often unknown until an outbreak situation.", "output": "humans." }, { "input": "The newly emerging severe acute respiratory syndrome coronavirus ( SARS - CoV ) and reemerging influenza virus cause disproportionate disease in the aged, who are also notoriously difficult to successfully vaccinate, likely due to immunosenescence.", "output": "severe acute respiratory syndrome coronavirus, SARS - CoV." }, { "input": "To protect against future emerging strains, vaccine platforms should induce broad cross - reactive immunity that is sufficient to protect from homologous and heterologous challenge in all ages.", "output": "There is no related enetity." }, { "input": "From initial studies, we hypothesized that attenuated Venezuelan equine encephalitis virus ( VEE ) replicon particle ( VRP ) vaccine glycoproteins mediated vaccine failure in the aged.", "output": "Venezuelan equine encephalitis virus, VEE." }, { "input": "We then compared the efficacies of vaccines bearing attenuated ( VRP ( 3014 ) ) or wild - type VEE glycoproteins ( VRP ( 3000 ) ) in young and aged mice within novel models of severe SARS - CoV pathogenesis.", "output": "VEE, mice, SARS - CoV." }, { "input": "Aged animals receiving VRP ( 3000 ) - based vaccines were protected from SARS - CoV disease, while animals receiving the VRP ( 3014 ) - based vaccines were not.", "output": "SARS - CoV." }, { "input": "The superior protection for the aged observed with VRP ( 3000 ) - based vaccines was confirmed in a lethal influenza virus challenge model.", "output": "There is no related enetity." }, { "input": "While the VRP ( 3000 ) vaccine ' s immune responses in the aged were sufficient to protect against lethal homologous and heterologous challenge, our data suggest that innate defects within the VRP ( 3014 ) platform mediate vaccine failure.", "output": "There is no related enetity." }, { "input": "Exploration into the mechanism ( s ) of successful vaccination in the immunosenescent should aid in the development of successful vaccine strategies for other viral diseases disproportionately affecting the elderly, like West Nile virus, influenza virus, norovirus, or other emerging viruses of the future.", "output": "West Nile virus." }, { "input": "Reovirus infection or ectopic expression of outer capsid protein micro1 induces apoptosis independently of the cellular proapoptotic proteins Bax and Bak.", "output": "There is no related enetity." }, { "input": "Mammalian orthoreoviruses induce apoptosis in vivo and in vitro; however, the specific mechanism by which apoptosis is induced is not fully understood.", "output": "Mammalian orthoreoviruses." }, { "input": "Recent studies have indicated that the reovirus outer capsid protein mu1 is the primary determinant of reovirus - induced apoptosis.", "output": "There is no related enetity." }, { "input": "Ectopically expressed mu1 induces apoptosis and localizes to intracellular membranes.", "output": "There is no related enetity." }, { "input": "Here we report that ectopic expression of mu1 activated both the extrinsic and intrinsic apoptotic pathways with activation of initiator caspases - 8 and - 9 and downstream effector caspase - 3.", "output": "There is no related enetity." }, { "input": "Activation of both pathways was required for mu1 - induced apoptosis, as specific inhibition of either caspase - 8 or caspase - 9 abolished downstream effector caspase - 3 activation.", "output": "There is no related enetity." }, { "input": "Similar to reovirus infection, ectopic expression of mu1 caused release into the cytosol of cytochrome c and smac / DIABLO from the mitochondrial intermembrane space.", "output": "There is no related enetity." }, { "input": "Pancaspase inhibitors did not prevent cytochrome c release from cells expressing mu1, indicating that caspases were not required.", "output": "There is no related enetity." }, { "input": "Additionally, mu1 - or reovirus - induced release of cytochrome c occurred efficiently in Bax ( - / - ) Bak ( - / - ) mouse embryonic fibroblasts ( MEFs ).", "output": "mouse." }, { "input": "Finally, we found that reovirus - induced apoptosis occurred in Bax ( - / - ) Bak ( - / - ) MEFs, indicating that reovirus - induced apoptosis occurs independently of the proapoptotic Bcl - 2 family members Bax and Bak.", "output": "There is no related enetity." }, { "input": "Assembly and immunological properties of Newcastle disease virus - like particles containing the respiratory syncytial virus F and G proteins.", "output": "Newcastle disease virus, respiratory syncytial virus." }, { "input": "Human respiratory syncytial virus ( RSV ) is a serious respiratory pathogen in infants and young children as well as elderly and immunocompromised populations.", "output": "Human respiratory syncytial virus, RSV." }, { "input": "However, no RSV vaccines are available.", "output": "RSV." }, { "input": "We have explored the potential of virus - like particles ( VLPs ) as an RSV vaccine candidate.", "output": "RSV." }, { "input": "VLPs composed entirely of RSV proteins were produced at levels inadequate for their preparation as immunogens.", "output": "RSV." }, { "input": "However, VLPs composed of the Newcastle disease virus ( NDV ) nucleocapsid and membrane proteins and chimera proteins containing the ectodomains of RSV F and G proteins fused to the transmembrane and cytoplasmic domains of NDV F and HN proteins, respectively, were quantitatively prepared from avian cells.", "output": "Newcastle disease virus, NDV, RSV, NDV." }, { "input": "Immunization of mice with these VLPs, without adjuvant, stimulated robust, anti - RSV F and G protein antibody responses.", "output": "mice, RSV." }, { "input": "IgG2a / IgG1 ratios were very high, suggesting predominantly T ( H ) 1 responses.", "output": "There is no related enetity." }, { "input": "In contrast to infectious RSV immunization, neutralization antibody titers were robust and stable for 4 months.", "output": "RSV." }, { "input": "Immunization with a single dose of VLPs resulted in the complete protection of mice from RSV replication in lungs.", "output": "mice, RSV." }, { "input": "Upon RSV intranasal challenge of VLP - immunized mice, no enhanced lung pathology was observed, in contrast to the pathology observed in mice immunized with formalin - inactivated RSV.", "output": "RSV, mice, mice, RSV." }, { "input": "These results suggest that these VLPs are effective RSV vaccines in mice, in contrast to other nonreplicating RSV vaccine candidates.", "output": "RSV, mice, RSV." }, { "input": "Domain structure of Lassa virus L protein.", "output": "Lassa virus." }, { "input": "The 200 - kDa L protein of arenaviruses plays a central role in viral genome replication and transcription.", "output": "There is no related enetity." }, { "input": "This study aimed at providing evidence for the domain structure of L protein by combining bioinformatics with a stepwise mutagenesis approach using the Lassa virus minireplicon system.", "output": "Lassa virus." }, { "input": "Potential interdomain linkers were predicted using various algorithms.", "output": "There is no related enetity." }, { "input": "The prediction was challenged by insertion of flexible sequences into the predicted linkers.", "output": "There is no related enetity." }, { "input": "Insertion of 5 or 10 amino acid residues was tolerated at seven sites ( S407, G446, G467, G774, G939, S1952, and V2074 in Lassa virus AV ).", "output": "Lassa virus AV." }, { "input": "At two of these sites, G467 and G939, L protein could be split into an N - terminal and a C - terminal part, which were able to trans - complement each other and reconstitute a functional complex upon coexpression.", "output": "There is no related enetity." }, { "input": "Coimmunoprecipitation studies revealed physical interaction between the N - and C - terminal domains, irrespective of whether L protein was split at G467 or G939.", "output": "There is no related enetity." }, { "input": "In confocal immunofluorescence microscopy, the N - terminal domains showed a dot - like, sometimes perinuclear, cytoplasmic distribution similar to that of full - length L protein, while the C - terminal domains were homogenously distributed in cytoplasm.", "output": "There is no related enetity." }, { "input": "The latter were redistributed into the dot - like structures upon coexpression with the corresponding N - terminal domain.", "output": "There is no related enetity." }, { "input": "In conclusion, this study demonstrates two interdomain linkers in Lassa virus L protein, at G467 and G939, suggesting that L protein is composed of at least three structural domains spanning residues 1 to 467, 467 to 939, and 939 to 2220.", "output": "Lassa virus." }, { "input": "The first domain seems to mediate accumulation of L protein into cytoplasmic dot - like structures.", "output": "There is no related enetity." }, { "input": "Reverse genetics generation of chimeric infectious Junin / Lassa virus is dependent on interaction of homologous glycoprotein stable signal peptide and G2 cytoplasmic domains.", "output": "There is no related enetity." }, { "input": "The Arenaviridae are a diverse and globally distributed collection of viruses that are maintained primarily by rodent reservoirs.", "output": "There is no related enetity." }, { "input": "Junin virus ( JUNV ) and Lassa virus ( LASV ) can both cause significant outbreaks of severe and often fatal human disease throughout their respective areas of endemicity.", "output": "Junin virus, JUNV, Lassa virus, LASV, human." }, { "input": "In an effort to improve upon the existing live attenuated JUNV Candid1 vaccine, we generated a genetically homogenous stock of this virus from cDNA copies of the virus S and L segments by using a reverse genetics system.", "output": "JUNV." }, { "input": "Further, these cDNAs were used in combination with LASV cDNAs to successfully generate two recombinant Candid1 JUNV / LASV chimeric viruses ( via envelope glycoprotein [ GPC ] exchange ).", "output": "LASV, JUNV, LASV." }, { "input": "It was found that while the GPC extravirion domains were readily exchangeable, homologous stable signal peptide ( SSP ) and G2 transmembrane and cytoplasmic tail domains were essential for correct GPC maturation and production of infectious chimeric viruses.", "output": "There is no related enetity." }, { "input": "The switching of the JUNV and LASV G1 / G2 ectodomains within the Candid1 vaccine background did not alter the attenuated phenotype of the vaccine strain in a lethal mouse model.", "output": "JUNV, LASV, mouse." }, { "input": "These recombinant chimeric viruses shed light on the fundamental requirements of arenavirus GPC maturation and may serve as a strategy for the development of bivalent JUNV and LASV vaccine candidates.", "output": "JUNV, LASV." }, { "input": "B7 - mediated costimulation of CD4 T cells constrains cytomegalovirus persistence.", "output": "There is no related enetity." }, { "input": "Cytomegalovirus ( CMV ) utilizes multiple strategies to modulate immunity and promote lifelong, persistent / latent infection, including suppressing T cell activation pathways.", "output": "There is no related enetity." }, { "input": "Here we examined the role of B7 costimulatory ligands in establishing immune detente from both the host and virus perspectives.", "output": "There is no related enetity." }, { "input": "Mice lacking both B7. 1 and B7. 2 showed reduced early expansion of CMV - specific CD4 T cells, consequently allowing for enhanced levels of persistent virus replication.", "output": "Mice." }, { "input": "In turn, a CMV mutant lacking expression of the m138 and m147. 5 gene products, which restrict B7. 1 and B7. 2 expression in infected antigen - presenting cells, induced a more robust CD4 T cell response and showed decreased persistence.", "output": "There is no related enetity." }, { "input": "Together, these data reveal a requirement for B7 - mediated signaling in regulating the CMV - specific CD4 T cell response and establishing host - virus equilibrium.", "output": "There is no related enetity." }, { "input": "Upregulation of CXCL10 in human dorsal root ganglia during experimental and natural varicella - zoster virus infection.", "output": "human, varicella - zoster virus." }, { "input": "Varicella - zoster virus ( VZV ) reactivation causes herpes zoster, which is accompanied by an influx of lymphocytes into affected ganglia, but the stimulus for this infiltrate is not known.", "output": "VZV." }, { "input": "We report that VZV infection of ganglia leads to increased CXCL10 production in vitro, in an explant ganglion model and in naturally infected dorsal root ganglia ( DRG ) during herpes zoster.", "output": "VZV." }, { "input": "Lymphocytes expressing the receptor for CXCL10, CXCR3, were also observed throughout naturally infected ganglia during herpes zoster, including immediately adjacent to neurons.", "output": "There is no related enetity." }, { "input": "This study identifies VZV - induced CXCL10 as a potential driver of T lymphocyte recruitment into DRG during herpes zoster.", "output": "VZV - induced." }, { "input": "Persistent Friend virus replication and disease in Apobec3 - deficient mice expressing functional B - cell - activating factor receptor.", "output": "Friend virus, mice." }, { "input": "Rfv3 is an autosomal dominant gene that influences the recovery of resistant mice from Friend retrovirus ( FV ) infection by limiting viremia and promoting a more potent neutralizing antibody response.", "output": "mice, Friend retrovirus, FV." }, { "input": "We previously reported that Rfv3 is encoded by Apobec3, an innate retrovirus restriction factor.", "output": "There is no related enetity." }, { "input": "However, it was recently suggested that the Rfv3 susceptible phenotype of high viremia at 28 days postinfection ( dpi ) was more dominantly controlled by the B - cell - activating factor receptor ( BAFF - R ), a gene that is linked to but located outside the genetically mapped region containing Rfv3.", "output": "There is no related enetity." }, { "input": "Although one prototypical Rfv3 susceptible mouse strain, A / WySn, indeed contains a dysfunctional BAFF - R, two other Rfv3 susceptible strains, BALB / c and A. BY, express functional BAFF - R genes, determined on the basis of genotyping and B - cell immunophenotyping.", "output": "mouse." }, { "input": "Furthermore, transcomplementation studies in ( C57BL / 6 [ B6 ] x BALB / c ) F ( 1 ) and ( B6 x A. BY ) F ( 1 ) mice revealed that the B6 Apobec3 gene significantly influences recovery from FV viremia, cellular infection, and disease at 28 dpi.", "output": "mice, FV." }, { "input": "Finally, the Rfv3 phenotypes of prototypic B6, A. BY, A / WySn, and BALB / c mouse strains correlate with reported Apobec3 mRNA expression levels.", "output": "mouse." }, { "input": "Overall, these findings argue against the generality of BAFF - R polymorphisms as a dominant mechanism to explain the Rfv3 recovery phenotype and further strengthen the evidence that Apobec3 encodes Rfv3.", "output": "There is no related enetity." }, { "input": "Characterization of cross - reactive CD8 + T - cell recognition of HLA - A2 - restricted HIV - Gag ( SLYNTVATL ) and HCV - NS5b ( ALYDVVSKL ) epitopes in individuals infected with human immunodeficiency and hepatitis C viruses.", "output": "human immunodeficiency, hepatitis C viruses." }, { "input": "The immunologic mechanisms underlying the faster progression of hepatitis C virus ( HCV ) disease in the presence of human immunodeficiency virus ( HIV ) coinfection are not clearly understood.", "output": "HCV, human immunodeficiency virus, HIV." }, { "input": "T - cell cross - reactivity between HCV and influenza virus - specific epitopes has been associated with rapid progression of HCV disease ( S. Urbani, B. Amadei, P. Fisicaro, M. Pilli, G. Missale, A. Bertoletti, and C. Ferrari, J. Exp. Med. 201: 675 - 680, 2005 ).", "output": "HCV, HCV." }, { "input": "We asked whether T - cell cross - reactivity between HCV and HIV could exist during HCV / HIV coinfection and affect pathogenesis.", "output": "HIV, HCV, HIV." }, { "input": "Our search for amino acid sequence homology between the HCV and HIV proteomes revealed two similar HLA - A2 - restricted epitopes, HIV - Gag ( SLYNTVATL [ HIV - SL9 ] ) and HCV - NS5b ( ALYDVVSKL [ HCV - AL9 ] ).", "output": "HIV, HCV, HCV." }, { "input": "We found that 4 out of 20 HLA - A2 - positive ( HLA - A2 ( + ) ) HIV - infected individuals had CD8 ( + ) T cells that recognized both the HIV - SL9 and HCV - AL9 epitopes.", "output": "HIV, HIV." }, { "input": "However, the AL9 epitope was generally shown to be a weak agonist.", "output": "There is no related enetity." }, { "input": "Although HCV - monoinfected individuals in our study did not show AL9 - specific responses, we found that about half of HCV / HIV - coinfected individuals had dual responses to both epitopes.", "output": "HIV." }, { "input": "High dual T - cell recognition among coinfected subjects was usually due to separate T - cell populations targeting each epitope, as determined by pentamer staining.", "output": "There is no related enetity." }, { "input": "The one individual demonstrating cross - reactive T cells to both epitopes showed the most advanced degree of liver disease.", "output": "There is no related enetity." }, { "input": "In coinfected individuals, we observed a positive correlation between the magnitudes of T - cell responses to both the SL9 and the AL9 epitopes, which was also positively associated with the clinical parameter of liver damage.", "output": "There is no related enetity." }, { "input": "Thus, we find that HIV infection induces T cells that can cross - react to heterologous viruses or prime for T cells that are closely related in sequence.", "output": "There is no related enetity." }, { "input": "However, the induction of cross - reactive T cells may not be associated with control of disease caused by the heterologous virus.", "output": "There is no related enetity." }, { "input": "This demonstrates that degeneracy of HIV - specific T cells may play a role in the immunopathology of HCV / HIV coinfection.", "output": "HCV, HIV." }, { "input": "T cell - mediated protection against lethal 2009 pandemic H1N1 influenza virus infection in a mouse model.", "output": "lethal 2009 pandemic H1N1 influenza virus." }, { "input": "Genetic mutation and reassortment of influenza virus gene segments, in particular those of hemagglutinin ( HA ) and neuraminidase ( NA ), that lead to antigenic drift and shift are the major strategies for influenza virus to escape preexisting immunity.", "output": "influenza virus, influenza virus." }, { "input": "The most recent example of such phenomena is the first pandemic of H1N1 influenza of the 21st century, which started in 2009.", "output": "H1N1 influenza." }, { "input": "Cross - reactive antibodies raised against H1N1 viruses circulating before 1930 show protective activity against the 2009 pandemic virus.", "output": "H1N1 viruses, 2009 pandemic virus." }, { "input": "Cross - reactive T - cell responses can also contribute to protection, but in vivo support of this view is lacking.", "output": "There is no related enetity." }, { "input": "To explore the protection mechanisms in vivo, we primed mice with H1 and H3 influenza virus isolates and rechallenged them with a virus derived from the 2009 H1N1 A / CA / 04 / 09 virus, named CA / E3 / 09.", "output": "H1, H3 influenza virus, 2009 H1N1 A / CA / 04 / 09 virus." }, { "input": "We found that priming with influenza viruses of both H1 and H3 homo - and heterosubtypes protected against lethal CA / E3 / 09 virus challenge.", "output": "H1." }, { "input": "Convalescent - phase sera from these primed mice conferred no neutralization activity in vitro and no protection in vivo.", "output": "There is no related enetity." }, { "input": "However, T - cell depletion studies suggested that both CD4 and CD8 T cells contributed to the protection.", "output": "There is no related enetity." }, { "input": "Taken together, these results indicate that cross - reactive T cells established after initial priming with distally related viruses can be a vital component for prevention of disease and control of pandemic H1N1 influenza virus infection.", "output": "pandemic H1N1 influenza virus." }, { "input": "Our results highlight the importance of establishing cross - reactive T - cell responses for protecting against existing or newly emerging pandemic influenza viruses.", "output": "There is no related enetity." }, { "input": "Association of TRIM22 with the type 1 interferon response and viral control during primary HIV - 1 infection.", "output": "HIV - 1." }, { "input": "Type 1 interferons ( IFNs ) induce the expression of the tripartite interaction motif ( TRIM ) family of E3 ligases, but the contribution of these antiviral factors to HIV pathogenesis is not completely understood.", "output": "HIV." }, { "input": "We hypothesized that the increased expression of select type 1 IFN and TRIM isoforms is associated with a significantly lower likelihood of HIV - 1 acquisition and viral control during primary HIV - 1 infection.", "output": "HIV - 1, HIV - 1." }, { "input": "We measured IFN - alpha, IFN - Beta, myxovirus resistance protein A ( MxA ), human TRIM5alpha ( huTRIM5alpha ), and TRIM22 mRNA levels in peripheral blood mononuclear cells ( PBMCs ) of high - risk, HIV - 1 - uninfected participants and HIV - 1 - positive study participants.", "output": "human, HIV - 1, HIV - 1." }, { "input": "Samples were available for 32 uninfected subjects and 28 infected persons, all within 1 year of infection.", "output": "There is no related enetity." }, { "input": "HIV - 1 - positive participants had higher levels of IFN - Beta ( P = 0. 0005 ), MxA ( P = 0. 007 ), and TRIM22 ( P = 0. 01 ) and lower levels of huTRIM5alpha ( P & lt; 0. 001 ) than did HIV - 1 - negative participants.", "output": "HIV - 1, HIV - 1." }, { "input": "TRIM22 but not huTRIM5alpha correlated positively with type 1 IFN ( IFN - alpha, IFN - Beta, and MxA ) ( all P & lt; 0. 0001 ).", "output": "There is no related enetity." }, { "input": "In a multivariate model, increased MxA expression showed a significant positive association with viral load ( P = 0. 0418 ).", "output": "There is no related enetity." }, { "input": "Furthermore, TRIM22 but not huTRIM5alpha, IFN - alpha, IFN - Beta, or MxA showed a negative correlation with plasma viral load ( P = 0. 0307 ) and a positive correlation with CD4 ( + ) T - cell counts ( P = 0. 0281 ).", "output": "There is no related enetity." }, { "input": "In vitro studies revealed that HIV infection induced TRIM22 expression in PBMCs obtained from HIV - negative donors.", "output": "HIV, HIV." }, { "input": "Stable TRIM22 knockdown resulted in increased HIV - 1 particle release and replication in Jurkat reporter cells.", "output": "HIV - 1." }, { "input": "Collectively, these data suggest concordance between type 1 IFN and TRIM22 but not huTRIM5alpha expression in PBMCs and that TRIM22 likely acts as an antiviral effector in vivo.", "output": "There is no related enetity." }, { "input": "Determinants that specify the integration pattern of retrotransposon Tf1 in the fbp1 promoter of Schizosaccharomyces pombe.", "output": "Schizosaccharomyces pombe." }, { "input": "Long terminal repeat ( LTR ) retrotransposons are closely related to retroviruses and, as such, are important models for the study of viral integration and target site selection.", "output": "There is no related enetity." }, { "input": "The transposon Tf1 of Schizosaccharomyces pombe integrates with a strong preference for the promoters of polymerase II ( Pol II ) - transcribed genes.", "output": "Schizosaccharomyces pombe." }, { "input": "Previous work in vivo with plasmid - based targets revealed that the patterns of insertion were promoter specific and highly reproducible.", "output": "There is no related enetity." }, { "input": "To determine which features of promoters are recognized by Tf1, we studied integration in a promoter that has been characterized.", "output": "There is no related enetity." }, { "input": "The promoter of fbp1 has two upstream activating sequences, UAS1 and UAS2.", "output": "There is no related enetity." }, { "input": "We found that integration was targeted to two windows, one 180 nucleotides ( nt ) upstream and the other 30 to 40 nt downstream of UAS1.", "output": "There is no related enetity." }, { "input": "A series of deletions in the promoter showed that the integration activities of these two regions functioned autonomously.", "output": "There is no related enetity." }, { "input": "Integration assays of UAS2 and of a synthetic promoter demonstrated that strong promoter activity alone was not sufficient to direct integration.", "output": "There is no related enetity." }, { "input": "The factors that modulate the transcription activities of UAS1 and UAS2 include the activators Atf1p, Pcr1p, and Rst2p as well as the repressors Tup11p, Tup12p, and Pka1p.", "output": "There is no related enetity." }, { "input": "Strains lacking each of these proteins revealed that Atf1p alone mediated the sites of integration.", "output": "There is no related enetity." }, { "input": "These data indicate that Atf1p plays a direct and specific role in targeting integration in the promoter of fbp1.", "output": "There is no related enetity." }, { "input": "Phylloplane location of glucosinolates in Barbarea spp.", "output": "There is no related enetity." }, { "input": "( Brassicaceae ) and misleading assessment of host suitability by a specialist herbivore.", "output": "There is no related enetity." }, { "input": "Glucosinolates are plant secondary metabolites used in host plant recognition by insects specialized on Brassicaceae, such as the diamondback moth ( DBM ), Plutella xylostella.", "output": "diamondback moth, DBM, Plutella xylostella." }, { "input": "Their perception as oviposition cues by females would seem to require their occurrence on the leaf surface, yet previous studies have reached opposite conclusions about whether glucosinolates are actually present on the surface of crucifer leaves.", "output": "There is no related enetity." }, { "input": "DBM oviposits extensively on Barbarea vulgaris, despite its larvae not being able to survive on this plant because of its content of feeding - deterrent saponins.", "output": "DBM, Barbarea vulgaris." }, { "input": "Glucosinolates and saponins in plant tissue and mechanically removed surface waxes from leaves of Barbarea spp. were analyzed with high - performance liquid chromatography ( HPLC ) and liquid chromatography - mass spectrometry ( LC - MS ).", "output": "There is no related enetity." }, { "input": "Surface waxes from leaves of Barbarea spp. contained glucosinolates, but not feeding - deterrent saponins.", "output": "There is no related enetity." }, { "input": "Our research is the first to show that glucosinolates are present on the leaf surface of Barbarea spp., but not in other crucifers investigated, resolving some conflicting results from previous studies.", "output": "There is no related enetity." }, { "input": "Our research is also the first to quantify glucosinolates on the leaf surface of a crucifer, and to show that the concentrations of glucosinolates found on the leaf surface of Barbarea spp. are sufficient to be perceived by ovipositing DBM.", "output": "DBM." }, { "input": "Improved nitrogen nutrition enhances root uptake, root - to - shoot translocation and remobilization of zinc ( ( 65 ) Zn ) in wheat.", "output": "There is no related enetity." }, { "input": "This study focussed on the effect of increasing nitrogen ( N ) supply on root uptake and root - to - shoot translocation of zinc ( Zn ) as well as retranslocation of foliar - applied Zn in durum wheat ( Triticum durum ).", "output": "durum wheat, Triticum durum." }, { "input": "Nutrient solution experiments were conducted to examine the root uptake and root - to - shoot translocation of ( 65 ) Zn in seedlings precultured with different N supplies.", "output": "There is no related enetity." }, { "input": "In additional experiments, the effect of varied N nutrition on retranslocation of foliar - applied ( 65 ) Zn was tested at both the vegetative and generative stages.", "output": "There is no related enetity." }, { "input": "When N supply was increased, the ( 65 ) Zn uptake by roots was enhanced by up to threefold and the ( 65 ) Zn translocation from roots to shoots increased by up to eightfold, while plant growth was affected to a much smaller degree.", "output": "There is no related enetity." }, { "input": "Retranslocation of ( 65 ) Zn from old into young leaves and from flag leaves to grains also showed marked positive responses to increasing N supply.", "output": "There is no related enetity." }, { "input": "The results demonstrate that the N - nutritional status of wheat affects major steps in the route of Zn from the growth medium to the grain, including its uptake, xylem transport and remobilization via phloem.", "output": "There is no related enetity." }, { "input": "Thus, N is a critical player in the uptake and accumulation of Zn in plants, which deserves special attention in biofortification of food crops with Zn.", "output": "There is no related enetity." }, { "input": "Dynamic changes of canopy - scale mesophyll conductance to CO2 diffusion of flower as affected by CO2 concentration and abscisic acid.", "output": "There is no related enetity." }, { "input": "Leaf - level measurements have shown that mesophyll conductance ( g ( m ) ) can vary rapidly in response to CO2 and other environmental factors, but similar studies at the canopy - scale are missing.", "output": "There is no related enetity." }, { "input": "Here, we report the effect of short - term variation of CO2 concentration on canopy - scale g ( m ) and other CO2 exchange parameters of sunflower ( Helianthus annuus L. ) stands in the presence and absence of abscisic acid ( ABA ) in their nutrient solution.", "output": "sunflower, Helianthus annuus." }, { "input": "g ( m ) was estimated from gas exchange and on - line carbon isotope discrimination ( Delta ( obs ) ) in a ^ 1 ^ 3CO2 / ^ 1 ^ 2CO2 ) gas exchange mesocosm.", "output": "There is no related enetity." }, { "input": "The isotopic contribution of ( photo ) respiration to stand - scale Delta ( obs ) was determined with the experimental approach of Tcherkez et al.", "output": "There is no related enetity." }, { "input": "Without ABA, short - term exposures to different CO2 concentrations ( C ( a ) 100 to 900 mumol mol - ^ 1 ) had little effect on canopy - scale g ( m ).", "output": "There is no related enetity." }, { "input": "But, addition of ABA strongly altered the CO2 - response: g ( m ) was high ( approx. 0. 5 mol CO2 m - ^ 2 s - ^ 1 ) at C ( a ) & lt; 200 mumol mol - ^ 1 and decreased to & lt; 0. 1 mol CO2 m - ^ 2 s - ^ 1 at C ( a ) > 400 mumol mol - ^ 1.", "output": "There is no related enetity." }, { "input": "In the absence of ABA, the contribution of ( photo ) respiration to stand - scale Delta ( obs ) was high at low C ( a ) ( 7. 2 % ) and decreased to & lt; 2 % at C ( a ) > 400 mumol mol - ^ 1.", "output": "There is no related enetity." }, { "input": "Treatment with ABA halved this effect at all C ( a ).", "output": "There is no related enetity." }, { "input": "Hormone receptor - like in 96 and Broad - Complex modulate phenobarbital induced transcription of cytochrome P450 CYP6D1 in Drosophila S2 cells.", "output": "Drosophila." }, { "input": "Phenobarbital ( PB ) is a prototypical inducer for studies of xenobiotic responses in animals.", "output": "There is no related enetity." }, { "input": "In mammals, the nuclear receptors constitutive androstane receptor ( CAR ) and pregnane X receptor ( PXR ) have been identified as key transcription factors regulating PB induced transcription of xenobiotic responsive genes.", "output": "There is no related enetity." }, { "input": "In insects, much less is known about the transcription factors involved in regulating PB induced transcription, although CAR and PXR have a single orthologue hormone receptor - like in 96 ( HR96 ) in Drosophila melanogaster.", "output": "Drosophila melanogaster." }, { "input": "Using dual luciferase reporter assays in Drosophila Schneider ( S2 ) cells, constructs containing variable lengths of the promoter of the PB inducible cytochrome P450 CYP6D1 were evaluated in the presence and absence of PB.", "output": "Drosophila." }, { "input": "The promoter region between - 330 and - 280 ( relative to the position of transcription start site, + 1 ) was found to be critical for PB induction.", "output": "There is no related enetity." }, { "input": "Putative binding sites for Drosophila Broad - Complex ( BR - C ) and deformed ( Dfd ) were identified within this promoter region using TFsearch.", "output": "Drosophila." }, { "input": "RNA interference ( RNAi ) treatment of S2 cells in conjunction with CYP6D1 promoter assays showed that suppression of Drosophila HR96 and BR - C transcription in S2 cells resulted in a significant decrease and increase, respectively, of PB induction.", "output": "Drosophila." }, { "input": "Effects of HR96 and BR - C in mediating PB induction were PB specific and PB dependent.", "output": "There is no related enetity." }, { "input": "This represents new functional evidence that Drosophila HR96 and BR - C can act as an activator and repressor, respectively, in regulating PB induced transcription in insects.", "output": "Drosophila." }, { "input": "Double - antigen sandwich ELISA for the detection of anti - hepatitis C virus antibodies.", "output": "hepatitis C virus." }, { "input": "A double - antigen sandwich ELISA was developed a detection of HCV antibodies by a recombinant multi - epitope HCV antigen and a biotin - streptavidin amplification system.", "output": "HCV, HCV." }, { "input": "Three plasma specimens from 1708 individuals who were suspected previously to be HCV - positive using an HCV antibody diagnostic kit ( Chuangxin, Xiamen, China ) displayed negative results when using the ELISA.", "output": "HCV, HCV." }, { "input": "These results were validated by a recombinant immunoblotting assay ( two were negative, and one was indeterminate ).", "output": "There is no related enetity." }, { "input": "Among 889 blood specimens donated for clinical evaluation, 246 were positive and 630 were negative using the ELISA.", "output": "There is no related enetity." }, { "input": "The sensitivity and specificity of the ELISA were 98. 7 % and 100 %, respectively.", "output": "There is no related enetity." }, { "input": "In 43 donors and 14 patients with chronic hepatitis C, the detectable rates for HCV IgM by both ELISA and the HCV anti - IgM detection reagents ( Huimin, Shenyang, China ) were 100 %, and the detectable rate for HCV IgG using an indirect HCV - antibody detection kit ( GWK, Beijing, China ) was 98. 3 %.", "output": "HCV, HCV, HCV, HCV." }, { "input": "Thus, the double - antigen sandwich ELISA exhibits strong specificity and sensitivity and has been approved by the China State Food and Drug Administration ( SFDA ).", "output": "There is no related enetity." }, { "input": "The performance of the double - antigen sandwich ELISA was similar to the Ortho ELISA 3. 0.", "output": "There is no related enetity." }, { "input": "It did not give false - negative results otherwise IgM was undetectable using an indirect HCV - antibody detection kit.", "output": "HCV." }, { "input": "This ELISA provides another method for the detection of HCV antibodies.", "output": "HCV." }, { "input": "Detection of infectious myonecrosis virus using monoclonal antibody specific to N and C fragments of the capsid protein expressed heterologously.", "output": "infectious myonecrosis virus." }, { "input": "The gene encoding the capsid protein in ORF1 of the genome of infectious myonecrosis virus ( IMNV ) ( GenBank AY570982 ) was amplified into three parts named CP - N ( nucleotides 2248 - 3045 ), CP - I ( nucleotides 3046 - 3954 ) and CP - C ( nucleotides 3955 - 4953 ).", "output": "infectious myonecrosis virus, IMNV." }, { "input": "The CP - N fragment was inserted into expression vector pTYB1 while CP - I and CP - C were each inserted into expression vector pGEX - 6P - 1 for transformation of BL21 E. coli strain.", "output": "BL21 E . coli." }, { "input": "After induction, intein - CP - N ( 84 kDa ), glutathione - S - transferase ( GST ) - CP - I ( 60 kDa ) and GST - CP - C ( 62 kDa ) fusion proteins were produced.", "output": "There is no related enetity." }, { "input": "They were separated by SDS - PAGE and electroeluted before immunization of Swiss mice for monoclonal antibody ( MAb ) production.", "output": "There is no related enetity." }, { "input": "Two MAbs specific to CP - N and one MAb specific to CP - C were selected for use for detection of natural IMNV infections in Penaeus vannamei by dot blotting, Western blotting and immunohistochemistry.", "output": "IMNV." }, { "input": "There was no cross - reaction with shrimp tissues or common shrimp viruses including white spot syndrome virus ( WSSV ), yellow head virus ( YHV ), Taura syndrome virus ( TSV ), Penaeus monodon nucleopolyhedrovirus ( PemoNPV ), Penaeus stylirostris densovirus ( PstDNV ) and Penaeus monodon densovirus ( PmDNV ).", "output": "white spot syndrome virus, WSSV, yellow head virus, YHV, Taura syndrome virus, TSV, Penaeus monodon nucleopolyhedrovirus, PemoNPV." }, { "input": "The detection sensitivities of the MAbs were approximately 6 fmol / spot of purified recombinant intein - CP - N protein and 8 fmol / spot of GST - CP - C as determined by dot blotting.", "output": "There is no related enetity." }, { "input": "A combination of all three MAbs resulted in a twofold increase in sensitivity over use of any single MAb.", "output": "There is no related enetity." }, { "input": "However, this sensitivity was approximately 10 times lower than that of one - step RT - PCR using the same sample.", "output": "There is no related enetity." }, { "input": "Immunohistochemical analysis using MAbs specific to CP - N and CP - C in IMNV - infected shrimp revealed intense staining patterns in muscles, the lymphoid organ, gills, the heart, hemocytes and connective tissue.", "output": "IMNV." }, { "input": "Real time PCR method for simultaneous detection, quantitation and differentiation of capripoxviruses.", "output": "There is no related enetity." }, { "input": "The genus Capripoxvirus ( CaPV ) comprises three members namely, sheep poxvirus ( SPPV ), goat poxvirus ( GTPV ) and lumpy skin disease virus ( LSDV ) affecting sheep, goats and cattle, respectively.", "output": "sheep poxvirus, SPPV, goat poxvirus, GTPV, lumpy skin disease virus, LSDV, sheep, goats, cattle." }, { "input": "CaPV infections produce similar symptoms in sheep and goats, and the three viruses cannot be distinguished serologically.", "output": "sheep, goats." }, { "input": "Since there are conflicting opinions regarding the host specificity of CaPVs, particularly for goatpox and sheeppox viruses, the development of rapid genotyping tools will facilitate more accurate disease diagnosis and surveillance for better management of capripox outbreaks.", "output": "goatpox, sheeppox viruses." }, { "input": "This paper describes a species - specific, real time polymerase chain reaction ( PCR ), based on unique molecular markers that were found in the G - protein - coupled chemokine receptor ( GPCR ) gene sequences of CaPVs, that uses dual hybridization probes for their simultaneous detection, quantitation and genotyping.", "output": "There is no related enetity." }, { "input": "The assay can differentiate between CaPV strains based on differences in the melting point temperature ( Tm ) obtained after fluorescence melting curve analysis ( FMCA ).", "output": "There is no related enetity." }, { "input": "It is highly sensitive and presents low intra - and inter - run variation.", "output": "There is no related enetity." }, { "input": "This real time PCR assay will make a significant contribution to CaPV diagnosis and to the better understanding of the epidemiology of CaPVs by enabling rapid genotyping and gene - based classification of viral strains and unequivocal identification of isolates.", "output": "There is no related enetity." }, { "input": "Multiplex PCR for rapid detection of serotype A foot - and - mouth disease virus variants with amino acid deletion at position 59 of the capsid protein VP3.", "output": "serotype A foot - and - mouth disease virus." }, { "input": "In India, there has been co - circulation, extinction and emergence of genotypes / lineages within serotype A foot - and - mouth disease ( FMD ) virus.", "output": "FMD." }, { "input": "At present an antigenically heterogeneous, unique lineage within genotype VII dominates the field outbreaks.", "output": "There is no related enetity." }, { "input": "This genetic cluster has amino acid deletion at position 59 of VP3 ( VP3 ( 59 ) - deletion group ), considered to be critical antigenically.", "output": "There is no related enetity." }, { "input": "The emergence of this group warrants rapid and accurate detection to facilitate early planning and implementation of an effective control policy.", "output": "There is no related enetity." }, { "input": "A rapid multiplex PCR assay was developed for detection of the dominating VP3 ( 59 ) - deletion group with 100 % sensitivity and specificity, even before generating sequence data and confirmatory phylogenetic analysis.", "output": "There is no related enetity." }, { "input": "This development is important for surveillance of FMD in India.", "output": "FMD." }, { "input": "Multiplex RT - PCR for rapid detection and differentiation of class I and class II Newcastle disease viruses.", "output": "class I, class II Newcastle disease viruses." }, { "input": "A multiplex RT - PCR was developed for detection and differentiation of class I and class II strains of Newcastle disease virus ( NDV ).", "output": "class I, class II strains of Newcastle disease virus ( NDV )." }, { "input": "The method was shown to have high specificity and sensitivity.", "output": "There is no related enetity." }, { "input": "The results obtained from the multiplex RT - PCR for a total of 67 NDV field isolates obtained in 2009 were consistent with those obtained by nucleotide sequencing and phylogenetic analysis.", "output": "NDV." }, { "input": "A phylogenetic tree based on the partial sequences of the F gene revealed that the 67 field isolates of NDV could be divided into two classes.", "output": "NDV." }, { "input": "Twenty - seven NDV isolates were grouped into class I, and two genotypes were identified.", "output": "NDV, class I." }, { "input": "Most of the class I isolates were determined to be of genotype 3, with the exception of isolate NDV09 - 034, which belonged to genotype 2.", "output": "class I, NDV09 - 034." }, { "input": "Forty class II NDV isolates were divided into three genotypes, namely genotype VII ( 27 isolates ), genotype I ( 2 isolates ) and genotype II ( 11 isolates ).", "output": "class II NDV isolates." }, { "input": "Isolates of genotypes I and II in class II were shown to be related to commercial vaccine strains used commonly in China.", "output": "There is no related enetity." }, { "input": "All isolates of genotype VII were predicted to be virulent, on the basis of the sequence motif at the cleavage site of the F gene.", "output": "There is no related enetity." }, { "input": "This genotype has become predominantly responsible for most outbreaks of ND in China in recent years.", "output": "There is no related enetity." }, { "input": "In conclusion, this multiplex RT - PCR provides a new assay for rapid detection and differentiation of both classes of NDV isolates.", "output": "NDV isolates." }, { "input": "Detection of Tomato black ring virus by real - time one - step RT - PCR.", "output": "Tomato black ring virus." }, { "input": "A TaqMan - based real - time one - step RT - PCR assay was developed for the rapid detection of Tomato black ring virus ( TBRV ), a significant plant pathogen which infects a wide range of economically important crops.", "output": "Tomato black ring virus, TBRV." }, { "input": "Primers and a probe were designed against existing genomic sequences to amplify a 72 bp fragment from RNA - 2.", "output": "There is no related enetity." }, { "input": "The assay amplified all isolates of TBRV tested, but no amplification was observed from the RNA of other nepovirus species or healthy host plants.", "output": "TBRV." }, { "input": "The detection limit of the assay was estimated to be around nine copies of the TBRV target region in total RNA.", "output": "TBRV." }, { "input": "A comparison with conventional RT - PCR and ELISA, indicated that ELISA, the current standard test method, lacked specificity and reacted to all nepovirus species tested, while conventional RT - PCR was approximately ten - fold less sensitive than the real - time RT - PCR assay.", "output": "There is no related enetity." }, { "input": "Finally, the real - time RT - PCR assay was tested using five different RT - PCR reagent kits and was found to be robust and reliable, with no significant differences in sensitivity being found.", "output": "There is no related enetity." }, { "input": "The development of this rapid assay should aid in quarantine and post - border surveys for regulatory agencies.", "output": "There is no related enetity." }, { "input": "Cross - genotypic polyclonal anti - HCV antibodies from human ascitic fluid.", "output": "HCV, human." }, { "input": "Many anti - HCV antibodies are available, but more are needed for research and clinical applications.", "output": "HCV." }, { "input": "This study examines whether ascitic fluid from cirrhotic patients could be a source of reagent - grade antibodies.", "output": "There is no related enetity." }, { "input": "Ascitic fluid from 29 HCV patients was screened by ELISA for anti - HCV antibodies against three viral proteins: core, NS4B, and NS5A.", "output": "HCV, HCV." }, { "input": "Significant patient - to - patient variability in anti - HCV antibody titers was observed.", "output": "HCV." }, { "input": "Total ascitic fluid IgG purified by Protein - A chromatography reacted with HCV proteins in immunoblots, cell extracts, and replicon - expressing cells.", "output": "HCV." }, { "input": "Affinity - purification using synthetic peptides as bait allowed the preparation of cross - genotypic antibodies directed against pre - selected regions of HCV core, NS4B, and NS5A proteins.", "output": "There is no related enetity." }, { "input": "The performance of the polyclonal antibodies was comparable to that of monoclonal antibodies.", "output": "There is no related enetity." }, { "input": "Anti - NS4B antibody preparations reacted with genotype 1a, 1b, and 2a NS4B proteins in immunoblots and allowed NS4B to be localized in replicon - expressing cells.", "output": "There is no related enetity." }, { "input": "Ascitic fluid is an abundant source of human polyclonal cross - genotypic antibodies that can be used as an alternative to blood.", "output": "human." }, { "input": "This study shows the utility of selectively purifying human polyclonal antibodies from ascitic fluid.", "output": "human." }, { "input": "Affinity purification allows antibodies to be selected that are comparable to monoclonal antibodies in their ability to react with targeted regions of viral proteins.", "output": "There is no related enetity." }, { "input": "A versatile vector for the production of pseudotyped viruses expressing gp120 antigens from different clades of primary HIV - 1 isolates.", "output": "HIV - 1." }, { "input": "A novel HIV - 1 Env expression vector ( SF162 - Z ) was developed by introducing two new cloning sites on the backbone of an existing vector that produces a full length Env from HIV - 1 SF162 isolate.", "output": "HIV - 1, HIV - 1." }, { "input": "These sites facilitate the swapping of the gp120 portion of the SF162 Env with matching gp120 antigens from HIV - 1 isolates of different genetic clades.", "output": "HIV - 1." }, { "input": "Final production of functional pseudotyped viruses will express chimeric Env antigens, including gp41 of the parental SF162 and gp120 from other primary isolates.", "output": "There is no related enetity." }, { "input": "This system is useful for testing the neutralizing sensitivity of partial env gene products frequently identified in viral quasi species in patients infected with HIV or when only partial gp120 gene products are available.", "output": "HIV." }, { "input": "Catabolite control protein A controls hydrogen peroxide production and cell death in Streptococcus sanguinis.", "output": "Streptococcus sanguinis." }, { "input": "Streptococcus sanguinis is a commensal oral bacterium producing hydrogen peroxide ( H2O2 ) that is dependent on pyruvate oxidase ( Spx ) activity.", "output": "Streptococcus sanguinis." }, { "input": "In addition to its well - known role in bacterial antagonism during interspecies competition, H2O2 causes cell death in about 10 % of the S. sanguinis population.", "output": "S . sanguinis." }, { "input": "As a consequence of H2O2 - induced cell death, largely intact chromosomal DNA is released into the environment.", "output": "There is no related enetity." }, { "input": "This extracellular DNA ( eDNA ) contributes to the self - aggregation phenotype under aerobic conditions.", "output": "There is no related enetity." }, { "input": "To further investigate the regulation of spx gene expression, we assessed the role of catabolite control protein A ( CcpA ) in spx expression control.", "output": "There is no related enetity." }, { "input": "We report here that CcpA represses spx expression.", "output": "There is no related enetity." }, { "input": "An isogenic DeltaccpA mutant showed elevated spx expression, increased Spx abundance, and H2O2 production, whereas the wild type did not respond with altered spx expression in the presence of glucose and other carbohydrates.", "output": "There is no related enetity." }, { "input": "Since H2O2 is directly involved in the release of eDNA and bacterial cell death, the presented data suggest that CcpA is a central control element in this important developmental process in S. sanguinis.", "output": "S . sanguinis." }, { "input": "Genome sequence of strain HTCC2083, a novel member of the marine clade Roseobacter.", "output": "There is no related enetity." }, { "input": "Strain HTCC2083 was isolated from Oregon seawater using dilution - to - extinction culturing and represents a novel member of the Roseobacter clade.", "output": "There is no related enetity." }, { "input": "The draft genome sequence of HTCC2083 is presented here.", "output": "There is no related enetity." }, { "input": "The genome is predicted to contain genes for aerobic anoxygenic phototrophy, sulfite - oxidizing chemolithotrophy, anapleurotic CO ( 2 ) fixation, carbon monoxide oxidation, and dimethylsulfoniopropionate ( DMSP ) utilization.", "output": "There is no related enetity." }, { "input": "Cadherin domains in the polysaccharide - degrading marine bacterium Saccharophagus degradans 2 - 40 are carbohydrate - binding modules.", "output": "Saccharophagus degradans 2 - 40." }, { "input": "The complex polysaccharide - degrading marine bacterium Saccharophagus degradans strain 2 - 40 produces putative proteins that contain numerous cadherin and cadherin - like domains involved in intercellular contact interactions.", "output": "There is no related enetity." }, { "input": "The current study reveals that both domain types exhibit reversible calcium - dependent binding to different complex polysaccharides which serve as growth substrates for the bacterium.", "output": "There is no related enetity." }, { "input": "Distinct roles of multiple NDH - 1 complexes in the cyanobacterial electron transport network as revealed by kinetic analysis of P700 + reduction in various Ndh - deficient mutants of Synechocystis sp. strain PCC6803.", "output": "Synechocystis sp . strain PCC6803." }, { "input": "While methyl viologen had only a small effect on P700 ( + ) rereduction kinetics after far - red pulses in KCN - treated wild - type Synechocystis sp. strain PCC6803 and an NdhF3 / NdhF4 ( NdhF3 / F4 ) - defective mutant, it involved a rather slow P700 ( + ) rereduction in an NdhF1 - defective mutant.", "output": "Synechocystis sp . strain PCC6803." }, { "input": "This strongly indicates that ( i ) active electron flow from metabolites to plastoquinone is suppressed upon deletion of ndhF1 and ( ii ) photosystem 1 - mediated cyclic electron transport is dependent on NdhF3 / F4 - type NDH - 1 complexes.", "output": "There is no related enetity." }, { "input": "Adhesive activity of the haemophilus cryptic genospecies cha autotransporter is modulated by variation in tandem Peptide repeats.", "output": "There is no related enetity." }, { "input": "The Haemophilus cryptic genospecies is an important cause of maternal genital tract and neonatal systemic infections and initiates infection by colonizing the genital or respiratory epithelium.", "output": "There is no related enetity." }, { "input": "In recent work, we identified a unique Haemophilus cryptic genospecies protein called Cha, which mediates efficient adherence to genital and respiratory epithelia.", "output": "There is no related enetity." }, { "input": "The Cha adhesin belongs to the trimeric autotransporter family and contains an N - terminal signal peptide, an internal passenger domain that harbors adhesive activity, and a C - terminal membrane anchor domain.", "output": "There is no related enetity." }, { "input": "The passenger domain in Cha contains clusters of YadA - like head domains and neck motifs as well as a series of tandem 28 - amino - acid peptide repeats.", "output": "There is no related enetity." }, { "input": "In the current study, we report that variation in peptide repeat number gradually modulates Cha adhesive activity, associated with a direct effect on the length of Cha fibers on the bacterial cell surface.", "output": "There is no related enetity." }, { "input": "The N - terminal 404 residues of the Cha passenger domain mediate binding to host cells and also facilitate bacterial aggregation through intermolecular Cha - Cha binding.", "output": "There is no related enetity." }, { "input": "As the tandem peptide repeats expand, the Cha fiber becomes longer and Cha adherence activity decreases.", "output": "There is no related enetity." }, { "input": "The expansion and contraction of peptide repeats represent a novel mechanism for modulating adhesive capacity, potentially balancing the need of the organism to colonize the genital and respiratory tracts with the ability to attach to alternative substrates, disperse within the host, or evade the host immune system.", "output": "There is no related enetity." }, { "input": "Complete genome sequence of strain HTCC2503T of Parvularcula bermudensis, the type species of the order Parvularculales in the class Alphaproteobacteria.", "output": "HTCC2503T, Parvularcula bermudensis." }, { "input": "The order Parvularculales represents the seventh order in the class Alphaproteobacteria.", "output": "There is no related enetity." }, { "input": "Parvularcula bermudensis, the type species of the order, was isolated from the Sargasso Sea using dilution - to - extinction culturing.", "output": "Parvularcula bermudensis." }, { "input": "We present here the complete genome sequence of Parvularcula bermudensis HTCC2503 ( T ), which contains genes for carotenoid biosynthesis, dimethylsulfoniopropionate demethylase, and transduction - like gene transfer agents.", "output": "Parvularcula bermudensis HTCC2503 ( T )." }, { "input": "Complete genome sequence of Corynebacterium pseudotuberculosis I19, a strain isolated from a cow in Israel with bovine mastitis.", "output": "Corynebacterium pseudotuberculosis I19, cow." }, { "input": "This work reports the completion and annotation of the genome sequence of Corynebacterium pseudotuberculosis I19, isolated from an Israeli dairy cow with severe clinical mastitis.", "output": "Corynebacterium pseudotuberculosis I19, cow." }, { "input": "To present the whole - genome sequence, a de novo assembly approach using 33 million short ( 25 - bp ) mate - paired SOLiD reads only was applied.", "output": "There is no related enetity." }, { "input": "Furthermore, the automatic, functional, and manual annotations were attained with the use of several algorithms in a multistep process.", "output": "There is no related enetity." }, { "input": "X - ray structure and site - directed mutagenesis analysis of the Escherichia coli colicin M immunity protein.", "output": "Escherichia coli." }, { "input": "Colicin M ( ColM ), which is produced by some Escherichia coli strains to kill competitor strains from the same or related species, was recently shown to inhibit cell wall peptidoglycan biosynthesis through enzymatic degradation of its lipid II precursor.", "output": "Escherichia coli." }, { "input": "ColM - producing strains are protected from the toxin that they produce by coexpression of a specific immunity protein, named Cmi, whose mode of action still remains to be identified.", "output": "There is no related enetity." }, { "input": "We report here the resolution of the crystal structure of Cmi, which is composed of four Beta strands and four alpha helices.", "output": "There is no related enetity." }, { "input": "This rather compact structure revealed a disulfide bond between residues Cys31 and Cys107.", "output": "There is no related enetity." }, { "input": "Interestingly, these two cysteines and several other residues appeared to be conserved in the sequences of several proteins of unknown function belonging to the YebF family which exhibit 25 to 35 % overall sequence similarity with Cmi.", "output": "There is no related enetity." }, { "input": "Site - directed mutagenesis was performed to assess the role of these residues in the ColM immunity - conferring activity of Cmi, which showed that the disulfide bond and residues from the C - terminal extremity of the protein were functionally essential.", "output": "There is no related enetity." }, { "input": "The involvement of DsbA oxidase in the formation of the Cmi disulfide bond is also demonstrated.", "output": "There is no related enetity." }, { "input": "Complete genome sequence of Bifidobacterium bifidum S17.", "output": "Bifidobacterium bifidum S17." }, { "input": "Here, we report on the first completely annotated genome sequence of a Bifidobacterium bifidum strain.", "output": "Bifidobacterium bifidum." }, { "input": "B. bifidum S17, isolated from feces of a breast - fed infant, was shown to strongly adhere to intestinal epithelial cells and has potent anti - inflammatory activity in vitro and in vivo.", "output": "B . bifidum S17." }, { "input": "The genome sequence will provide new insights into the biology of this potential probiotic organism and allow for the characterization of the molecular mechanisms underlying its beneficial properties.", "output": "There is no related enetity." }, { "input": "Complete genome sequence of strain HTCC2170, a novel member of the genus Maribacter in the family Flavobacteriaceae.", "output": "HTCC2170." }, { "input": "Strain HTCC2170 was isolated from surface waters off the Oregon coast using dilution - to - extinction culturing.", "output": "HTCC2170." }, { "input": "Here, we present the finished genome sequence of a marine bacterium, Maribacter sp. strain HTCC2170.", "output": "marine bacterium, Maribacter sp . strain HTCC2170." }, { "input": "Strain sp.", "output": "There is no related enetity." }, { "input": "HTCC2170 is predicted to be a facultatively aerobic chemoorganotroph that, based on genomic sequence analysis, is capable of macromolecule degradation and anaerobic respiration.", "output": "HTCC2170." }, { "input": "Characterization of the Bacteroides CTnDOT regulatory protein RteC.", "output": "There is no related enetity." }, { "input": "Excision of the Bacteroides conjugative transposon CTnDOT is stimulated by tetracycline.", "output": "There is no related enetity." }, { "input": "It was shown previously that a gene, rteC, is necessary for tetracycline - stimulated transcriptional regulation of the orf2c operon, which contains the excision genes.", "output": "There is no related enetity." }, { "input": "The protein encoded by this gene, RteC, did not have primary amino acid sequence homology to any known proteins in the databases.", "output": "There is no related enetity." }, { "input": "Accordingly, we sought structural homologs of RteC.", "output": "There is no related enetity." }, { "input": "A three - dimensional structure prediction by Robetta suggested that RteC might have two domains and that the C - terminal domain might have a winged helix motif.", "output": "There is no related enetity." }, { "input": "Based on the Robetta prediction, the human transcriptional factors E2F - 4 and DP2 were identified as the most likely structural homologs of RteC.", "output": "human." }, { "input": "We made alanine substitutions within the putative DNA binding helix 3 region of RteC.", "output": "There is no related enetity." }, { "input": "Assays of orf2c:: uidA activation by alanine mutants indicated that residues 174, 175, 178, 180, and 184 in helix 3 might contact the upstream region of P ( E ).", "output": "There is no related enetity." }, { "input": "The upstream region of orf2c contained two inverted - repeat half sites.", "output": "There is no related enetity." }, { "input": "Mutational analysis of these half sites showed that both half sites are important for activity.", "output": "There is no related enetity." }, { "input": "Thus, we have identified the DNA binding portion of RteC and the DNA site to which it binds.", "output": "There is no related enetity." }, { "input": "Draft genome sequence of the anoxygenic filamentous phototrophic bacterium Oscillochloris trichoides subsp. DG - 6.", "output": "Oscillochloris trichoides subsp . DG - 6." }, { "input": "Oscillochloris trichoides is a mesophilic, filamentous, photoautotrophic, nonsulfur, diazotrophic bacterium which is capable of carbon dioxide fixation via the reductive pentose phosphate cycle and possesses no assimilative sulfate reduction.", "output": "Oscillochloris trichoides." }, { "input": "Here, we present the draft genome sequence of Oscillochloris trichoides subsp. DG - 6, the type strain of the species, which has permitted the prediction of genes for carbon and nitrogen metabolism and for the light - harvesting apparatus.", "output": "Oscillochloris trichoides subsp . DG - 6." }, { "input": "Impact of density and environmental factors on population fluctuations in a migratory passerine.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Populations of plants and animals typically fluctuate because of the combined effects of density - dependent and density - independent processes.", "output": "There is no related enetity." }, { "input": "The study of these processes is complicated by the fact that population sizes are typically not known exactly, because population counts are subject to sampling variance.", "output": "There is no related enetity." }, { "input": "Although the existence of sampling variance is broadly acknowledged, relatively few studies on time - series data have accounted for it, which can result in wrong inferences about population processes.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "To increase our understanding of population dynamics, we analysed time series from six Central European populations of the migratory red - backed shrike Lanius collurio by simultaneously assessing the strength of density dependence, process and sampling variance.", "output": "red - backed shrike, Lanius collurio." }, { "input": "In addition, we evaluated hypotheses predicting effects of factors presumed to operate on the breeding grounds, at stopover sites in eastern Africa during fall and spring migration and in the wintering grounds in southern Africa.", "output": "There is no related enetity." }, { "input": "We used both simple and state - space formulations of the Gompertz equation to model population size.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Across populations and modelling approaches, we found consistent evidence for negative density - dependent population regulation.", "output": "There is no related enetity." }, { "input": "Further, process variance contributed substantially to variation in population size, while sampling variance did not.", "output": "There is no related enetity." }, { "input": "Environmental conditions in eastern and southern Africa appear to influence breeding population size, as rainfall in the Sahel during fall migration and in the south African wintering areas were positively related to population size in the following spring in four of six populations.", "output": "There is no related enetity." }, { "input": "In contrast, environmental conditions in the breeding grounds were not related to population size.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Our findings suggest negative density - dependent regulation of red - backed shrike breeding populations and are consistent with the long - standing hypothesis that conditions in the African staging and wintering areas influence population numbers of species breeding in Europe.", "output": "red - backed shrike." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "This study highlights the importance of jointly investigating density - dependent and density - independent processes to improve our understanding of factors influencing population fluctuations in space and time.", "output": "There is no related enetity." }, { "input": "Intraspecific trait variation and covariation in a widespread tree species ( Nothofagus pumilio ) in southern Chile.", "output": "Nothofagus pumilio." }, { "input": "* The focus of the trait - based approach to study community ecology has mostly been on trait comparisons at the interspecific level.", "output": "There is no related enetity." }, { "input": "Here we quantified intraspecific variation and covariation of leaf mass per area ( LMA ) and wood density ( WD ) in monospecific forests of the widespread tree species Nothofagus pumilio to determine its magnitude and whether it is related to environmental conditions and ontogeny.", "output": "Nothofagus pumilio." }, { "input": "We also discuss probable mechanisms controlling the trait variation found.", "output": "There is no related enetity." }, { "input": "* We collected leaf and stem woody tissues from 30 - 50 trees of different ages ( ontogeny ) from each of four populations at differing elevations ( i. e. temperatures ) and placed at each of three locations differing in soil moisture.", "output": "There is no related enetity." }, { "input": "* The total variation in LMA ( coefficient of variation ( CV ) = 21. 14 % ) was twice that of WD ( CV = 10. 52 % ).", "output": "There is no related enetity." }, { "input": "The total variation in traits was never less than 23 % when compared with interspecific studies.", "output": "There is no related enetity." }, { "input": "Differences in elevation ( temperature ) for the most part explained variation in LMA, while differences in soil moisture and ontogeny explained the variation in WD.", "output": "There is no related enetity." }, { "input": "Traits covaried similarly in the altitudinal gradient only.", "output": "There is no related enetity." }, { "input": "* Functional traits of N. pumilio exhibited nonnegligible variation; LMA varied for the most part with temperature, while WD mostly varied with moisture and ontogeny.", "output": "N . pumilio." }, { "input": "We demonstrate that environmental variation can cause important trait variation without species turnover.", "output": "There is no related enetity." }, { "input": "Systemic virus - induced gene silencing allows functional characterization of maize genes during biotrophic interaction with Ustilago maydis.", "output": "maize, Ustilago maydis." }, { "input": "Infection of maize ( Zea mays ) plants with the corn smut fungus Ustilago maydis leads to the formation of large tumors on the stem, leaves and inflorescences.", "output": "maize, Zea mays, corn, Ustilago maydis." }, { "input": "In this biotrophic interaction, plant defense responses are actively suppressed by the pathogen, and previous transcriptome analyses of infected maize plants showed massive and stage - specific changes in host gene expression during disease progression.", "output": "maize." }, { "input": "To identify maize genes that are functionally involved in the interaction with U. maydis, we adapted a virus - induced gene silencing ( VIGS ) system based on the brome mosaic virus ( BMV ) for maize.", "output": "maize, U . maydis, maize." }, { "input": "Conditions were established that allowed successful U. maydis infection of BMV - preinfected maize plants.", "output": "U . maydis." }, { "input": "This set - up enabled quantification of VIGS and its impact on U. maydis infection using a quantitative real - time PCR ( qRT - PCR ) - based readout.", "output": "U . maydis." }, { "input": "In proof - of - principle experiments, an U. maydis - induced terpene synthase was shown to negatively regulate disease development while a protein involved in cell death inhibition was required for full virulence of U. maydis.", "output": "U . maydis." }, { "input": "The results suggest that this system is a versatile tool for the rapid identification of maize genes that determine compatibility with U. maydis.", "output": "maize, U . maydis." }, { "input": "The second face of a known player: Arabidopsis silencing suppressor AtXRN4 acts organ - specifically.", "output": "Arabidopsis." }, { "input": "Plant viruses exploit the symplastic transport pathway provided by plasmodesmata by encoding for specialized movement proteins, which interact with host factors to enable viral intracellular and intercellular spread.", "output": "There is no related enetity." }, { "input": "Stable expression of the Potato leaf roll virus movement protein MP17 in Arabidopsis results in a carbohydrate export block and stunted growth.", "output": "Potato leaf roll virus, Arabidopsis." }, { "input": "To identify host factors essential for viral infection, we screened a progeny population of EMS ( ethyl methanesulfonate ) - mutagenized Arabidopsis expressing a MP17: GFP fusion for suppressor mutants with restored wild type - like phenotype.", "output": "Arabidopsis." }, { "input": "Two suppressor mutants showed decreased susceptibility against Turnip mosaic virus and post - transcriptional silencing of MP17: GFP RNA in source leaves.", "output": "Turnip mosaic virus." }, { "input": "Map based cloning identified in both lines mutations in XRN4 ( Exoribonuclease 4 ), which was previously described as a suppressor of transgene silencing in source leaves.", "output": "There is no related enetity." }, { "input": "Importantly, silencing of MP17: GFP was not present in cotyledons and roots of the two suppressor mutants, which was confirmed in a third xrn4 T - DNA knock out line.", "output": "There is no related enetity." }, { "input": "Subsequent analysis of MP17: GFP transcript stability in xrn2 and xrn3 mutants indicated an essential role of AtXRN2 for silencing suppression in roots / cotyledons while AtXRN3 appears to act similar to AtXRN4 in source leaves, only.", "output": "There is no related enetity." }, { "input": "Overall, these findings point towards an organ - specific regulation of gene silencing in Arabidopsis.", "output": "Arabidopsis." }, { "input": "Haplotype analysis of the genes encoding glutamine synthetase plastic isoforms and their association with nitrogen - use - and yield - related traits in bread wheat.", "output": "bread wheat." }, { "input": "Glutamine synthetase ( GS ) plays a key role in the growth, nitrogen ( N ) use and yield potential of cereal crops.", "output": "There is no related enetity." }, { "input": "Investigating the haplotype variation of GS genes and its association with agronomic traits may provide useful information for improving wheat N - use efficiency and yield.", "output": "wheat." }, { "input": "We isolated the promoter and coding region sequences of the plastic glutamine synthetase isoform ( GS2 ) genes located on chromosomes 2A, 2B and 2D in bread wheat.", "output": "bread wheat." }, { "input": "By analyzing nucleotide sequence variations of the coding region, two, six and two haplotypes were distinguished for TaGS2 - A1 ( a and b ), TaGS2 - B1 ( a - f ) and TaGS2 - D1 ( a and b ), respectively.", "output": "There is no related enetity." }, { "input": "By analyzing the frequency data of different haplotypes and their association with N use and agronomic traits, four major and favorable TaGS2 haplotypes ( A1b, B1a, B1b, D1a ) were revealed.", "output": "There is no related enetity." }, { "input": "These favorable haplotypes may confer better seedling growth, better agronomic performance, and improved N uptake during vegetative growth or grain N concentration.", "output": "There is no related enetity." }, { "input": "Our data suggest that certain TaGS2 haplotypes may be valuable in breeding wheat varieties with improved agronomic performance and N - use efficiency.", "output": "wheat." }, { "input": "The molecular basis for venation patterning of pigmentation and its effect on pollinator attraction in flowers of Antirrhinum.", "output": "There is no related enetity." }, { "input": "Pigment stripes associated with veins ( venation ) is a common flower colour pattern.", "output": "There is no related enetity." }, { "input": "The molecular genetics and function of venation were investigated in the genus Antirrhinum, in which venation is determined by Venosa ( encoding an R2R3MYB transcription factor ).", "output": "There is no related enetity." }, { "input": "Pollinator preferences were measured by field tests with Antirrhinum majus.", "output": "There is no related enetity." }, { "input": "Venosa function was examined using in situ hybridization and transient overexpression.", "output": "There is no related enetity." }, { "input": "The origin of the venation trait was examined by molecular phylogenetics.", "output": "There is no related enetity." }, { "input": "Venation and full - red flower colouration provide a comparable level of advantage for pollinator attraction relative to palely pigmented or white lines.", "output": "There is no related enetity." }, { "input": "Ectopic expression of Venosa confers pigmentation outside the veins.", "output": "There is no related enetity." }, { "input": "Venosa transcript is produced only in small areas of the corolla between the veins and the adaxial epidermis.", "output": "There is no related enetity." }, { "input": "Phylogenetic analyses suggest that venation patterning is an ancestral trait in Antirrhinum.", "output": "There is no related enetity." }, { "input": "Different accessions of three species with full - red pigmentation with or without venation patterning have been found.", "output": "There is no related enetity." }, { "input": "Epidermal - specific venation is defined through overlapping expression domains of the MYB ( myoblastoma ) and bHLH ( basic Helix - Loop - Helix ) co - regulators of anthocyanin biosynthesis, with the bHLH providing epidermal specificity and Venosa vein specificity.", "output": "There is no related enetity." }, { "input": "Venation may be the ancestral trait, with full - red pigmentation a derived, polyphyletic trait.", "output": "There is no related enetity." }, { "input": "Venation patterning is probably not fixed once species evolve full - red floral pigmentation.", "output": "There is no related enetity." }, { "input": "High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane.", "output": "sugarcane." }, { "input": "Modern sugarcane ( Saccharum spp. ) is the leading sugar crop and a primary energy crop.", "output": "sugarcane, Saccharum spp .." }, { "input": "It has the highest level of ' vertical ' redundancy ( 2n = 12x = 120 ) of all polyploid plants studied to date.", "output": "There is no related enetity." }, { "input": "It was produced about a century ago through hybridization between two autopolyploid species, namely S. officinarum and S. spontaneum.", "output": "S . officinarum, S . spontaneum." }, { "input": "In order to investigate the genome dynamics in this highly polyploid context, we sequenced and compared seven hom ( oe ) ologous haplotypes ( bacterial artificial chromosome clones ).", "output": "There is no related enetity." }, { "input": "Our analysis revealed a high level of gene retention and colinearity, as well as high gene structure and sequence conservation, with an average sequence divergence of 4 % for exons.", "output": "There is no related enetity." }, { "input": "Remarkably, all of the hom ( oe ) ologous genes were predicted as being functional ( except for one gene fragment ) and showed signs of evolving under purifying selection, with the exception of genes within segmental duplications.", "output": "There is no related enetity." }, { "input": "By contrast, transposable elements displayed a general absence of colinearity among hom ( oe ) ologous haplotypes and appeared to have undergone dynamic expansion in Saccharum, compared with sorghum, its close relative in the Andropogonea tribe.", "output": "There is no related enetity." }, { "input": "These results reinforce the general trend emerging from recent studies indicating the diverse and nuanced effect of polyploidy on genome dynamics.", "output": "There is no related enetity." }, { "input": "Aerenchyma formation in the rice stem and its promotion by H2O2.", "output": "rice." }, { "input": "* Gas spaces ( aerenchyma ) form as an adaptation to submergence to facilitate gas exchange.", "output": "There is no related enetity." }, { "input": "In rice ( Oryza sativa ), aerenchyma develop by cell death and lysis, which are poorly understood at the cellular level.", "output": "rice, Oryza sativa." }, { "input": "* Aerenchyma formation was studied in rice stems by light microscopy.", "output": "rice." }, { "input": "It was analyzed in response to submergence, ethylene and hydrogen peroxide ( H ( 2 ) O ( 2 ) ) treatment, and in the MT2b:: Tos17 mutant.", "output": "There is no related enetity." }, { "input": "O ( 2 ) * ( - ) was detected with nitroblue tetrazolium and an epinephrine assay.", "output": "There is no related enetity." }, { "input": "H ( 2 ) O ( 2 ) was detected with 3, 3 ' - diaminobenzidine.", "output": "There is no related enetity." }, { "input": "* Aerenchyma develop constitutively in all internodes of the deep - water rice variety Pin Gaew 56, but are absent from the nodes.", "output": "rice." }, { "input": "Constitutive aerenchyma formation was also observed in two lowland rice varieties, albeit to a lesser degree.", "output": "rice." }, { "input": "A larger number of aerenchyma are present in older internodes, and at the top of each internode, revealing developmental gradients.", "output": "There is no related enetity." }, { "input": "Submergence or treatment with the ethylene - releasing compound ethephon promoted aerenchyma formation in all genotypes analyzed.", "output": "There is no related enetity." }, { "input": "Pre - aerenchymal cells contain less starch, no chloroplasts, thinner cell walls and produce elevated levels of O ( 2 ) * ( - ) and H ( 2 ) O ( 2 ) compared with other parenchymal cells.", "output": "There is no related enetity." }, { "input": "Ethephon promotes O ( 2 ) * ( - ) formation and H ( 2 ) O ( 2 ) promotes aerenchyma formation in a dose - dependent manner.", "output": "There is no related enetity." }, { "input": "Further - more, genetic downregulation of the H ( 2 ) O ( 2 ) scavenger MT2b enhances aerenchyma formation.", "output": "There is no related enetity." }, { "input": "* Aerenchyma formation is mediated by reactive oxygen species.", "output": "There is no related enetity." }, { "input": "Nitric oxide participates in cold - responsive phosphosphingolipid formation and gene expression in Arabidopsis thaliana.", "output": "Arabidopsis thaliana." }, { "input": "Chilling triggers rapid molecular responses that permit the maintenance of plant cell homeostasis and plant adaptation.", "output": "There is no related enetity." }, { "input": "Recent data showed that nitric oxide ( NO ) is involved in plant acclimation and tolerance to cold.", "output": "There is no related enetity." }, { "input": "The participation of NO in the early transduction of the cold signal in Arabidopsis thaliana was investigated.", "output": "Arabidopsis thaliana." }, { "input": "The production of NO after a short exposure to cold was assessed using the NO - sensitive fluorescent probe 4, 5 - diamino fluoresceine diacetate and chemiluminescence.", "output": "There is no related enetity." }, { "input": "Pharmacological and genetic approaches were used to analyze NO sources and NO - mediated changes in cold - regulated gene expression, phosphatidic acid ( PtdOH ) synthesis and sphingolipid phosphorylation.", "output": "There is no related enetity." }, { "input": "NO production was detected after 1 - 4h of chilling.", "output": "There is no related enetity." }, { "input": "It was impaired in the nia1nia2 nitrate reductase mutant.", "output": "There is no related enetity." }, { "input": "Moreover, NO accumulation was not observed in H7 plants overexpressing the A. thaliana nonsymbiotic hemoglobin Arabidopsis haemoglobin 1 ( AHb1 ).", "output": "A . thaliana." }, { "input": "Cold - regulated gene expression was affected in nia1nia2 and H7 plants.", "output": "There is no related enetity." }, { "input": "The synthesis of PtdOH upon chilling was not modified by NO depletion.", "output": "There is no related enetity." }, { "input": "By contrast, the formation of phytosphingosine phosphate and ceramide phosphate, two phosphorylated sphingolipids that are transiently synthesized upon chilling, was negatively regulated by NO.", "output": "There is no related enetity." }, { "input": "Taken together, these data suggest a new function for NO as an intermediate in gene regulation and lipid - based signaling during cold transduction.", "output": "There is no related enetity." }, { "input": "Identification of a novel mitochondrial protein, short postembryonic roots 1 ( SPR1 ), involved in root development and iron homeostasis in Oryza sativa.", "output": "Oryza sativa." }, { "input": "* A rice mutant, Oryza sativa short postembryonic roots 1 ( Osspr1 ), has been characterized.", "output": "rice, Oryza sativa short postembryonic roots 1, Osspr1." }, { "input": "It has short postembryonic roots, including adventitious and lateral roots, and a lower iron content in its leaves.", "output": "There is no related enetity." }, { "input": "* OsSPR1 was identified by map - based cloning.", "output": "OsSPR1." }, { "input": "It encodes a novel mitochondrial protein with the Armadillo - like repeat domain.", "output": "There is no related enetity." }, { "input": "* Osspr1 mutants exhibited decreased root cell elongation.", "output": "There is no related enetity." }, { "input": "The iron content of the mutant shoots was significantly altered compared with that of wild - type shoots.", "output": "There is no related enetity." }, { "input": "A similar pattern of alteration of manganese and zinc concentrations in shoots was also observed.", "output": "There is no related enetity." }, { "input": "Complementation of the mutant confirmed that OsSPR1 is involved in post - embryonic root elongation and iron homeostasis in rice.", "output": "OsSPR1." }, { "input": "OsSPR1 was found to be ubiquitously expressed in various tissues throughout the plant.", "output": "OsSPR1." }, { "input": "The transcript abundance of various genes involved in iron uptake and signaling via both strategies I and II was similar in roots of wild - type and mutant plants, but was higher in the leaves of mutant plants.", "output": "There is no related enetity." }, { "input": "* Thus, a novel mitochondrial protein that is involved in root elongation and plays a role in metal ion homeostasis has been identified.", "output": "There is no related enetity." }, { "input": "Genomic profiling of carbohydrate metabolism in the ectomycorrhizal fungus Tuber melanosporum.", "output": "Tuber melanosporum." }, { "input": "* Primary carbohydrate metabolism plays a special role related to carbon / nitrogen exchange, as well as metabolic support of fruiting body development, in ectomycorrhizal macrofungi.", "output": "There is no related enetity." }, { "input": "In this study, we used information retrieved from the recently sequenced Tuber melanosporum genome, together with transcriptome analysis data and targeted validation experiments, to construct the first genome - wide catalogue of the proteins supporting carbohydrate metabolism in a plant - symbiotic ascomycete.", "output": "Tuber melanosporum." }, { "input": "* More than 100 genes coding for enzymes of the glycolysis, pentose phosphate, tricarboxylic acid, glyoxylate and methylcitrate pathways, glycogen, trehalose and mannitol metabolism and cell wall precursor were annotated.", "output": "There is no related enetity." }, { "input": "Transcriptional regulation of these pathways in different stages of the T. melanosporum lifecycle was investigated using whole - genome oligoarray expression data together with real - time reverse transcription - polymerase chain reaction analysis of selected genes.", "output": "T . melanosporum." }, { "input": "* The most significant results were the identification of methylcitrate cycle genes and of an acid invertase, the first enzyme of this kind to be described in a plant - symbiotic filamentous fungus.", "output": "There is no related enetity." }, { "input": "* A subset of transcripts coding for trehalose, glyoxylate and methylcitrate enzymes was up - regulated in fruiting bodies, whereas genes involved in mannitol and glycogen metabolism were preferentially expressed in mycelia and ectomycorrhizas, respectively.", "output": "There is no related enetity." }, { "input": "These data indicate a high degree of lifecycle stage specialization for particular branches of carbohydrate metabolism in T. melanosporum.", "output": "T . melanosporum." }, { "input": "An analytical model of non - photorespiratory CO2release in the light and dark in leaves of C3species based on stoichiometric flux balance.", "output": "There is no related enetity." }, { "input": "Leaf respiration continues in the light but at a reduced rate.", "output": "There is no related enetity." }, { "input": "This inhibition is highly variable, and the mechanisms are poorly known, partly due to the lack of a formal model that can generate testable hypotheses.", "output": "There is no related enetity." }, { "input": "We derived an analytical model for non - photorespiratory CO2 release by solving steady - state supply / demand equations for ATP, NADH and NADPH, coupled to a widely used photosynthesis model.", "output": "There is no related enetity." }, { "input": "We used this model to evaluate causes for suppression of respiration by light.", "output": "There is no related enetity." }, { "input": "The model agrees with many observations, including highly variable suppression at saturating light, greater suppression in mature leaves, reduced assimilatory quotient ( ratio of net CO2 and O2 exchange ) concurrent with nitrate reduction and a Kok effect ( discrete change in quantum yield at low light ).", "output": "There is no related enetity." }, { "input": "The model predicts engagement of non - phosphorylating pathways at moderate to high light, or concurrent with processes that yield ATP and NADH, such as fatty acid or terpenoid synthesis.", "output": "There is no related enetity." }, { "input": "Suppression of respiration is governed largely by photosynthetic adenylate balance, although photorespiratory NADH may contribute at sub - saturating light.", "output": "There is no related enetity." }, { "input": "Key questions include the precise diel variation of anabolism and the ATP: 2e - ratio for photophosphorylation.", "output": "There is no related enetity." }, { "input": "Our model can focus experimental research and is a step towards a fully process - based model of CO2 exchange.", "output": "There is no related enetity." }, { "input": "Complement opsonization enhances friend virus infection of B cells and thereby amplifies the virus - specific CD8 + T cell response.", "output": "There is no related enetity." }, { "input": "B cells are one of the targets of Friend virus ( FV ) infection, a well - established mouse model often used to study retroviral infections in vivo.", "output": "retroviral." }, { "input": "Although B cells may be effective in stimulating cytotoxic T lymphocyte responses, studies involving their role in FV infection have mainly focused on neutralizing antibody production.", "output": "There is no related enetity." }, { "input": "Here we show that polyclonal activation of B cells promotes their infection with FV both in vitro and in vivo.", "output": "There is no related enetity." }, { "input": "Furthermore, we demonstrate that complement opsonization of Friend murine leukemia virus ( F - MuLV ) enhances infection of B cells, which correlates with increased potency of B cells to activate FV - specific CD8 ( + ) T cells.", "output": "murine leukemia virus ( F - MuLV )." }, { "input": "Genetic analysis of B55alpha / Cdc55 protein phosphatase 2A subunits: association with the adenovirus E4orf4 protein.", "output": "There is no related enetity." }, { "input": "The human adenovirus E4orf4 protein is toxic in both human tumor cells and Saccharomyces cerevisiae.", "output": "human, human, Saccharomyces cerevisiae." }, { "input": "Previous studies indicated that most of this toxicity is dependent on an interaction of E4orf4 protein with the B55 class of regulatory subunits of protein phosphatase 2A ( PP2A ) and in yeast with the B55 homolog Cdc55.", "output": "yeast." }, { "input": "We have found previously that E4orf4 inhibits PP2A activity against at least some substrates.", "output": "There is no related enetity." }, { "input": "In an attempt to understand the mechanism of this inhibition, we used a genetic approach to identify residues in the seven - bladed Beta - propeller proteins B55alpha and Cdc55 required for E4orf4 binding.", "output": "There is no related enetity." }, { "input": "In both cases, amino - terminal polypeptides composed only of blade 1 and at least part of blade 2 were found to bind E4orf4 and overexpression blocked E4orf4 toxicity in yeast.", "output": "yeast." }, { "input": "Furthermore, certain amino acid substitutions in blades 1 and 2 within full - length B55alpha and Cdc55 resulted in loss of E4orf4 binding.", "output": "There is no related enetity." }, { "input": "Recent mutational analysis has suggested that segments of blades 1 and 2 present on the top face of B55alpha form part of the & quot; substrate - binding groove. & quot; Additionally, these segments are in close proximity to the catalytic C subunit of the PP2A holoenzyme.", "output": "There is no related enetity." }, { "input": "Thus, our results are consistent with the hypothesis that E4orf4 binding could affect the access of substrates, resulting in the failure to dephosphorylate some PP2A substrates.", "output": "There is no related enetity." }, { "input": "Stepwise loss of fluorescent core protein V from human adenovirus during entry into cells.", "output": "human adenovirus." }, { "input": "Human adenoviruses ( Ads ) replicate and assemble particles in the nucleus.", "output": "Human adenoviruses ( Ads )." }, { "input": "They organize a linear double - strand DNA genome into a condensed core with about 180 nucleosomes, by the viral proteins VII ( pVII ), pX, and pV attaching the DNA to the capsid.", "output": "There is no related enetity." }, { "input": "Using reverse genetics, we generated a novel, nonconditionally replicating Ad reporter by inserting green fluorescent protein ( GFP ) at the amino terminus of pV.", "output": "There is no related enetity." }, { "input": "Purified Ad2 - GFP - pV virions had an oversized complete genome and incorporated about 38 GFP - pV molecules per virion, which is about 25 % of the pV levels in Ad2.", "output": "There is no related enetity." }, { "input": "GFP - pV cofractionated with the DNA core, like pV, and newly synthesized GFP - pV had a subcellular localization indistinguishable from that of pV, indicating that GFP - pV is a valid reporter for pV.", "output": "There is no related enetity." }, { "input": "Ad2 - GFP - pV completed the replication cycle, although at lower yields than Ad2.", "output": "There is no related enetity." }, { "input": "Incoming GFP - pV ( or pV ) was not imported into the nucleus.", "output": "There is no related enetity." }, { "input": "Virions lost GFP - pV at two points during the infection process: at entry into the cytosol and at the nuclear pore complex, where capsids disassemble.", "output": "There is no related enetity." }, { "input": "Disassembled capsids, positive for the conformation - specific antihexon antibody R70, were devoid of GFP - pV.", "output": "There is no related enetity." }, { "input": "The loss of GFP - pV was reduced by the macrolide antibiotic leptomycin B ( LMB ), which blocks nuclear export and adenovirus attachment to the nuclear pore complex.", "output": "adenovirus." }, { "input": "LMB inhibited the appearance of R70 epitopes on Ad2 and Ad2 - GFP - pV, indicating that the loss of GFP - pV from Ad2 - GFP - pV is an authentic step in the adenovirus uncoating program.", "output": "adenovirus." }, { "input": "Ad2 - GFP - pV is genetically complete and hence enables detailed analyses of infection and spreading dynamics in cells and model organisms or assessment of oncolytic adenoviral potential.", "output": "adenoviral." }, { "input": "The spatial scaling of habitat selection by African elephants.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Understanding and accurately predicting the spatial patterns of habitat use by organisms is important for ecological research, biodiversity conservation and ecosystem management.", "output": "There is no related enetity." }, { "input": "However, this understanding is complicated by the effects of spatial scale, because the scale of analysis affects the quantification of species - environment relationships.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We therefore assessed the influence of environmental context ( i. e. the characteristics of the landscape surrounding a site ), varied over a large range of scales ( i. e. ambit radii around focal sites ), on the analysis and prediction of habitat selection by African elephants in Kruger National Park, South Africa.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We focused on the spatial scaling of the elephants ' response to their main resources, forage and water, and found that the quantification of habitat selection strongly depended on the scales at which environmental context was considered.", "output": "There is no related enetity." }, { "input": "Moreover, the inclusion of environmental context at characteristic scales ( i. e. those at which habitat selectivity was maximized ) increased the predictive capacity of habitat suitability models.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "The elephants responded to their environment in a scale - dependent and perhaps hierarchical manner, with forage characteristics driving habitat selection at coarse spatial scales, and surface water at fine spatial scales.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Furthermore, the elephants exhibited sexual habitat segregation, mainly in relation to vegetation characteristics.", "output": "There is no related enetity." }, { "input": "Male elephants preferred areas with high tree cover and low herbaceous biomass, whereas this pattern was reversed for female elephants.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "We show that the spatial distribution of elephants can be better understood and predicted when scale - dependent species - environment relationships are explicitly considered.", "output": "There is no related enetity." }, { "input": "This demonstrates the importance of considering the influence of spatial scale on the analysis of spatial patterning in ecological phenomena.", "output": "There is no related enetity." }, { "input": "Is hunting mortality additive or compensatory to natural mortality?", "output": "There is no related enetity." }, { "input": "Effects of experimental harvest on the survival and cause - specific mortality of willow ptarmigan.", "output": "willow ptarmigan." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "The effects of harvest on the annual and seasonal survival of willow ptarmigan Lagopus lagopus L. were tested in a large - scale harvest experiment.", "output": "willow ptarmigan, Lagopus lagopus." }, { "input": "Management units were randomly assigned to one of three experimental treatments: 0 %, 15 % or 30 % harvest.", "output": "There is no related enetity." }, { "input": "Seasonal quotas were based on the experimental treatment and estimates of bird density before the hunting season.", "output": "There is no related enetity." }, { "input": "Survival rates and hazard functions for radio - marked ptarmigan were then estimated under the competing risks of harvest and natural mortality.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "The partially compensatory mortality hypothesis was supported: annual survival of ptarmigan was 0 * 54 + / - 0 * 08 SE under 0 % harvest, 0 * 47 + / - 0 * 06 under 15 % harvest, and was reduced to 0 * 30 + / - 0 * 05 under 30 % harvest.", "output": "There is no related enetity." }, { "input": "Harvest mortality increased linearly from 0 * 08 + / - 0 * 05, 0 * 27 + / - 0 * 05 and 0 * 42 + / - 0 * 06 from 0 % to 30 % harvest, whereas natural mortality was 0 * 38 + / - 0 * 08, 0 * 25 + / - 0 * 05 and 0 * 28 + / - 0 * 06 under the same treatments.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Realized risk of harvest mortality was 0 * 08 - 0 * 12 points higher than our set harvest treatments of 0 - 30 % because birds were exposed to risk if they moved out of protected areas.", "output": "There is no related enetity." }, { "input": "The superadditive hypothesis was supported because birds in the 30 % harvest treatment had higher natural mortality during winter after the hunting season.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Natural mortality was mainly because of raptor predation, with two seasonal peaks in fall and spring.", "output": "There is no related enetity." }, { "input": "Natural and harvest mortality coincided during early autumn with little potential for compensation during winter months.", "output": "There is no related enetity." }, { "input": "Peak risk of harvest mortality was 5x higher than natural mortality.", "output": "There is no related enetity." }, { "input": "Low natural mortality during winter suggests that most late season harvest would be additive mortality.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Environmental correlates of natural mortality of ptarmigan included seasonal changes in snow cover, onset of juvenile dispersal, and periods of territorial activity.", "output": "There is no related enetity." }, { "input": "Natural mortality of ptarmigan was highest during autumn movements and nesting by gyrfalcons Falco rusticolus L.", "output": "gyrfalcons, Falco rusticolus." }, { "input": "Mortality was low when gyrfalcons had departed for coastal wintering sites, and during summer when ptarmigan were attending nests and broods.", "output": "gyrfalcons." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "Our experimental results have important implications for harvest management of upland gamebirds.", "output": "There is no related enetity." }, { "input": "Seasonal quotas based on proportional harvest were effective and should be set at = < 15 % of August populations for regional management plans.", "output": "There is no related enetity." }, { "input": "Under threshold harvest of a reproductive surplus, 15 % harvest would be sustainable at productivity rates > = 2 * 5 young per pair.", "output": "There is no related enetity." }, { "input": "Impacts of winter harvest could be minimized by closing the hunting season in early November or by reducing late season quotas.", "output": "There is no related enetity." }, { "input": "Possible contributions of TERMINAL FLOWER 1 to the evolution of rosette flowering in Leavenworthia ( Brassicaceae ).", "output": "There is no related enetity." }, { "input": "Leavenworthia crassa is a rosette flowering species that differs from inflorescence flowering species, such as Arabidopsis thaliana, in having elongated pedicels and shortened interfloral internodes on the main axis.", "output": "Leavenworthia crassa, Arabidopsis thaliana." }, { "input": "Based on previous experiments, we hypothesized that changes to the L. crassa TFL1 ortholog, LcrTFL1, were important in the evolution of rosette flowering.", "output": "There is no related enetity." }, { "input": "We isolated LcrTFL1 and introduced a genomic construct into tfl1 mutant A. thaliana plants.", "output": "A . thaliana." }, { "input": "We also generated and analyzed EGFP - LcrTFL1 reporter - fusion lines, and LcrTFL1 / LcrLFY doubly transgenic lines.", "output": "There is no related enetity." }, { "input": "The transgene rescued the mutant defects, but manifested gain - of - function phenotypes.", "output": "There is no related enetity." }, { "input": "However, LcrTFL1 lines differed from 35S: TFL1 lines in several regards.", "output": "There is no related enetity." }, { "input": "Defects in floral meristem identity establishment were observed, as was the production of flowers with extra petals.", "output": "There is no related enetity." }, { "input": "We also noted features that resemble rosette flowering: LcrTFL1 lines produced significantly shorter interfloral internodes and significantly longer pedicels than either wild - type or 35S: TFL1 plants.", "output": "There is no related enetity." }, { "input": "Our data show that there are substantive differences in the regulation and / or function of TFL1 orthologs between A. thaliana and L. crassa.", "output": "A . thaliana, L . crassa." }, { "input": "These may reflect changes that occurred during the evolution of rosette flowering in Leavenworthia, but, if so, our results show that additional, as - yet - unidentified genes were involved in this instance of architectural evolution.", "output": "There is no related enetity." }, { "input": "Gene expression changes during short day induced terminal bud formation in Norway spruce.", "output": "Norway spruce." }, { "input": "The molecular basis for terminal bud formation in autumn is not well understood in conifers.", "output": "There is no related enetity." }, { "input": "By combining suppression subtractive hybridization and monitoring of gene expression by qRT - PCR analysis, we aimed to identify genes involved in photoperiodic control of growth cessation and bud set in Norway spruce.", "output": "Norway spruce." }, { "input": "Close to 1400 ESTs were generated and their functional distribution differed between short day ( SD - 12 h photoperiod ) and long day ( LD - 24 h photoperiod ) libraries.", "output": "There is no related enetity." }, { "input": "Many genes with putative roles in protection against stress appeared differentially regulated under SD and LD, and also differed in transcript levels between 6 and 20 SDs.", "output": "There is no related enetity." }, { "input": "Of these, PaTFL1 ( TERMINAL FLOWER LIKE 1 ) showed strongly increased transcript levels at 6 SDs.", "output": "There is no related enetity." }, { "input": "PaCCCH ( CCCH - TYPE ZINC FINGER ) and PaCBF2 & amp; 3 ( C - REPEAT BINDING FACTOR 2 & amp; 3 ) showed a later response at 20 SDs, with increased and decreased transcript levels, respectively.", "output": "There is no related enetity." }, { "input": "For rhythmically expressed genes such as CBFs, such differences might represent a phase shift in peak expression, but might also suggest a putative role in response to SD.", "output": "There is no related enetity." }, { "input": "Multivariate analyses revealed strong differences in gene expression between LD, 6 SD and 20 SD.", "output": "There is no related enetity." }, { "input": "The robustness of the gene expression patterns was verified in 6 families differing in bud - set timing under natural light with gradually decreasing photoperiod.", "output": "There is no related enetity." }, { "input": "Role of nitric oxide in hydrogen peroxide - dependent induction of abiotic stress tolerance by brassinosteroids in cucumber.", "output": "cucumber." }, { "input": "Brassinosteroids ( BRs ) can induce plant tolerance to a variety of abiotic stresses by triggering the generation of H ( 2 ) O ( 2 ) as a signalling molecule in cucumber leaves.", "output": "cucumber." }, { "input": "Whether nitric oxide ( NO ) also plays a signalling role and, if so, what is the relationship between NO and H ( 2 ) O ( 2 ) in BR - induced stress tolerance are unknown.", "output": "There is no related enetity." }, { "input": "Involvement of NO and H ( 2 ) O ( 2 ) in BR - induced tolerance was examined.", "output": "There is no related enetity." }, { "input": "NO accumulation and defence related gene transcripts were monitored by confocal laser - scanning microscopy and qRT - PCR, respectively.", "output": "There is no related enetity." }, { "input": "NO content was elevated after treatment with 24 - epibrassinolide ( EBR ) and reduced with the inhibition of BR biosynthesis.", "output": "There is no related enetity." }, { "input": "EBR - induced NO production was blocked by pre - treatment with inhibitor of NADPH oxidase and a reactive oxygen species scavenger.", "output": "There is no related enetity." }, { "input": "On the other hand, EBR - induced H ( 2 ) O ( 2 ) generation was not sensitive to NO scavenger or inhibitor of NO production.", "output": "There is no related enetity." }, { "input": "Scavenging or inhibition of NO production inhibited EBR - induced tolerance to photo - oxidative and cold stress and partly blocked EBR - induced expression and activities of several antioxidant enzymes.", "output": "There is no related enetity." }, { "input": "Pre - treatment of the exogenous NO precursor, on the other hand, led to both increased stress tolerance and increased expression of antioxidant enzymes.", "output": "There is no related enetity." }, { "input": "These results strongly suggest that NO plays an important role in H ( 2 ) O ( 2 ) - dependent induction of plant stress tolerance by BR.", "output": "There is no related enetity." }, { "input": "The Arabidopsis tt19 - 4 mutant differentially accumulates proanthocyanidin and anthocyanin through a 3 ' amino acid substitution in glutathione S - transferase.", "output": "There is no related enetity." }, { "input": "The Arabidopsis transparent testa ( tt ) mutant tt19 - 4 shows reduced seed coat colour, but stains darkly with DMACA and accumulates anthocyanins in aerial tissues.", "output": "There is no related enetity." }, { "input": "Positional cloning showed that tt19 - 4 was allelic to tt19 - 1 and has a G - to - T mutation in a conserved 3 ' - domain in the TT19 - 4 gene.", "output": "There is no related enetity." }, { "input": "Soluble and unextractable seed proanthocyanidins and hydrolysis of unextractable proanthocyanidin differ between wild - type Col - 4 and both mutants.", "output": "There is no related enetity." }, { "input": "However, seed quercetins, unextractable proanthocyanidin hydrolysis, and seedling anthocyanin content, and flavonoid gene expression differ between tt19 - 1 and tt19 - 4.", "output": "There is no related enetity." }, { "input": "Transformation of tt19 - 1 with a TT19 - 4 cDNA results in vegetative anthocyanins, whereas TT19 - 4 cDNA cannot complement the proanthocyanidin and pale seed coat phenotype of tt19 - 1.", "output": "There is no related enetity." }, { "input": "Both recombinant TT19 and TT19 - 4 enzymes are functional GSTs and are localized in the cytosol, but TT19 did not function with wide range of flavonoids and natural products to produce conjugation products.", "output": "There is no related enetity." }, { "input": "We suggest that the dark seed coat of Arabidopsis is related to soluble proanthocyanidin content and that quercetin holds the key to the function of TT19.", "output": "There is no related enetity." }, { "input": "In addition, TT19 appears to have a 5 ' GSH - binding domain influencing both anthocyanin and proanthocyanidin accumulation and a 3 ' domain affecting proanthocyanidin accumulation by a single amino acid substitution.", "output": "There is no related enetity." }, { "input": "Insights into membrane association of Klebsiella pneumoniae NifL under nitrogen - fixing conditions from mutational analysis.", "output": "Klebsiella pneumoniae." }, { "input": "In Klebsiella pneumoniae nitrogen fixation is tightly controlled in response to ammonium and molecular oxygen by the NifL / NifA regulatory system.", "output": "Klebsiella pneumoniae." }, { "input": "Under repressing conditions, NifL inhibits the nif - specific transcriptional activator NifA by direct protein - protein interaction, whereas under anaerobic and nitrogen - limited conditions sequestration of reduced NifL to the cytoplasmic membrane impairs inhibition of cytoplasmic NifA by NifL.", "output": "There is no related enetity." }, { "input": "We report here on a genetic screen to identify amino acids of NifL essential for sequestration to the cytoplasmic membrane under nitrogen - fixing conditions.", "output": "There is no related enetity." }, { "input": "Overall, 11, 500 mutated nifL genes of three independently generated pools were screened for those conferring a Nif ( - ) phenotype.", "output": "There is no related enetity." }, { "input": "Based on the respective amino acid changes of nonfunctional derivatives obtained in the screen, and taking structural data into account as well, several point mutations were introduced into nifL by site - directed mutagenesis.", "output": "There is no related enetity." }, { "input": "The majority of amino acid changes resulting in a significant nif gene inhibition were located in the N - terminal domain ( N46D, Q57L, Q64R, N67S, N69S, R80C, and W87G ) and the Q - linker ( K271E ).", "output": "There is no related enetity." }, { "input": "Further analyses demonstrated that positions N69, R80, and W87 are essential for binding the FAD cofactor, whereas primarily Q64 and N46, but also Q57 and N67, appear to be crucial for direct membrane contact of NifL under oxygen and nitrogen limitation.", "output": "There is no related enetity." }, { "input": "Based on these findings, we propose that those four amino acids most likely located on the protein surface, as well as the presence of the FAD cofactor, are crucial for the correct overall protein conformation and respective surface charge, allowing NifL sequestration to the cytoplasmic membrane under derepressing conditions.", "output": "There is no related enetity." }, { "input": "Complex regulation of symbiotic functions is coordinated by MucR and quorum sensing in Sinorhizobium meliloti.", "output": "There is no related enetity." }, { "input": "In Sinorhizobium meliloti, the production of exopolysaccharides such as succinoglycan and exopolysaccharide II ( EPS II ) enables the bacterium to invade root nodules on Medicago sativa and establish a nitrogen - fixing symbiosis.", "output": "Medicago sativa." }, { "input": "While extensive research has focused on succinoglycan, less is known concerning the regulation of EPS II or the mechanism by which it mediates entrance into the host plant.", "output": "There is no related enetity." }, { "input": "Previously, we reported that the ExpR / Sin quorum - sensing system is required to produce the symbiotically active low - molecular - weight fraction of this exopolysaccharide.", "output": "There is no related enetity." }, { "input": "Here, we show that this system induces EPS II production by increasing expression of the expG - expC operon, encoding both a transcriptional regulator ( ExpG ) and a glycosyl transferase ( ExpC ).", "output": "There is no related enetity." }, { "input": "ExpG derepresses EPS II production at the transcriptional level from MucR, a RosR homolog, while concurrently elevating expression of expC, resulting in the synthesis of the low - molecular - weight form.", "output": "There is no related enetity." }, { "input": "While the ExpR / Sin system abolishes the role of MucR on EPS II production, it preserves a multitude of other quorum - sensing - independent regulatory functions which promote the establishment of symbiosis.", "output": "There is no related enetity." }, { "input": "In planktonic S. meliloti, MucR properly coordinates a diverse set of bacterial behaviors by repressing a variety of genes intended for expression during symbiosis and enhancing the bacterial ability to induce root nodule formation.", "output": "There is no related enetity." }, { "input": "Quorum sensing precisely modulates the functions of MucR to take advantage of both the production of symbiotically active EPS II as well as the proper coordination of bacterial behavior required to promote symbiosis.", "output": "There is no related enetity." }, { "input": "Biochemical characterization of UDP - Gal: GlcNAc - pyrophosphate - lipid Beta - 1, 4 - Galactosyltransferase WfeD, a new enzyme from Shigella boydii type 14 that catalyzes the second step in O - antigen repeating - unit synthesis.", "output": "Shigella boydii." }, { "input": "The O antigen is the outer part of the lipopolysaccharide ( LPS ) in the outer membrane of Gram - negative bacteria and contains many repeats of an oligosaccharide unit.", "output": "There is no related enetity." }, { "input": "It contributes to antigenic variability and is essential to the full function and virulence of bacteria.", "output": "There is no related enetity." }, { "input": "Shigella is a Gram - negative human pathogen that causes diarrhea in humans.", "output": "human, humans." }, { "input": "The O antigen of Shigella boydii type 14 consists of repeating oligosaccharide units with the structure [ - > 6 - d - Galpalpha1 - > 4 - d - GlcpABeta1 - > 6 - d - GalpBeta1 - > 4 - d - GalpBeta1 - > 4 - d - GlcpNAcBeta1 - > ] n.", "output": "Shigella boydii." }, { "input": "The wfeD gene in the O - antigen gene cluster of Shigella boydii type 14 was proposed to encode a galactosyltransferase ( GalT ) involved in O - antigen synthesis.", "output": "Shigella boydii." }, { "input": "We confirmed here that the wfeD gene product is a Beta4 - GalT that synthesizes the GalBeta1 - 4GlcNAcalpha - R linkage.", "output": "There is no related enetity." }, { "input": "WfeD was expressed in Escherichia coli, and the activity was characterized by using UDP - [ ^ 3H ] Gal as the donor substrate as well as the synthetic acceptor substrate GlcNAcalpha - pyrophosphate - ( CH2 ) 11 - O - phenyl.", "output": "Escherichia coli." }, { "input": "The enzyme product was analyzed by liquid chromatography - mass spectrometry ( LC - MS ), high - performance liquid chromatography ( HPLC ), nuclear magnetic resonance ( NMR ), and galactosidase digestion.", "output": "There is no related enetity." }, { "input": "The enzyme was shown to be specific for the UDP - Gal donor substrate and required pyrophosphate in the acceptor substrate.", "output": "There is no related enetity." }, { "input": "Divalent metal ions such as Mn ^ 2 ( + ), Ni ^ 2 ( + ), and, surprisingly, also Pb ^ 2 ( + ) enhanced the enzyme activity.", "output": "There is no related enetity." }, { "input": "Mutational analysis showed that the Glu101 residue within a DxD motif is essential for activity, possibly by forming the catalytic nucleophile.", "output": "There is no related enetity." }, { "input": "The Lys211 residue was also shown to be required for activity and may be involved in the binding of the negatively charged acceptor substrate.", "output": "There is no related enetity." }, { "input": "Our study revealed that the Beta4 - GalT WfeD is a novel enzyme that has virtually no sequence similarity to mammalian Beta4 - GalT, although it catalyzes a similar reaction.", "output": "There is no related enetity." }, { "input": "Plasma membrane Ca ^ 2 + transporters mediate virus - induced acquired resistance to oxidative stress.", "output": "There is no related enetity." }, { "input": "This paper reports the phenomenon of acquired cross - tolerance to oxidative stress in plants and investigates the activity of specific Ca ^ 2 + transport systems mediating this phenomenon.", "output": "There is no related enetity." }, { "input": "Nicotiana benthamiana plants were infected with Potato virus X ( PVX ) and exposed to oxidative [ either ultraviolet ( UV - C ) or H2O2 ] stress.", "output": "Nicotiana benthamiana, Potato virus X, PVX." }, { "input": "Plant adaptive responses were assessed by the combined application of a range of electrophysiological ( non - invasive microelectrode ion flux measurements ), biochemical ( Ca ^ 2 + - and H + - ATPase activity ), imaging ( fluorescence lifetime imaging measurements of changes in intracellular Ca ^ 2 + concentrations ), pharmacological and cytological transmission electrone microscopy techniques.", "output": "There is no related enetity." }, { "input": "Virus - infected plants had a better ability to control UV - induced elevations in cytosolic - free Ca ^ 2 + and prevent structural and functional damage of chloroplasts.", "output": "There is no related enetity." }, { "input": "Taken together, our results suggest a high degree of crosstalk between UV and pathogen - induced oxidative stresses, and highlight the crucial role of Ca ^ 2 + efflux systems in acquired resistance to oxidative stress in plants.", "output": "There is no related enetity." }, { "input": "Involvement of extracellular oxidative burst in salicylic acid - induced stomatal closure in Arabidopsis.", "output": "Arabidopsis." }, { "input": "Salicylic acid ( SA ), a ubiquitous phenolic phytohormone, is involved in many plant physiological processes including stomatal movement.", "output": "There is no related enetity." }, { "input": "We analysed SA - induced stomatal closure, production of reactive oxygen species ( ROS ) and nitric oxide ( NO ), cytosolic calcium ion ( [ Ca ^ 2 + ] ( cyt ) ) oscillations and inward - rectifying potassium ( K + ( in ) ) channel activity in Arabidopsis.", "output": "Arabidopsis." }, { "input": "SA - induced stomatal closure was inhibited by pre - treatment with catalase ( CAT ) and superoxide dismutase ( SOD ), suggesting the involvement of extracellular ROS.", "output": "There is no related enetity." }, { "input": "A peroxidase inhibitor, SHAM ( salicylhydroxamic acid ) completely abolished SA - induced stomatal closure whereas neither an inhibitor of NADPH oxidase ( DPI ) nor atrbohD atrbohF mutation impairs SA - induced stomatal closures.", "output": "There is no related enetity." }, { "input": "3, 3 ' - Diaminobenzidine ( DAB ) and nitroblue tetrazolium ( NBT ) stainings demonstrated that SA induced H2O2 and O2 - production.", "output": "There is no related enetity." }, { "input": "Guard cell ROS accumulation was significantly increased by SA, but that ROS was suppressed by exogenous CAT, SOD and SHAM.", "output": "There is no related enetity." }, { "input": "NO scavenger 2 - ( 4 - carboxyphenyl ) - 4, 4, 5, 5 - tetramethylimidazoline - 1 - oxyl - 3 - oxide ( cPTIO ) suppressed the SA - induced stomatal closure but did not suppress guard cell ROS accumulation whereas SHAM suppressed SA - induced NO production.", "output": "There is no related enetity." }, { "input": "SA failed to induce [ Ca ^ 2 + ] ( cyt ) oscillations in guard cells whereas K + ( in ) channel activity was suppressed by SA.", "output": "There is no related enetity." }, { "input": "These results indicate that SA induces stomatal closure accompanied with extracellular ROS production mediated by SHAM - sensitive peroxidase, intracellular ROS accumulation and K + ( in ) channel inactivation.", "output": "There is no related enetity." }, { "input": "Effect of soil acidity, soil strength and macropores on root growth and morphology of perennial grass species differing in acid - soil resistance.", "output": "There is no related enetity." }, { "input": "It is unclear whether roots of acid - soil resistant plants have significant advantages, compared with acid - soil sensitive genotypes, when growing in high - strength, acid soils or in acid soils where macropores may allow the effects of soil acidity and strength to be avoided.", "output": "There is no related enetity." }, { "input": "The responses of root growth and morphology to soil acidity, soil strength and macropores by seedlings of five perennial grass genotypes differing in acid - soil resistance were determined, and the interaction of soil acidity and strength for growth and morphology of roots was investigated.", "output": "There is no related enetity." }, { "input": "Soil acidity and strength altered root length and architecture, root hair development, and deformed the root tip, especially in acid - soil sensitive genotypes.", "output": "There is no related enetity." }, { "input": "Root length was restricted to some extent by soil acidity in all genotypes, but the adverse impact of soil acidity on root growth by acid - soil resistant genotypes was greater at high levels of soil strength.", "output": "There is no related enetity." }, { "input": "Roots reacted to soil acidity when growing in macropores, but elongation through high - strength soil was improved.", "output": "There is no related enetity." }, { "input": "Soil strength can confound the effect of acidity on root growth, with the sensitivity of acid - resistant genotypes being greater in high - strength soils.", "output": "There is no related enetity." }, { "input": "This highlights the need to select for genotypes that resist both acidity and high soil strength.", "output": "There is no related enetity." }, { "input": "Enhanced formation of methane in plant cell cultures by inhibition of cytochrome c oxidase.", "output": "There is no related enetity." }, { "input": "The claim of methane ( CH4 ) formation in plants has caused much controversy and debate within the scientific community over the past 4 years.", "output": "There is no related enetity." }, { "input": "Here, using both stable isotope and concentration measurements, we demonstrate that CH4 formation occurs in plant cell cultures that were grown in the dark under sterile conditions.", "output": "There is no related enetity." }, { "input": "Under non - stress conditions the plant cell cultures produced trace amounts [ 0. 3 - 0. 6 ng g - ^ 1 dry weight ( DW ) h - ^ 1 ] of CH4 but these could be increased by one to two orders of magnitude ( up to 12 ng g - ^ 1 DW h - ^ 1 ) when sodium azide, a compound known to disrupt electron transport flow at the cytochrome c oxidase ( complex IV ) in plant mitochondria, was added to the cell cultures.", "output": "There is no related enetity." }, { "input": "The addition of other electron transport chain ( ETC ) inhibitors did not result in significant CH4 formation indicating that a site - specific disturbance of the ETC at complex IV causes CH4 formation in plant cells.", "output": "There is no related enetity." }, { "input": "Our study is an important first step in providing more information on non - microbial CH4 formation from living plants particularly under abiotic stress conditions that might affect the electron transport flow at the cytochrome c oxidase in plant mitochondria.", "output": "There is no related enetity." }, { "input": "Microbial and viral pathogens in colorectal cancer.", "output": "There is no related enetity." }, { "input": "The heterogenetic and sporadic nature of colorectal cancer has led to many epidemiological associations with causes of this disease.", "output": "There is no related enetity." }, { "input": "As our understanding of the underlying molecular processes in colorectal - cancer develops, the concept of microbial - epithelial interactions as an oncogenic trigger might provide a plausible hypothesis for the pathogenesis of colorectal cancer.", "output": "There is no related enetity." }, { "input": "By contrast with other cancers of the gastrointestinal tract ( gastric carcinoma, mucosa - associated lymphoid - tissue lymphoma ), a direct causal link between microbial infection ( bacteria and viruses ) and colorectal carcinoma has not been established.", "output": "There is no related enetity." }, { "input": "Studies support the involvement of these organisms in oncogenesis, however, in colorectal cancer, clinical data are lacking.", "output": "There is no related enetity." }, { "input": "Here, we discuss current evidence ( both in vitro and clinical studies ), and focus on a putative role for bacterial and viral pathogens as a cause of colorectal cancer.", "output": "There is no related enetity." }, { "input": "Activation and localization of protein kinase C in Neurospora crassa.", "output": "Neurospora crassa." }, { "input": "The Neurosporacrassa protein kinase C ( NPKC ) is reported to be a regulator of light responsive genes.", "output": "Neurosporacrassa." }, { "input": "It phosphorylates the light receptor WC - 1 and regulates the levels of the circadian clock protein FRQ and transcription of the light - induced albino - 2 gene.", "output": "There is no related enetity." }, { "input": "In mammals, the conventional and novel isoforms of PKC are activated by diacylglycerol ( DAG ), which induces PKC translocation from the cytoplasm to membranes.", "output": "There is no related enetity." }, { "input": "To investigate the interaction of NPKC and DAG in Neurospora, we constructed a strain that expresses a PKC - GFP fusion protein.", "output": "There is no related enetity." }, { "input": "We found that NPKC localizes to growing tips and sub - apical plasma membrane in actively growing hyphae, and actively participates in septum development.", "output": "There is no related enetity." }, { "input": "NPKC is activated by exogenous DAG and phorbol esters, and translocates to the plasma membrane from the cytoplasm.", "output": "There is no related enetity." }, { "input": "We have previously reported that choline depletion of the chol - 1 mutant of Neurospora increases DAG levels and lengthens the period of the circadian rhythm of conidiation.", "output": "There is no related enetity." }, { "input": "We have found that the activity of NPKC is rhythmic, and that NPKC levels are increased on choline depletion.", "output": "There is no related enetity." }, { "input": "However, over - expression of NPKC did not lengthen the conidiation period, indicating that PKC in Neurospora may not be responsible for the lengthened period in low choline cultures.", "output": "There is no related enetity." }, { "input": "Cercozoa comprises both EF - 1alpha - containing and EFL - containing members.", "output": "There is no related enetity." }, { "input": "Elongation factor 1alpha ( EF - 1alpha ) and elongation factor - like protein ( EFL ) are considered to be functionally equivalent proteins involved in peptide synthesis.", "output": "There is no related enetity." }, { "input": "Eukaryotes can be fundamentally divided into ' EF - 1alpha - containing ' and ' EFL - containing ' types.", "output": "There is no related enetity." }, { "input": "Recently, EF - 1alpha and EFL genes have been surveyed across the diversity of eukaryotes to explore the origin and evolution of EFL genes.", "output": "There is no related enetity." }, { "input": "Although the phylum Cercozoa is a diverse group, gene data for either EFL or EF - 1alpha are absent from all cercozoans except chlorarachniophytes which were previously defined as EFL - containing members.", "output": "There is no related enetity." }, { "input": "Our survey revealed that two members of the cercozoan subphylum Filosa ( Thaumatomastix sp. and strain YPF610 ) are EFL - containing members.", "output": "There is no related enetity." }, { "input": "Importantly, we identified EF - 1alpha genes from two members of Filosa ( Paracercomonas marina and Paulinella chromatophora ) and a member of the other subphylum Endomyxa ( Filoreta japonica ).", "output": "Paracercomonas marina, Paulinella chromatophora, Filoreta japonica." }, { "input": "All cercozoan EFL homologues could not be recovered as a monophyletic group in maximum - likelihood and Bayesian analyses, suggesting that lateral gene transfer was involved in the EFL evolution in this protist assemblage.", "output": "There is no related enetity." }, { "input": "In contrast, EF - 1alpha analysis successfully recovered a monophyly of three homologues sampled from the two cercozoan subphyla.", "output": "There is no related enetity." }, { "input": "Based on the results, we postulate that cercozoan EF - 1alpha genes have been vertically inherited, and the current EFL - containing species may have secondarily lost their EF - 1alpha genes.", "output": "There is no related enetity." }, { "input": "Ecological conditions in wintering and passage areas as determinants of timing of spring migration in trans - Saharan migratory birds.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Climate change has been associated with shifts in the timing of biological events, including the spring arrival of migratory birds.", "output": "There is no related enetity." }, { "input": "Early arrival at breeding sites is an important life - history trait, usually associated with higher breeding success and therefore, susceptible to selection and evolution in response to changing climatic conditions.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Here, we examine the effect of changes in the environmental conditions of wintering and passage areas on the mean passage time of 13 trans - Saharan passerines during their spring migration through the western Mediterranean over the 15 years from 1993 to 2007.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We found that most of the species studied have been advancing the timing of their passage in recent years.", "output": "There is no related enetity." }, { "input": "However, annual variation in the mean date of passage was positively correlated with vegetation growth ( measured as the normalized difference vegetation index [ NDVI ] ) both in the Sahel ( the region of departure ) and in northern Africa ( the passage area ).", "output": "There is no related enetity." }, { "input": "Thus, migration dates were delayed in years with high primary productivity in passage and wintering zones.", "output": "There is no related enetity." }, { "input": "All species seem to respond similarly to NDVI in the Sahel; however, late migrants were less affected by ecological conditions in northern Africa than those migrating earlier, suggesting differences based on species ecology.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Mean timing of passage was not related to the North Atlantic Oscillation ( NAO ), El Nino - Southern Oscillation ( ENSO ), temperature or NDVI in the species - specific wintering areas ( the overwintering region ) when analysed in combination with the other covariates.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Our findings show that ecological conditions in the winter quarters ( specifically the Sahel ) and en route are relevant factors influencing trends in the passage dates of trans - Saharan migratory birds on the southern fringe of Europe.", "output": "There is no related enetity." }, { "input": "Possible long - term consequences for late arriving spring migrants are discussed.", "output": "There is no related enetity." }, { "input": "Effects of early horn growth on reproduction and hunting mortality in female chamois.", "output": "chamois." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Environmental conditions during early development can affect the growth patterns of vertebrates, influencing future survival and reproduction.", "output": "There is no related enetity." }, { "input": "In long - lived mammals, females that experience poor environmental conditions early in life may delay primiparity.", "output": "There is no related enetity." }, { "input": "In female bovids, annual horn growth increments may provide a record of age - specific reproduction and body growth.", "output": "There is no related enetity." }, { "input": "Horn length, however, may also be a criterion used by hunters in selecting animals to harvest, possibly leading to artificial selection.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We studied three populations of chamois ( Rupicapra rupicapra ) in the western Alps to explore the relationships between female horn length and early growth, age of primiparity and age - specific reproduction.", "output": "chamois, Rupicapra rupicapra." }, { "input": "We also compared the risk of harvest to reproductive status and horn length.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Early horn growth was positively correlated with body mass in pre - reproductive females and with reproduction in very young and senescent adults.", "output": "There is no related enetity." }, { "input": "Females with strong early horn growth attained primiparity at an earlier age than those with weak early growth.", "output": "There is no related enetity." }, { "input": "Horn length did not affect hunter selection, but we found a strong hunter preference for nonlactating females.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Our research highlights the persistent effects of early development on reproductive performance in mammals.", "output": "There is no related enetity." }, { "input": "Moderate sport harvests are unlikely to affect the evolution of phenotypic traits and reproductive strategies in female chamois.", "output": "chamois." }, { "input": "A policy of penalizing hunters that harvest lactating females, however, may increase the harvest of 2 - year - old females, which have high reproductive potential.", "output": "There is no related enetity." }, { "input": "FungiFun: a web - based application for functional categorization of fungal genes and proteins.", "output": "There is no related enetity." }, { "input": "FungiFun assigns functional annotations to fungal genes or proteins and performs gene set enrichment analysis.", "output": "There is no related enetity." }, { "input": "Based on three different classification methods ( FunCat, GO and KEGG ), FungiFun categorizes genes and proteins for several fungal species on different levels of annotation detail.", "output": "There is no related enetity." }, { "input": "It is web - based and accessible to users without any programming skills.", "output": "There is no related enetity." }, { "input": "FungiFun is the first tool offering gene set enrichment analysis including the FunCat categorization.", "output": "There is no related enetity." }, { "input": "Two biological datasets for Aspergillus fumigatus and Candida albicans were analyzed using FungiFun, providing an overview of the usage and functions of the tool.", "output": "Aspergillus fumigatus, Candida albicans." }, { "input": "FungiFun is freely accessible at https: / / www. omnifung. hki - jena. de / FungiFun /.", "output": "There is no related enetity." }, { "input": "Cleavage of resveratrol in fungi: characterization of the enzyme Rco1 from Ustilago maydis.", "output": "Ustilago maydis." }, { "input": "Ustilago maydis, the causative agent of corn smut disease, contains two genes encoding members of the carotenoid cleavage oxygenase family, a group of enzymes that cleave double bonds in different substrates.", "output": "Ustilago maydis, corn smut." }, { "input": "One of them, Cco1, was formerly identified as a Beta - carotene cleaving enzyme.", "output": "There is no related enetity." }, { "input": "Here we elucidate the function of the protein encoded by the second gene, termed here as Ustilago maydis Resveratrol cleavage oxygenase 1 ( Um Rco1 ).", "output": "Ustilago maydis." }, { "input": "In vitro incubations of heterologously expressed and purified UM Rco1 with different carotenoid and stilbene substrates demonstrate that it cleaves the interphenyl Calpha - CBeta double bond of the phytoalexin resveratrol and its derivative piceatannol.", "output": "There is no related enetity." }, { "input": "Um Rco1 exhibits a high degree of substrate specificity, as suggested by the lack of activity on carotenoids and the other resveratrol - related compounds tested.", "output": "There is no related enetity." }, { "input": "The activity of Um Rco1 was confirmed by incubation of U. maydis rco1 deletion and over - expression strains with resveratrol.", "output": "U . maydis." }, { "input": "Furthermore, treatment with resveratrol resulted in striking alterations of cell morphology.", "output": "There is no related enetity." }, { "input": "However, pathogenicity assays indicated that Um rco1 is largely dispensable for biotrophic development.", "output": "There is no related enetity." }, { "input": "Our work reveals Um Rco1 as the first eukaryotic resveratrol cleavage enzyme identified so far.", "output": "There is no related enetity." }, { "input": "Moreover, Um Rco1 represents a subfamily of fungal enzymes likely involved in the degradation of stilbene compounds, as suggested by the cleavage of resveratrol by homologs from Aspergillus fumigatus, Chaetomium globosum and Botryotinia fuckeliana.", "output": "Aspergillus fumigatus, Chaetomium globosum, Botryotinia fuckeliana." }, { "input": "Medical schools in sub - Saharan Africa.", "output": "There is no related enetity." }, { "input": "Small numbers of graduates from few medical schools, and emigration of graduates to other countries, contribute to low physician presence in sub - Saharan Africa.", "output": "There is no related enetity." }, { "input": "The Sub - Saharan African Medical School Study examined the challenges, innovations, and emerging trends in medical education in the region.", "output": "There is no related enetity." }, { "input": "We identified 168 medical schools; of the 146 surveyed, 105 ( 72 % ) responded.", "output": "There is no related enetity." }, { "input": "Findings from the study showed that countries are prioritising medical education scale - up as part of health - system strengthening, and we identified many innovations in premedical preparation, team - based education, and creative use of scarce research support.", "output": "There is no related enetity." }, { "input": "The study also drew attention to ubiquitous faculty shortages in basic and clinical sciences, weak physical infrastructure, and little use of external accreditation.", "output": "There is no related enetity." }, { "input": "Patterns recorded include the growth of private medical schools, community - based education, and international partnerships, and the benefit of research for faculty development.", "output": "There is no related enetity." }, { "input": "Ten recommendations provide guidance for efforts to strengthen medical education in sub - Saharan Africa.", "output": "There is no related enetity." }, { "input": "Diversity, distribution and biogeography of testate amoebae in China: implications for ecological studies in Asia.", "output": "There is no related enetity." }, { "input": "Testate amoebae are a group of shelled protozoa that occur in high density populations in wet environments.", "output": "There is no related enetity." }, { "input": "More than 1900 testate amoebae species or subspecies have been reported in published literature over the last 200 years, from many regions of the world.", "output": "There is no related enetity." }, { "input": "Testate amoebae are classified as Lobosea or Filosea respectively, according to the presence of lobose or filiform pseudopodia.", "output": "There is no related enetity." }, { "input": "Testate amoebae have proved an interesting group of indicator organisms in palaeoenvironmental studies and have also been used as bioindicators of human impact on ecosystems.", "output": "human." }, { "input": "Until recently, the testate amoebae of China were unknown to most western scientists, but our knowledge has improved greatly over the past 20 years.", "output": "There is no related enetity." }, { "input": "This paper summarizes the testate amoebae research in China along with relevant data from other countries in Asia, and provides the necessary context for future research.", "output": "There is no related enetity." }, { "input": "Translation efficiency of antiterminator proteins is a determinant for the difference in glucose repression of two Beta - glucoside phosphotransferase system gene clusters in Corynebacterium glutamicum R.", "output": "Corynebacterium glutamicum R." }, { "input": "Corynebacterium glutamicum R has two Beta - glucoside phosphoenolpyruvate, carbohydrate phosphotransferase systems ( PTS ) encoded by bglF and bglF2 located in the respective clusters, bglF - bglA - bglG and bglF2 - bglA2 - bglG2.", "output": "Corynebacterium glutamicum R." }, { "input": "Previously, we reported that whereas Beta - glucoside - dependent induction of bglF is strongly repressed by glucose, glucose repression of bglF2 is very weak.", "output": "There is no related enetity." }, { "input": "Here, we reveal the mechanism behind the different effects of glucose on the two bgl genes.", "output": "There is no related enetity." }, { "input": "Deletion of the ribonucleic antiterminator sequence and transcriptional terminator located upstream of the translation initiation codon of bglF markedly relieved the glucose repression of a bglF - lacZ fusion, indicating that glucose affects the antitermination mechanism that is responsible for the Beta - glucoside - dependent induction of the bglF cluster.", "output": "There is no related enetity." }, { "input": "The glucose repression of bglF mRNA was also relieved by introducing a multicopy plasmid carrying the bglG gene encoding an antiterminator of the bglF cluster.", "output": "There is no related enetity." }, { "input": "Moreover, replacement of the GUG translation initiation codon of bglG with AUG was effective in relieving the glucose repression of bglF and bglG.", "output": "There is no related enetity." }, { "input": "Inversely, expression of bglF2 and bglG2 was subject to strict glucose repression in a mutant strain in which the AUG translation initiation codon of bglG2 encoding antiterminator of the bglF2 cluster was replaced with GUG.", "output": "There is no related enetity." }, { "input": "These results suggest that the translation initiation efficiency of the antiterminator proteins, at least in part, determines whether the target genes are subject to glucose repression.", "output": "There is no related enetity." }, { "input": "We also found that bglF expression was induced by glucose in the BglG - overexpressing strains, which may be explained by the ability of BglF to transport glucose.", "output": "There is no related enetity." }, { "input": "argC Orthologs from Rhizobiales show diverse profiles of transcriptional efficiency and functionality in Sinorhizobium meliloti.", "output": "Sinorhizobium meliloti." }, { "input": "Several factors can influence ortholog replacement between closely related species.", "output": "There is no related enetity." }, { "input": "We evaluated the transcriptional expression and metabolic performance of ortholog substitution complementing a Sinorhizobium meliloti argC mutant with argC from Rhizobiales ( Agrobacterium tumefaciens, Rhizobium etli, and Mesorhizobium loti ).", "output": "Sinorhizobium meliloti, Agrobacterium tumefaciens, Rhizobium etli, Mesorhizobium loti." }, { "input": "The argC gene is necessary for the synthesis of arginine, an amino acid that is central to protein and cellular metabolism.", "output": "There is no related enetity." }, { "input": "Strains were obtained carrying plasmids with argC orthologs expressed under the speB and argC ( S. meliloti ) and lac ( Escherichia coli ) promoters.", "output": "S . meliloti, Escherichia coli." }, { "input": "Complementation analysis was assessed by growth, transcriptional activity, enzymatic activity, mRNA levels, specific detection of ArgC proteomic protein, and translational efficiency.", "output": "There is no related enetity." }, { "input": "The argC orthologs performed differently in each complementation, reflecting the diverse factors influencing gene expression and the ability of the ortholog product to function in a foreign metabolic background.", "output": "There is no related enetity." }, { "input": "Optimal complementation was directly related to sequence similarity with S. meliloti, and was inversely related to species signature, with M. loti argC showing the poorest performance, followed by R. etli and A. tumefaciens.", "output": "S . meliloti, M . loti, R . etli, A . tumefaciens." }, { "input": "Different copy numbers of genes and amounts of mRNA and protein were produced, even with genes transcribed from the same promoter, indicating that coding sequences play a role in the transcription and translation processes.", "output": "There is no related enetity." }, { "input": "These results provide relevant information for further genomic analyses and suggest that orthologous gene substitutions between closely related species are not completely functionally equivalent.", "output": "There is no related enetity." }, { "input": "Genetic and mass spectrometry analyses of the unusual type IV - like pili of the archaeon Methanococcus maripaludis.", "output": "Methanococcus maripaludis." }, { "input": "The structure of pili from the archaeon Methanococcus maripaludis is unlike that of any bacterial pili.", "output": "Methanococcus maripaludis." }, { "input": "However, genetic analysis of the genes involved in the formation of these pili has been lacking until this study.", "output": "There is no related enetity." }, { "input": "Pili were isolated from a nonflagellated ( DeltaflaK ) mutant and shown by sodium dodecyl sulfate - polyacrylamide gel electrophoresis to consist primarily of subunits with an apparent molecular mass of 17 kDa.", "output": "There is no related enetity." }, { "input": "In - frame deletions were created in three genes, MMP0233, MMP0236, and MMP0237, which encode proteins with bacterial type IV pilin - like signal peptides previously identified by in silico methodology as likely candidates for pilus structural proteins.", "output": "There is no related enetity." }, { "input": "Deletion of MMP0236 or MMP0237 resulted in mutant cells completely devoid of pili on the cell surface, while deletion of the third pilin - like gene, MMP0233, resulted in cells greatly reduced in the number of pili on the surface.", "output": "There is no related enetity." }, { "input": "Complementation with the deleted gene in each case returned the cells to a piliated state.", "output": "There is no related enetity." }, { "input": "Surprisingly, mass spectrometry analysis of purified pili identified the major structural pilin as another type IV pilin - like protein, MMP1685, whose gene is located outside the first pilus locus.", "output": "There is no related enetity." }, { "input": "This protein was found to be glycosylated with an N - linked branched pentasaccharide glycan.", "output": "There is no related enetity." }, { "input": "Deletion and complementation analysis confirmed that MMP1685 is required for piliation.", "output": "There is no related enetity." }, { "input": "XerCD - mediated site - specific recombination leads to loss of the 57 - kilobase gonococcal genetic island.", "output": "There is no related enetity." }, { "input": "Most strains of Neisseria gonorrhoeae carry the 57 - kb gonococcal genetic island ( GGI ), as do a few strains of Neisseria meningitidis.", "output": "Neisseria gonorrhoeae, Neisseria meningitidis." }, { "input": "The GGI is inserted into the chromosome at the dif site ( difA ) and is flanked by a partial repeat of the dif site ( difB ).", "output": "There is no related enetity." }, { "input": "Since dif is a sequence recognized by the site - specific recombinases XerC and XerD and the GGI shows evidence of horizontal acquisition, we hypothesized that the GGI may be acquired or lost by XerCD - mediated site - specific recombination.", "output": "There is no related enetity." }, { "input": "We show that while the GGI flanked by wild - type dif sites, difA and difB, is not readily lost from the gonococcal chromosome, the substitution of difB with another copy of difA allows the frequent excision and loss of the GGI.", "output": "There is no related enetity." }, { "input": "In mutants carrying two difA sites ( difA ( + ) difA ( + ) ), the GGI can be detected as an extrachromosomal circle that exists transiently.", "output": "There is no related enetity." }, { "input": "A mutation of xerD diminished GGI excision from the chromosome of a difA ( + ) difA ( + ) strain, while mutations in recA or type IV secretion genes had no effect on the loss of the GGI.", "output": "There is no related enetity." }, { "input": "These data indicate that the GGI is maintained by the replication of the chromosome and that GGI excision and loss are dependent upon the dif sequence and xerD.", "output": "There is no related enetity." }, { "input": "The detection of a circular form of the GGI in a wild - type strain suggests that GGI excision may occur naturally and could function to facilitate GGI transfer.", "output": "There is no related enetity." }, { "input": "These data suggest a model of GGI excision and loss explaining the absence of the GGI from some gonococcal strains and the maintenance of variant GGIs in some gonococcal and meningococcal isolates.", "output": "meningococcal." }, { "input": "Opposing contributions of polynucleotide phosphorylase and the membrane protein NlpI to biofilm formation by Salmonella enterica serovar Typhimurium.", "output": "Salmonella enterica serovar Typhimurium." }, { "input": "CsgD and cyclic - 3 ', 5 ' - di - guanylate are key regulators of biofilm formation in Salmonella enterica serovar Typhimurium.", "output": "Salmonella enterica serovar Typhimurium." }, { "input": "Our results show that polynucleotide phosphorylase and NlpI oppositely altered expression of CsgD.", "output": "There is no related enetity." }, { "input": "Polynucleotide phosphorylase and NlpI also had opposite effects on the expression of yjcC, which codes for a cyclic - 3 ', 5 ' - di - guanylate phosphodiesterase affecting CsgD expression.", "output": "There is no related enetity." }, { "input": "Demographic consequences of adult sex ratio in a reintroduced hihi population.", "output": "hihi." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Male - biased adult sex ratios are frequently observed in free - ranging populations and are known to cause changes in mating behaviours including increased male harassment of females, which can cause injury to females and / or alter female behaviour during breeding.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Although we can explain why such behaviours may evolve and have studied their impacts on individuals when it does, we know very little about the demographic consequences of harassment caused by changes in adult sex ratio.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Using a 12 - year longitudinal data set of a free - living and endangered New Zealand passerine, the hihi ( Notiomystis cincta ), we show that a changing adult sex ratio has little or no effect on adult female survival or the number of fledglings produced per female.", "output": "hihi, Notiomystis cincta." }, { "input": "This is despite clear evidence of male harassment of breeding females when the sex ratio was male biased ( up to three males per female ).", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "The length of the study and major fluctuations in sex ratio observed made it possible to obtain narrow confidence or credible intervals for effect sizes, showing that any effect of sex ratio on demographic rates were small.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Our results provide rare empirical evidence for the demographic consequences of biased adult sex ratios in the wild and particularly in a conservation context.", "output": "There is no related enetity." }, { "input": "Ebola haemorrhagic fever.", "output": "There is no related enetity." }, { "input": "Ebola viruses are the causative agents of a severe form of viral haemorrhagic fever in man, designated Ebola haemorrhagic fever, and are endemic in regions of central Africa.", "output": "Ebola viruses." }, { "input": "The exception is the species Reston Ebola virus, which has not been associated with human disease and is found in the Philippines.", "output": "Reston Ebola virus, human." }, { "input": "Ebola virus constitutes an important local public health threat in Africa, with a worldwide effect through imported infections and through the fear of misuse for biological terrorism.", "output": "Ebola virus." }, { "input": "Ebola virus is thought to also have a detrimental effect on the great ape population in Africa.", "output": "Ebola virus." }, { "input": "Case - fatality rates of the African species in man are as high as 90 %, with no prophylaxis or treatment available.", "output": "There is no related enetity." }, { "input": "Ebola virus infections are characterised by immune suppression and a systemic inflammatory response that causes impairment of the vascular, coagulation, and immune systems, leading to multiorgan failure and shock, and thus, in some ways, resembling septic shock.", "output": "Ebola virus." }, { "input": "Primate communities are structured more by dispersal limitation than by niches.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "A major goal in community ecology is to identify mechanisms that govern the assembly and maintenance of ecological communities.", "output": "There is no related enetity." }, { "input": "Current models of metacommunity dynamics differ chiefly in the relative emphasis placed on dispersal limitation and niche differentiation as causal mechanisms structuring ecological communities.", "output": "There is no related enetity." }, { "input": "Herein we investigate the relative roles of these two mechanisms in structuring primate communities in Africa, South America, Madagascar and Borneo.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We hypothesized that if dispersal limitation is important in structuring communities, then community similarity should depend on geographical proximity even after controlling for ecological similarity.", "output": "There is no related enetity." }, { "input": "Conversely, if communities are assembled primarily through niche processes, then community similarity should be determined by ecological similarity regardless of geographical proximity.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We performed Mantel and partial Mantel tests to investigate correlations among primate community similarity, ecological distance and geographical distance.", "output": "There is no related enetity." }, { "input": "Results showed significant and strongly negative relationships between diurnal primate community similarity and both ecological similarity and geographical distance in Madagascar, but significant and stronger negative relationships between community similarity and geographical distance in African, South American and Bornean metacommunities.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "We conclude that dispersal limitation is an important determinant of primate community structure and may play a stronger role in shaping the structure of some terrestrial vertebrate communities than niche differentiation.", "output": "There is no related enetity." }, { "input": "These patterns are consistent with neutral theory.", "output": "There is no related enetity." }, { "input": "We recommend tests of functional equivalence to determine the extent to which neutral theory may explain primate community composition.", "output": "There is no related enetity." }, { "input": "Candidate chemosensory ionotropic receptors in a Lepidoptera.", "output": "There is no related enetity." }, { "input": "A new family of candidate chemosensory ionotropic receptors ( IRs ) related to ionotropic glutamate receptors ( iGluRs ) was recently discovered in Drosophila melanogaster.", "output": "Drosophila melanogaster." }, { "input": "Through Blast analyses of an expressed sequenced tag library prepared from male antennae of the noctuid moth Spodoptera littoralis, we identified 12 unigenes encoding proteins related to D. melanogaster and Bombyx mori IRs.", "output": "Spodoptera littoralis, D . melanogaster, Bombyx mori." }, { "input": "Their full length sequences were obtained and the analyses of their expression patterns suggest that they were exclusively expressed or clearly enriched in chemosensory organs.", "output": "There is no related enetity." }, { "input": "The deduced protein sequences were more similar to B. mori and D. melanogaster IRs than to iGluRs and showed considerable variations in the predicted ligand - binding domains; none have the three glutamate - interacting residues found in iGluRs, suggesting different binding specificities.", "output": "B . mori, D . melanogaster." }, { "input": "Our data suggest that we identified members of the insect IR chemosensory receptor family in S. littoralis and we report here the first demonstration of IR expression in Lepidoptera.", "output": "S . littoralis." }, { "input": "The health of prisoners.", "output": "There is no related enetity." }, { "input": "More than 10 million people are incarcerated worldwide; this number has increased by about a million in the past decade.", "output": "There is no related enetity." }, { "input": "Mental disorders and infectious diseases are more common in prisoners than in the general population.", "output": "There is no related enetity." }, { "input": "High rates of suicide within prison and increased mortality from all causes on release have been documented in many countries.", "output": "There is no related enetity." }, { "input": "The contribution of prisons to illness is unknown, although shortcomings in treatment and aftercare provision contribute to adverse outcomes.", "output": "There is no related enetity." }, { "input": "Research has highlighted that women, prisoners aged 55 years and older, and juveniles present with higher rates of many disorders than do other prisoners.", "output": "There is no related enetity." }, { "input": "The contribution of initiatives to improve the health of prisoners by reducing the burden of infectious and chronic diseases, suicide, other causes of premature mortality and violence, and counteracting the cycle of reoffending should be further examined.", "output": "There is no related enetity." }, { "input": "Genome - wide inventory of metal homeostasis - related gene products including a functional phytochelatin synthase in the hypogeous mycorrhizal fungus Tuber melanosporum.", "output": "Tuber melanosporum." }, { "input": "Ectomycorrhizal fungi are thought to enhance mineral nutrition of their host plants and to confer increased tolerance toward toxic metals.", "output": "There is no related enetity." }, { "input": "However, a global view of metal homeostasis - related genes and pathways in these organisms is still lacking.", "output": "There is no related enetity." }, { "input": "Building upon the genome sequence of Tuber melanosporum and on transcriptome analyses, we set out to systematically identify metal homeostasis - related genes in this plant - symbiotic ascomycete.", "output": "Tuber melanosporum." }, { "input": "Candidate gene products ( 101 ) were subdivided into three major functional classes: ( i ) metal transport ( 58 ); ( ii ) oxidative stress defence ( 32 ); ( iii ) metal detoxification ( 11 ).", "output": "There is no related enetity." }, { "input": "The latter class includes a small - size metallothionein ( TmelMT ) that was functionally validated in yeast, and phytochelatin synthase ( TmelPCS ), the first enzyme of this kind to be described in filamentous ascomycetes.", "output": "yeast." }, { "input": "Recombinant TmelPCS was shown to support GSH - dependent, metal - activated phytochelatin synthesis in vitro and to afford increased Cd / Cu tolerance to metal hypersensitive yeast strains.", "output": "yeast." }, { "input": "Metal transporters, especially those related to Cu and Zn trafficking, displayed the highest expression levels in mycorrhizae, suggesting extensive translocation of both metals to root cells as well as to fungal metalloenzymes ( e. g., laccase ) that are strongly upregulated in symbiotic hyphae.", "output": "There is no related enetity." }, { "input": "Structural and functional insights into Aeropyrum pernix OppA, a member of a novel archaeal OppA subfamily.", "output": "Aeropyrum pernix." }, { "input": "In this study we gain insight into the structural and functional characterization of the Aeropyrum pernix oligopeptide - binding protein ( OppA ( Ap ) ) previously identified from the extracellular medium of an Aeropyrum pernix cell culture at late stationary phase.", "output": "Aeropyrum pernix, Aeropyrum pernix." }, { "input": "OppA ( Ap ) showed an N - terminal Q32 in a pyroglutamate form and C - terminal processing at the level of a threonine - rich region probably involved in protein membrane anchoring.", "output": "There is no related enetity." }, { "input": "Moreover, the OppA ( Ap ) protein released into the medium was identified as a & quot; nicked & quot; form composed of two tightly associated fragments detachable only under strong denaturing conditions.", "output": "There is no related enetity." }, { "input": "The cleavage site E569 - G570 seems be located on an exposed surface loop that is highly conserved in several three - dimensional ( 3D ) structures of dipeptide / oligopeptide - binding proteins from different sources.", "output": "There is no related enetity." }, { "input": "Structural and biochemical properties of the nicked protein were virtually indistinguishable from those of the intact form.", "output": "There is no related enetity." }, { "input": "Indeed, studies of the entire bacterially expressed OppA ( Ap ) protein owning the same N and C termini of the nicked form supported these findings.", "output": "There is no related enetity." }, { "input": "Moreover, in the middle exponential growth phase, OppA ( Ap ) was found as an intact cell membrane - associated protein.", "output": "There is no related enetity." }, { "input": "Interestingly, the native exoprotein OppA ( Ap ) was copurified with a hexapeptide ( EKFKIV ) showing both lysines methylated and possibly originating from an A. pernix endogenous stress - induced lipoprotein.", "output": "There is no related enetity." }, { "input": "Therefore, the involvement of OppA ( Ap ) in the recycling of endogenous proteins was suggested to be a potential physiological function.", "output": "There is no related enetity." }, { "input": "Finally, a new OppA from Sulfolobus solfataricus, SSO1288, was purified and preliminarily characterized, allowing the identification of a common structural / genetic organization shared by all & quot; true & quot; archaeal OppA proteins of the dipeptide / oligopeptide class.", "output": "Sulfolobus solfataricus." }, { "input": "Differential responses of Bacillus subtilis rRNA promoters to nutritional stress.", "output": "Bacillus subtilis." }, { "input": "The in vivo expression levels of four rRNA promoter pairs ( rrnp ( 1 ) p ( 2 ) ) of Bacillus subtilis were determined by employing single - copy lacZ fusions integrated at the amyE locus.", "output": "Bacillus subtilis." }, { "input": "The rrnO, rrnJ, rrnD, and rrnB promoters displayed unique growth rate regulation and stringent responses.", "output": "There is no related enetity." }, { "input": "Both lacZ activity and mRNA levels were highest for rrnO under all growth conditions tested, while rrnJ, rrnB, and rrnD showed decreasing levels of activity.", "output": "There is no related enetity." }, { "input": "During amino acid starvation induced by serine hydroxamate ( SHX ), only the strong rrnO and rrnJ promoters demonstrated stringent responses.", "output": "There is no related enetity." }, { "input": "Under the growth conditions used, the rrn promoters showed responses similar to the responses to carbon source limitation induced by alpha - methyl glucoside ( alpha - MG ).", "output": "There is no related enetity." }, { "input": "The ratio of P2 to P1 transcripts, determined by primer extension analysis, was high for the strong rrnO and rrnJ promoters, while only P2 transcripts were detected for the weak rrnD and rrnB promoters.", "output": "There is no related enetity." }, { "input": "Cloned P1 or P2 promoter fragments of rrnO or rrnJ were differentially regulated.", "output": "There is no related enetity." }, { "input": "In wild - type ( relA ( + ) ) and suppressor [ relA ( S ) ] strains under the conditions tested, only P2 responded to carbon source limitation by a decrease in RNA synthesis, correlating with an increase in ( p ) ppGpp levels and a decrease in the GTP concentration.", "output": "There is no related enetity." }, { "input": "The weak P1 promoter elements remain relaxed in the three genetic backgrounds [ relA ( + ), relA, relA ( S ) ] in the presence of alpha - MG.", "output": "There is no related enetity." }, { "input": "During amino acid starvation, P2 was stringently regulated in relA ( + ) and relA ( S ) cells, while only rrnJp ( 1 ) was also regulated, but to a lesser extent.", "output": "There is no related enetity." }, { "input": "Both the relA ( + ) and relA ( S ) strains showed ( p ) ppGpp accumulation after alpha - MG treatment but not after SHX treatment.", "output": "There is no related enetity." }, { "input": "These data reveal the complex nature of B. subtilis rrn promoter regulation in response to stress, and they suggest that the P2 promoters may play a more prominent role in the stringent response.", "output": "B . subtilis." }, { "input": "Primosomal proteins DnaD and DnaB are recruited to chromosomal regions bound by DnaA in Bacillus subtilis.", "output": "Bacillus subtilis." }, { "input": "The initiation of DNA replication requires the binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication, oriC.", "output": "There is no related enetity." }, { "input": "DnaA also binds to many sites around the chromosome, outside oriC, and acts as a transcription factor at several of these.", "output": "There is no related enetity." }, { "input": "In low - G + C Gram - positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, load the replicative helicase at oriC, and this depends on DnaA.", "output": "There is no related enetity." }, { "input": "DnaD and DnaB also are required to load the replicative helicase outside oriC during replication restart, independently of DnaA.", "output": "There is no related enetity." }, { "input": "Using chromatin immunoprecipitation, we found that DnaD and DnaB, but not the replicative helicase, are associated with many of the chromosomal regions bound by DnaA in Bacillus subtilis.", "output": "Bacillus subtilis." }, { "input": "This association was dependent on DnaA, and the order of recruitment was the same as that at oriC, but it was independent of a functional oriC and suggests that DnaD and DnaB do not require open complex formation for the stable association with DNA.", "output": "There is no related enetity." }, { "input": "These secondary binding regions for DnaA could be serving as a reservoir for excess DnaA, DnaD, and DnaB to help properly regulate replication initiation and perhaps are analogous to the proposed function of the datA locus in Escherichia coli.", "output": "Escherichia coli." }, { "input": "Alternatively, DnaD and DnaB might modulate the activity of DnaA at the secondary binding regions.", "output": "There is no related enetity." }, { "input": "All three of these proteins are widely conserved and likely have similar functions in a range of organisms.", "output": "There is no related enetity." }, { "input": "A LytM domain dictates the localization of proteins to the mother cell - forespore interface during bacterial endospore formation.", "output": "There is no related enetity." }, { "input": "A large number of proteins are known to reside at specific subcellular locations in bacterial cells.", "output": "There is no related enetity." }, { "input": "However, the molecular mechanisms by which many of these proteins are anchored at these locations remains unclear.", "output": "There is no related enetity." }, { "input": "During endospore formation in Bacillus subtilis, several integral membrane proteins are located specifically at the interface of the two adjacent cells of the developing sporangium, the mother cell and forespore.", "output": "Bacillus subtilis." }, { "input": "The mother cell membrane protein SpoIIIAH recognizes the cell - cell interface through an interaction with the forespore membrane protein SpoIIQ, and then the other proteins are positioned there by the SpoIIIAH - SpoIIQ complex.", "output": "There is no related enetity." }, { "input": "In this study, we investigated the molecular mechanisms underlying the formation of the SpoIIIAH - SpoIIQ complex.", "output": "There is no related enetity." }, { "input": "Using gel filtration chromatography and isothermal titration calorimetry, we measured the binding parameters that characterize the SpoIIIAH - SpoIIQ interaction in vitro.", "output": "There is no related enetity." }, { "input": "We also demonstrated that the interaction of SpoIIIAH and SpoIIQ is governed by their YscJ and degenerate LytM domains, respectively.", "output": "There is no related enetity." }, { "input": "Therefore, the LytM domain of SpoIIQ provides the positional cue that dictates the localization of mother cell membrane proteins to the mother cell - forespore interface.", "output": "There is no related enetity." }, { "input": "Spatial regulation of histidine kinases governing biofilm formation in Bacillus subtilis.", "output": "Bacillus subtilis." }, { "input": "Bacillus subtilis is able to form architecturally complex biofilms on solid medium due to the production of an extracellular matrix.", "output": "Bacillus subtilis." }, { "input": "A master regulator that controls the expression of the genes involved in matrix synthesis is Spo0A, which is activated by phosphorylation via a phosphorelay involving multiple histidine kinases.", "output": "There is no related enetity." }, { "input": "Here we report that four kinases, KinA, KinB, KinC, and KinD, help govern biofilm formation but that their contributions are partially masked by redundancy.", "output": "There is no related enetity." }, { "input": "We show that the kinases fall into two categories and that the members of each pair ( one pair comprising KinA and KinB and the other comprising KinC and KinD ) are partially redundant with each other.", "output": "There is no related enetity." }, { "input": "We also show that the kinases are spatially regulated: KinA and KinB are active principally in the older, inner regions of the colony, and KinC and KinD function chiefly in the younger, outer regions.", "output": "There is no related enetity." }, { "input": "These conclusions are based on the morphology of kinase mutants, real - time measurements of gene expression using luciferase as a reporter, and confocal microscopy using a fluorescent protein as a reporter.", "output": "There is no related enetity." }, { "input": "Our findings suggest that multiple signals from the older and younger regions of the colony are integrated by the kinases to determine the overall architecture of the biofilm community.", "output": "There is no related enetity." }, { "input": "Contributions of multiple binding sites and effector - independent binding to CodY - mediated regulation in Bacillus subtilis.", "output": "Bacillus subtilis." }, { "input": "CodY is a branched - chain amino acid - responsive transcriptional regulator that controls, directly or indirectly, the expression of more than 100 genes and operons in Bacillus subtilis.", "output": "Bacillus subtilis." }, { "input": "Using DNase I footprinting and gel - shift experiments, we identified two CodY - binding regions upstream of a B. subtilis gene ( bcaP, previously known as yhdG ) that encodes a transporter of branched - chain amino acids.", "output": "B . subtilis." }, { "input": "Mutational analysis revealed that both CodY - binding regions contribute to repression in vivo and do so independently of each other.", "output": "There is no related enetity." }, { "input": "Thus, a single CodY - binding site is apparently sufficient for substantial CodY - dependent regulation.", "output": "There is no related enetity." }, { "input": "By analyzing affinities of wild - type and mutant CodY - binding sites for CodY and their regulation by wild - type CodY and forms of CodY with various levels of activation by branched - chain amino acids, we concluded that unliganded CodY cannot repress transcription in vivo and that the level of endogenously produced effectors is sufficient for CodY - mediated regulation of promoters with stronger sites.", "output": "There is no related enetity." }, { "input": "Because the sites with higher affinity apparently respond to lower concentrations of CodY effectors and saturate faster as the concentrations of effectors increase, having two sites of binding with different affinities for CodY permits a promoter to respond to a wider range of intracellular concentrations of effectors.", "output": "There is no related enetity." }, { "input": "Differences in MinC / MinD sensitivity between polar and internal Z rings in Escherichia coli.", "output": "Escherichia coli." }, { "input": "In Escherichia coli the Z ring has the potential to assemble anywhere along the cell length but is restricted to midcell by the action of negative regulatory systems, including Min.", "output": "Escherichia coli." }, { "input": "In the current model for the Min system, the MinC / MinD division inhibitory complex is evenly distributed on the membrane and can disrupt Z rings anywhere in the cell; however, MinE spatially regulates MinC / MinD by restricting it to the cell poles, thus allowing Z ring formation at midcell.", "output": "There is no related enetity." }, { "input": "This model assumes that Z rings formed at different cellular locations have equal sensitivity to MinC / MinD in the absence of MinE.", "output": "There is no related enetity." }, { "input": "However, here we report evidence that differences in MinC / MinD sensitivity between polar and nonpolar Z rings exists even when there is no MinE.", "output": "There is no related enetity." }, { "input": "MinC / MinD at proper levels is able to block minicell production in Deltamin strains without increasing the cell length, indicating that polar Z rings are preferentially blocked.", "output": "There is no related enetity." }, { "input": "In the FtsZ - I374V strain ( which is resistant to MinC ( C ) / MinD ), wild - type morphology can be easily achieved with MinC / MinD in the absence of MinE.", "output": "FtsZ - I374V strain." }, { "input": "We also show that MinC / MinD at proper levels can rescue the lethal phenotype of a min slmA double deletion mutant, which we think is due to the elimination of polar Z rings ( or FtsZ structures ), which frees up FtsZ molecules for assembly of Z rings at internal sites to rescue division and growth.", "output": "There is no related enetity." }, { "input": "Taken together, these data indicate that polar Z rings are more susceptible to MinC / MinD than internal Z rings, even when MinE is absent.", "output": "There is no related enetity." }, { "input": "Altered regulation of the OmpF porin by Fis in Escherichia coli during an evolution experiment and between B and K - 12 strains.", "output": "Escherichia coli." }, { "input": "The phenotypic plasticity of global regulatory networks provides bacteria with rapid acclimation to a wide range of environmental conditions, while genetic changes in those networks provide additional flexibility as bacteria evolve across long time scales.", "output": "There is no related enetity." }, { "input": "We previously identified mutations in the global regulator - encoding gene fis that enhanced organismal fitness during a long - term evolution experiment with Escherichia coli.", "output": "Escherichia coli." }, { "input": "To gain insight into the effects of these mutations, we produced two - dimensional protein gels with strains carrying different fis alleles, including a beneficial evolved allele and one with an in - frame deletion.", "output": "There is no related enetity." }, { "input": "We found that Fis controls the expression of the major porin - encoding gene ompF in the E. coli B - derived ancestral strain used in the evolution experiment, a relationship that has not been described before.", "output": "E . coli." }, { "input": "We further showed that this regulatory connection evolved over two different time scales, perhaps explaining why it was not observed before.", "output": "There is no related enetity." }, { "input": "On the longer time scale, we showed that this regulation of ompF by Fis is absent from the more widely studied K - 12 strain and thus is specific to the B strain.", "output": "K - 12 strain, B strain." }, { "input": "On a shorter time scale, this regulatory linkage was lost during 20, 000 generations of experimental evolution of the B strain.", "output": "B strain." }, { "input": "Finally, we mapped the Fis binding sites in the ompF regulatory region, and we present a hypothetical model of ompF expression that includes its other known regulators.", "output": "There is no related enetity." }, { "input": "Fur and the novel regulator YqjI control transcription of the ferric reductase gene yqjH in Escherichia coli.", "output": "Escherichia coli." }, { "input": "Iron acquisition in aerobic habitats is complicated by the low solubility of ferric hydroxides.", "output": "There is no related enetity." }, { "input": "Siderophores that bind ferric iron with high affinity are used to mobilize iron.", "output": "There is no related enetity." }, { "input": "The reduction of ferric iron to the ferrous form can be coupled to the release of iron from siderophores.", "output": "There is no related enetity." }, { "input": "Iron is also stored intracellularly as a ferric mineral in proteins, such as ferritin, and must be reduced during release.", "output": "There is no related enetity." }, { "input": "In Escherichia coli, the yqjH gene encodes a putative ferric siderophore reductase that is also part of the Fur regulon.", "output": "Escherichia coli." }, { "input": "Here we show that YqjH has ferric reductase activity and is required for iron homeostasis in E. coli.", "output": "E . coli." }, { "input": "Divergently transcribed from yqjH is the yqjI gene, which encodes a novel member of the winged - helix family of transcriptional regulators and also contains an N - terminal extension similar to the Ni ( 2 + ) - binding C - terminal tail of SlyD.", "output": "There is no related enetity." }, { "input": "Deletion of yqjI leads to constitutive high - level activity of the yqjH and yqjI promoters.", "output": "There is no related enetity." }, { "input": "Purified YqjI binds inverted repeat target sequences within the yqjH and yqjI promoters.", "output": "There is no related enetity." }, { "input": "We also observed that YqjI - dependent transcriptional repression is reduced when cells are exposed to elevated nickel levels, resulting in increased expression of yqjH and yqjI.", "output": "There is no related enetity." }, { "input": "YqjI binding to nickel or iron reduces YqjI DNA - binding activity in vitro.", "output": "There is no related enetity." }, { "input": "Furthermore, we found that elevated nickel stress levels disrupt iron homeostasis in E. coli and that deletion of yqjH increases nickel toxicity.", "output": "E . coli." }, { "input": "Our results suggest that the YqjI protein controls expression of yqjH to help maintain iron homeostasis under conditions ( such as elevated cellular nickel levels ) that disrupt iron metabolism.", "output": "There is no related enetity." }, { "input": "Genome copy numbers and gene conversion in methanogenic archaea.", "output": "methanogenic archaea." }, { "input": "Previous studies revealed that one species of methanogenic archaea, Methanocaldococcus jannaschii, is polyploid, while a second species, Methanothermobacter thermoautotrophicus, is diploid.", "output": "methanogenic archaea, Methanocaldococcus jannaschii, Methanothermobacter thermoautotrophicus." }, { "input": "To further investigate the distribution of ploidy in methanogenic archaea, species of two additional genera - Methanosarcina acetivorans and Methanococcus maripaludis - were investigated.", "output": "methanogenic archaea, Methanosarcina acetivorans, Methanococcus maripaludis." }, { "input": "M. acetivorans was found to be polyploid during fast growth ( t ( D ) = 6 h; 17 genome copies ) and oligoploid during slow growth ( doubling time = 49 h; 3 genome copies ).", "output": "M . acetivorans." }, { "input": "M. maripaludis has the highest ploidy level found for any archaeal species, with up to 55 genome copies in exponential phase and ca.", "output": "M . maripaludis." }, { "input": "30 in stationary phase.", "output": "There is no related enetity." }, { "input": "A compilation of archaeal species with quantified ploidy levels reveals a clear dichotomy between Euryarchaeota and Crenarchaeota: none of seven euryarchaeal species of six genera is monoploid ( haploid ), while, in contrast, all six crenarchaeal species of four genera are monoploid, indicating significant genetic differences between these two kingdoms.", "output": "There is no related enetity." }, { "input": "Polyploidy in asexual species should lead to accumulation of inactivating mutations until the number of intact chromosomes per cell drops to zero ( called & quot; Muller ' s ratchet & quot; ).", "output": "There is no related enetity." }, { "input": "A mechanism to equalize the genome copies, such as gene conversion, would counteract this phenomenon.", "output": "There is no related enetity." }, { "input": "Making use of a previously constructed heterozygous mutant strain of the polyploid M. maripaludis we could show that in the absence of selection very fast equalization of genomes in M. maripaludis took place probably via a gene conversion mechanism.", "output": "M . maripaludis, M . maripaludis." }, { "input": "In addition, it was shown that the velocity of this phenomenon is inversely correlated to the strength of selection.", "output": "There is no related enetity." }, { "input": "Membrane topology and DNA - binding ability of the Streptococcal CpsA protein.", "output": "There is no related enetity." }, { "input": "Many streptococcal pathogens require a polysaccharide capsule for survival in the host during systemic infection.", "output": "There is no related enetity." }, { "input": "The highly conserved CpsA protein is proposed to be a transcriptional regulator of capsule production in streptococci, although the regulatory mechanism is unknown.", "output": "There is no related enetity." }, { "input": "Hydropathy plots of CpsA predict an integral membrane protein with 3 transmembrane domains and only 27 cytoplasmic residues, whereas other members of the LytR _ cpsA _ psr protein family are predicted to have a single transmembrane domain.", "output": "There is no related enetity." }, { "input": "This unique topology, with the short cytoplasmic domain, membrane localization, and large extracellular domain, suggests a novel mechanism of transcriptional regulation.", "output": "There is no related enetity." }, { "input": "Therefore, to determine the actual membrane topology of CpsA, specific protein domains were fused to beta - galactosidase or alkaline phosphatase.", "output": "There is no related enetity." }, { "input": "Enzymatic assays confirmed that the predicted membrane topology for CpsA is correct.", "output": "There is no related enetity." }, { "input": "To investigate how this integral membrane protein may be functioning in regulation of capsule transcription, purified full - length and truncated forms of CpsA were used in electrophoretic mobility shift assays to characterize the ability to bind the capsule operon promoter.", "output": "There is no related enetity." }, { "input": "Assays revealed that full - length, purified CpsA protein binds specifically to DNA containing the capsule promoter region.", "output": "There is no related enetity." }, { "input": "Furthermore, the large extracellular domain is not required for DNA binding, but all cytoplasmic regions of CpsA are necessary and sufficient for specific binding to the capsule operon promoter.", "output": "There is no related enetity." }, { "input": "This is the first demonstration of a member of this protein family interacting with its target DNA.", "output": "There is no related enetity." }, { "input": "Taken together, CpsA, as well as other members of the LytR _ cpsA _ psr protein family, appears to utilize a unique mechanism of transcriptional regulation.", "output": "There is no related enetity." }, { "input": "Identification of nocobactin NA biosynthetic gene clusters in Nocardia farcinica.", "output": "Nocardia farcinica." }, { "input": "We identified the biosynthetic gene clusters of the siderophore nocobactin NA.", "output": "There is no related enetity." }, { "input": "The nbt clusters, which were discovered as genes highly homologous to the mycobactin biosynthesis genes by the genomic sequencing of Nocardia farcinica IFM 10152, consist of 10 genes separately located at two genomic regions.", "output": "Nocardia farcinica IFM 10152." }, { "input": "The gene organization of the nbt clusters and the predicted functions of the nbt genes, particularly the cyclization and epimerization domains, were in good agreement with the chemical structure of nocobactin NA.", "output": "There is no related enetity." }, { "input": "Disruptions of the nbtA and nbtE genes, respectively, reduced and abolished the productivity of nocobactin NA.", "output": "There is no related enetity." }, { "input": "The heterologous expression of the nbtS gene revealed that this gene encoded a salicylate synthase.", "output": "There is no related enetity." }, { "input": "These results indicate that the nbt clusters are responsible for the biosynthesis of nocobactin NA.", "output": "There is no related enetity." }, { "input": "We also found putative IdeR - binding sequences upstream of the nbtA, - G, - H, - S, and - T genes, whose expression was more than 10 - fold higher in the low - iron condition than in the high - iron condition.", "output": "There is no related enetity." }, { "input": "These results suggest that nbt genes are regulated coordinately by IdeR protein in an iron - dependent manner.", "output": "There is no related enetity." }, { "input": "The DeltanbtE mutant was found to be impaired in cytotoxicity against J774A. 1 cells, suggesting that nocobactin NA production is required for virulence of N. farcinica.", "output": "N . farcinica." }, { "input": "Acyl - homoserine lactone binding to and stability of the orphan Pseudomonas aeruginosa quorum - sensing signal receptor QscR.", "output": "Pseudomonas aeruginosa." }, { "input": "The Pseudomonas aeruginosa transcription factor QscR responds to a variety of fatty acyl - homoserine lactones ( HSLs ), including N - 3 - oxododecanoyl - HSL ( 3OC12 - HSL ), which is produced and detected by the P. aeruginosa quorum - sensing circuit LasI and LasR.", "output": "Pseudomonas aeruginosa, P . aeruginosa." }, { "input": "As is true for LasR and many other acyl - HSL - dependent transcription factors, production of soluble QscR in sufficient amounts for purification requires growth of recombinant bacteria in the presence of an appropriate acyl - HSL.", "output": "There is no related enetity." }, { "input": "QscR is thought to bind 3OC12 - HSL relatively weakly compared to LasR, and unlike LasR, binding of purified QscR to target DNA was shown to strongly depend on exogenously added 3OC12 - HSL.", "output": "There is no related enetity." }, { "input": "We show that purified QscR is dimeric at sufficiently high concentrations and monomeric at lower concentrations.", "output": "There is no related enetity." }, { "input": "Furthermore, QscR bound 3OC12 - HSL more tightly than previously believed.", "output": "There is no related enetity." }, { "input": "Purified QscR retained 3OC12 - HSL, and at sufficiently high concentrations, it bound target DNA in the absence of added 3OC12 - HSL.", "output": "There is no related enetity." }, { "input": "We also obtained soluble QscR from recombinant Escherichia coli grown in the presence of N - 3 - oxohexanoyl - HSL ( 3OC6 - HSL ) instead of 3OC12 - HSL, and because 3OC6 - HSL bound much more loosely to QscR than other acyl - HSLs tested, we were able to exchange 3OC6 - HSL with other acyl - HSLs in vitro and then estimate binding affinities of QscR for different acyl - HSLs and for target DNA.", "output": "Escherichia coli." }, { "input": "Our data support a model whereby QscR polypeptides fold properly in the absence of an acyl - HSL, but soluble, acyl - HSL - free QscR does not accumulate because it is subject to rapid aggregation or proteolysis.", "output": "There is no related enetity." }, { "input": "Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent phage Dp - 1.", "output": "Streptococcus pneumoniae." }, { "input": "Streptococcus pneumoniae causes several diseases, including pneumonia, septicemia, and meningitis.", "output": "Streptococcus pneumoniae." }, { "input": "Phage Dp - 1 is one of the very few isolated virulent S. pneumoniae bacteriophages, but only a partial characterization is currently available.", "output": "S . pneumoniae." }, { "input": "Here, we confirmed that Dp - 1 belongs to the family Siphoviridae.", "output": "There is no related enetity." }, { "input": "Then, we determined its complete genomic sequence of 56, 506 bp.", "output": "There is no related enetity." }, { "input": "It encodes 72 open reading frames, of which 44 have been assigned a function.", "output": "There is no related enetity." }, { "input": "We have identified putative promoters, Rho - independent terminators, and several genomic clusters.", "output": "There is no related enetity." }, { "input": "We provide evidence that Dp - 1 may be using a novel DNA replication system as well as redirecting host protein synthesis through queuosine - containing tRNAs.", "output": "There is no related enetity." }, { "input": "Liquid chromatography - mass spectrometry analysis of purified phage Dp - 1 particles identified at least eight structural proteins.", "output": "There is no related enetity." }, { "input": "Finally, using comprehensive yeast two - hybrid screens, we identified 156 phage protein interactions, and this intraviral interactome was used to propose a structural model of Dp - 1.", "output": "There is no related enetity." }, { "input": "Role of the F1 region in the Escherichia coli aerotaxis receptor Aer.", "output": "Escherichia coli." }, { "input": "In Escherichia coli, the aerotaxis receptor Aer is an atypical receptor because it senses intracellular redox potential.", "output": "Escherichia coli." }, { "input": "The Aer sensor is a cytoplasmic, N - terminal PAS domain that is tethered to the membrane by a 47 - residue F1 linker.", "output": "There is no related enetity." }, { "input": "Here we investigated the function, topology, and orientation of F1 by employing random mutagenesis, cysteine scanning, and disulfide cross - linking.", "output": "There is no related enetity." }, { "input": "No native residue was obligatory for function, most deleterious substitutions had radically different side chain properties, and all F1 mutants but one were functionally rescued by the chemoreceptor Tar.", "output": "There is no related enetity." }, { "input": "Cross - linking studies were consistent with the predicted alpha - helical structure in the N - terminal F1 region and demonstrated trigonal interactions among the F1 linkers from three Aer monomers, presumably within trimer - of - dimer units, as well as binary interactions between subunits.", "output": "There is no related enetity." }, { "input": "Using heterodimer analyses, we also demonstrated the importance of arginine residues near the membrane interface, which may properly anchor the Aer protein in the membrane.", "output": "There is no related enetity." }, { "input": "By incorporating these data into a homology model of Aer, we developed a model for the orientation of the Aer F1 and PAS regions in an Aer lattice that is compatible with the known dimensions of the chemoreceptor lattice.", "output": "There is no related enetity." }, { "input": "We propose that the F1 region facilitates the orientation of PAS and HAMP domains during folding and thereby promotes the stability of the PAS and HAMP domains in Aer.", "output": "There is no related enetity." }, { "input": "Genome - wide identification of Phytophthora sojae SNARE genes and functional characterization of the conserved SNARE PsYKT6.", "output": "Phytophthora sojae." }, { "input": "Soluble N - ethylmaleimide - sensitive factor attachment protein receptors ( SNAREs ) are central components of the machinery mediating membrane fusion and key factors for vesicular trafficking in all eukaryotic cells.", "output": "There is no related enetity." }, { "input": "Taking advantage of the available whole genome sequence of the oomycete plant pathogen Phytophthora sojae, 35 genes encoding putative SNARE proteins were identified in the genome of this organism.", "output": "Phytophthora sojae." }, { "input": "PsYKT6, one of the most conserved SNARE proteins, was functionally characterized by homology - dependent gene silencing.", "output": "There is no related enetity." }, { "input": "The phenotype analysis showed that PsYKT6 is important for proper asexual development, sexual reproduction, and pathogenesis on host soybean cultivars.", "output": "soybean." }, { "input": "Oesophagogastric junction adenocarcinoma: which therapeutic approach?", "output": "There is no related enetity." }, { "input": "Gastric and oesophageal cancers are among the leading causes of cancer - related death worldwide.", "output": "There is no related enetity." }, { "input": "By contrast with the decreasing prevalence of gastric cancer, incidence and prevalence of oesophagogastric junction adenocarcinoma ( OGJA ) are rising rapidly in developed countries.", "output": "There is no related enetity." }, { "input": "We provide an update about treatment strategies for resectable OGJA.", "output": "There is no related enetity." }, { "input": "Here we review findings from the latest randomised trials and meta - analyses, and propose guidelines regarding endoscopic, surgical, and perioperative treatments.", "output": "There is no related enetity." }, { "input": "Through a team approach, members from all diagnostic and therapeutic disciplines, such as gastroenterologists, surgeons, oncologists, radiologists, and radiotherapists, can effectively administer a range of treatment modalities.", "output": "There is no related enetity." }, { "input": "Mating differentiation in Cryptococcus neoformans is negatively regulated by the Crk1 protein kinase.", "output": "Cryptococcus neoformans." }, { "input": "Cryptococcus neoformans is a heterothallic basidiomycete that grows vegetatively as yeast and filamentous hyphae are produced in the sexual state.", "output": "Cryptococcus neoformans, yeast." }, { "input": "Previous studies have shown that C. neoformans Cwc1 and Cwc2 are two central photoregulators which form a complex to inhibit the production of sexual filaments upon light treatment.", "output": "C . neoformans." }, { "input": "To reveal the detailed regulatory mechanisms, a genome wide mutagenesis screen was conducted and components in the Cwc1 / Cwc2 complex mediated pathway have been identified.", "output": "There is no related enetity." }, { "input": "In this study, one suppressor mutant, DJ22, is characterized and T - DNA is found to disrupt the C. neoformans CRK1 gene, a homologue of Saccharomyces cerevisiae IME2 and Ustilago maydis crk1.", "output": "C . neoformans, Saccharomyces cerevisiae, Ustilago maydis." }, { "input": "Ime2 is a meiosis - specific gene with the conserved Ser / Thr kinase domain and TXY dual phosphorylation site.", "output": "There is no related enetity." }, { "input": "Consistent with the findings of other suppressors in our screen, C. neoformans Crk1 plays a negative role in the mating process.", "output": "C . neoformans." }, { "input": "Dikaryotic filaments, basidia, and basidiospores are produced earlier in the crk1 mutant crosses and mating efficiency is also increased.", "output": "There is no related enetity." }, { "input": "Artificial elevation of the CRK1 mRNA level inhibits mating.", "output": "There is no related enetity." }, { "input": "Interestingly, monokaryotic fruiting is defective both in the MATalpha crk1 mutant and CRK1 overexpression strains.", "output": "There is no related enetity." }, { "input": "Our studies demonstrate that C. neoformans CRK1 gene functions as a negative regulator in the mating differentiation.", "output": "There is no related enetity." }, { "input": "& quot; Slime molds & quot; among the Tubulinea ( Amoebozoa ): molecular systematics and taxonomy of Copromyxa.", "output": "There is no related enetity." }, { "input": "Copromyxa protea is a dung - inhabiting amoeboid organism that aggregates to form simple macroscopic fruiting structures, sorocarps, which are composed of a single cell type.", "output": "Copromyxa protea." }, { "input": "In a recent effort to find the phylogenetic positions of the less well - known sorocarpic protists considered to be & quot; cellular slime molds, & quot; or aggregatively fruiting amoebae, we isolated C. protea and sequenced the nuclear - encoded small subunit ribosomal RNA gene from four samples collected from cattle farms in the central USA.", "output": "C . protea, cattle." }, { "input": "Phylogenetic analyses of these data place C. protea in the eukaryotic supergroup Amoebozoa together with the Tubulinea, in which there has been no previous report of an aggregative fruiting habit.", "output": "C . protea." }, { "input": "This is consistent with the morphology of the trophozoites.", "output": "There is no related enetity." }, { "input": "In fact, Copromyxa protea is found to be very closely related to Hartmannella cantabrigiensis and to a since lost amoeba isolate, Hartmannella sp. 4 / 3Da / 10.", "output": "Copromyxa protea, Hartmannella cantabrigiensis, Hartmannella sp . 4 / 3Da / 10." }, { "input": "This new grouping of Copromyxa + H. cantabrigiensis is sister to Glaeseria, which together are sister to the Amoebidae ( Amoeba + Chaos ).", "output": "H . cantabrigiensis." }, { "input": "We suggest renaming, H. cantabrigiensis as C. cantabrigiensis and designate isolate 4 / 3Da / 10 as C. protea.", "output": "C . cantabrigiensis, C . protea." }, { "input": "Future work is needed to see if these newly assigned members of the genus Copromyxa also show evidence of an ability to fruit.", "output": "There is no related enetity." }, { "input": "Improved accuracy of the transcriptional profiling method of age grading in Aedes aegypti mosquitoes under laboratory and semi - field cage conditions and in the presence of Wolbachia infection.", "output": "Aedes aegypti mosquitoes." }, { "input": "Transcriptional profiling is an effective method of predicting age in the mosquito Aedes aegypti in the laboratory, however, its effectiveness is limited to younger mosquitoes.", "output": "Aedes aegypti." }, { "input": "To address this we used a microarray to identify new gene candidates that show significant expression changes in older mosquitoes.", "output": "There is no related enetity." }, { "input": "These genes were then used to create a revised model, which upon evaluation in both laboratory and semi - field conditions, proved to have improved accuracy overall and for older mosquitoes.", "output": "There is no related enetity." }, { "input": "In association with the development of symbiont - based control strategies for Ae. aegypti, we also tested the model ' s accuracy for Wolbachia - infected mosquitoes and found no decline in performance.", "output": "Ae . aegypti." }, { "input": "Our findings suggest that the new model is a robust and powerful tool for age determination in Australian Ae. aegypti populations.", "output": "Ae . aegypti." }, { "input": "Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli.", "output": "Escherichia coli." }, { "input": "Cra ( catabolite repressor activator ) is a global regulator of the genes for carbon metabolism in Escherichia coli.", "output": "Escherichia coli." }, { "input": "To gain insights into the regulatory roles of Cra, attempts were made to identify the whole set of regulation targets using an improved genomic SELEX ( systematic evolution of ligands by exponential enrichment ) system.", "output": "There is no related enetity." }, { "input": "Surprisingly, a total of 164 binding sites were identified for Cra, 144 ( 88 % ) of which were newly identified.", "output": "There is no related enetity." }, { "input": "The majority of known targets were included in the SELEX chip pattern.", "output": "There is no related enetity." }, { "input": "The promoters examined by the lacZ reporter assay in vivo were all regulated by Cra.", "output": "There is no related enetity." }, { "input": "These two lines of evidence indicate that a total of as many as 178 promoters are under the control of Cra.", "output": "There is no related enetity." }, { "input": "The majority of Cra targets are the genes coding for the enzymes involved in central carbon metabolism, covering all the genes for the enzymes involved in glycolysis and metabolism downstream of glycolysis, including the tricarboxylic acid ( TCA ) cycle and aerobic respiration.", "output": "There is no related enetity." }, { "input": "Taken together, we propose that Cra plays a key role in balancing the levels of the enzymes for carbon metabolism.", "output": "There is no related enetity." }, { "input": "The three vibrio cholerae chromosome II - encoded ParE toxins degrade chromosome I following loss of chromosome II.", "output": "vibrio cholerae." }, { "input": "Three homologues of the plasmid RK2 ParDE toxin - antitoxin system are present in the Vibrio cholerae genome within the superintegron on chromosome II.", "output": "Vibrio cholerae." }, { "input": "Here we found that these three loci - two of which have identical open reading frames and regulatory sequences - encode functional toxin - antitoxin systems.", "output": "There is no related enetity." }, { "input": "The ParE toxins inhibit bacterial division and reduce viability, presumably due to their capacity to damage DNA.", "output": "There is no related enetity." }, { "input": "The in vivo effects of ParE1 / 3 mimic those of ParE2, which we have previously demonstrated to be a DNA gyrase inhibitor in vitro, suggesting that ParE1 / 3 is likewise a gyrase inhibitor, despite its relatively low degree of sequence identity.", "output": "There is no related enetity." }, { "input": "ParE - mediated DNA damage activates the V. cholerae SOS response, which in turn likely accounts for ParE ' s inhibition of cell division.", "output": "V . cholerae." }, { "input": "Each toxin ' s effects can be prevented by the expression of its cognate ParD antitoxin, which acts in a toxin - specific fashion both to block toxicity and to repress the expression of its parDE operon.", "output": "There is no related enetity." }, { "input": "Derepression of ParE activity in DeltaparAB2 mutant V. cholerae cells that have lost chromosome II contributes to the prominent DNA degradation that accompanies the death of these cells.", "output": "V . cholerae." }, { "input": "Overall, our findings suggest that the ParE toxins lead to the postsegregational killing of cells missing chromosome II in a manner that closely mimics postsegregational killing mediated by plasmid - encoded homologs.", "output": "There is no related enetity." }, { "input": "Thus, the parDE loci aid in the maintenance of the integrity of the V. cholerae superintegron and in ensuring the inheritance of chromosome II.", "output": "V . cholerae." }, { "input": "Climatic constraints on wintering bird distributions are modified by urbanization and weather.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Ecologists have long been interested in the role of climate in shaping species ' ranges, and in recent years, this relationship has taken on greater significance because of the need for accurate predictions of the effects of climate change on wildlife populations.", "output": "There is no related enetity." }, { "input": "Bioclimatic relationships, however, are potentially complicated by various environmental factors operating at multiple spatial and temporal scales.", "output": "There is no related enetity." }, { "input": "Here, we test the hypothesis that climatic constraints on bird distributions are modified by species - specific responses to weather, urbanization and use of supplemental food.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Our analyses focused on 18 bird species with data from over 3000 sites across the north - eastern United States and adjacent Canadian provinces.", "output": "There is no related enetity." }, { "input": "We use hierarchal occupancy modelling to quantify the effects of short - term weather variation and surrounding urbanization on food stress and probabilities of detection, and how these fine - scale changes modify the role that climate has on the distributions of wintering bird populations at regional scales.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Examining site occupancy and supplemental food use across the study region, we found that average minimum temperature was an important factor limiting bird distributions, supporting the hypothesis that the occupancy of wintering birds is limited by climatic constraints.", "output": "There is no related enetity." }, { "input": "We found that 15 of 18 species ( 83 % ) were more energetically stressed ( had a higher likelihood of visiting a feeder station ) as minimum temperature declined from the seasonal average.", "output": "There is no related enetity." }, { "input": "Because we found these patterns in populations that regularly visit supplemental food sites and were likely not food - limited, we suggest that resource availability is less important than climate in constraining wintering bird distributions.", "output": "There is no related enetity." }, { "input": "Across a winter season, local within - winter extinction probabilities were lower and colonization probabilities higher at warmer sites supporting the role of climate - mediated range shifts.", "output": "There is no related enetity." }, { "input": "Importantly, however, these relationships were modified by the degree of urbanization and species ' abilities to persist in human - modified landscapes.", "output": "human." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Our results suggest that urbanization and behavioural adaptation can modify the role of climate on bird ranges and should be included in future analyses of range shifts because of climate change.", "output": "There is no related enetity." }, { "input": "Molecular structure of the prothoracicotropic hormone gene in the northern house mosquito, Culex pipiens, and its expression analysis in association with diapause and blood feeding.", "output": "northern house mosquito, Culex pipiens." }, { "input": "We cloned the gene that encodes prothoracicotropic hormone ( PTTH ) in the northern house mosquito, Culex pipiens, and investigated its expression profile in short - day ( diapause - destined ) and long - day ( nondiapause - destined ) individuals from the fourth - instar larval stage to 2 months of adulthood, as well as after a blood meal.", "output": "northern house mosquito, Culex pipiens." }, { "input": "The deduced C. pipiens PTTH ( Cupip - PTTH ) amino acid sequence contains seven cysteines with a specific spacing pattern.", "output": "C . pipiens." }, { "input": "Sequence alignment suggests that Cupip - PTTH is 23 % identical to Drosophila melanogaster PTTH, but is > = 59 % identical to the PTTHs of other mosquitoes.", "output": "Drosophila melanogaster." }, { "input": "Cupip - PTTH has structural characteristics similar to those of Bombyx mori PTTH and some vertebrate nerve growth factors with cysteine - knot motifs.", "output": "Bombyx mori." }, { "input": "PTTH transcripts exhibit a daily cycling profile during the final ( fourth ) larval instar, with peak abundance occurring late in the scotophase.", "output": "There is no related enetity." }, { "input": "The fourth - larval instar stage is one day longer in short - day larvae than in long - day larvae, resulting in larger larvae and adults.", "output": "There is no related enetity." }, { "input": "This additional day of larval development is associated with one extra PTTH cycle.", "output": "There is no related enetity." }, { "input": "No cycling was observed in pupae, but PTTH transcripts were slightly higher in short - day pupae than in long - day pupae throughout much of the pupal stage.", "output": "There is no related enetity." }, { "input": "PTTH expression persisted at a nearly constant level in diapausing adult females for the first month but then dropped by - 50 %, while expression decreased at the beginning of adulthood in nondiapausing females and then remained at a low level as long as the females were denied a blood meal.", "output": "There is no related enetity." }, { "input": "However, when nondiapausing females were offered a blood meal, PTTH transcripts rose approximately 7 fold in 2 h and remained elevated for 24 h.", "output": "There is no related enetity." }, { "input": "A few diapausing females ( - 10 % ) will take a blood meal when placed in close proximity to a host, but much of the blood is ejected and such meals do not result in mature eggs.", "output": "There is no related enetity." }, { "input": "Yet, elevated PTTH mRNA expression was also observed in diapausing females that were force fed.", "output": "There is no related enetity." }, { "input": "Our results thus point to several distinctions in PTTH expression between short - day and long - day mosquitoes, but both types of females responded to a blood meal by elevating levels of PTTH mRNA.", "output": "There is no related enetity." }, { "input": "Molecular events of apical bud formation in white spruce, Picea glauca.", "output": "white spruce, Picea glauca." }, { "input": "Bud formation is an adaptive trait that temperate forest trees have acquired to facilitate seasonal synchronization.", "output": "There is no related enetity." }, { "input": "We have characterized transcriptome - level changes that occur during bud formation of white spruce [ Picea glauca ( Moench ) Voss ], a primarily determinate species in which preformed stem units contained within the apical bud constitute most of next season ' s growth.", "output": "white spruce, [ Picea glauca ( Moench ) Voss ]." }, { "input": "Microarray analysis identified 4460 differentially expressed sequences in shoot tips during short day - induced bud formation.", "output": "There is no related enetity." }, { "input": "Cluster analysis revealed distinct temporal patterns of expression, and functional classification of genes in these clusters implied molecular processes that coincide with anatomical changes occurring in the developing bud.", "output": "There is no related enetity." }, { "input": "Comparing expression profiles in developing buds under long day and short day conditions identified possible photoperiod - responsive genes that may not be essential for bud development.", "output": "There is no related enetity." }, { "input": "Several genes putatively associated with hormone signalling were identified, and hormone quantification revealed distinct profiles for abscisic acid ( ABA ), cytokinins, auxin and their metabolites that can be related to morphological changes to the bud.", "output": "There is no related enetity." }, { "input": "Comparison of gene expression profiles during bud formation in different tissues revealed 108 genes that are differentially expressed only in developing buds and show greater transcript abundance in developing buds than other tissues.", "output": "There is no related enetity." }, { "input": "These findings provide a temporal roadmap of bud formation in white spruce.", "output": "white spruce." }, { "input": "Linking irradiance - induced changes in pit membrane ultrastructure with xylem vulnerability to cavitation.", "output": "There is no related enetity." }, { "input": "The effect of shading on xylem hydraulic traits and xylem anatomy was studied in hybrid poplar ( Populus trichocarpa x deltoides, clone H11 - 11 ).", "output": "Populus trichocarpa x deltoides." }, { "input": "Hydraulic measurements conducted on stem segments of 3 - month - old saplings grown in shaded ( SH ) or control light ( C ) conditions indicated that shading resulted in more vulnerable and less efficient xylem.", "output": "There is no related enetity." }, { "input": "Air is thought to enter vessels through pores in inter - vessel pit membranes, thereby nucleating cavitation.", "output": "There is no related enetity." }, { "input": "Therefore, we tested if the ultrastructure and / or chemistry of pit membranes differed in SH and C plants.", "output": "There is no related enetity." }, { "input": "Transmission electron micrographs revealed that pit membranes were thinner in SH, which was paralleled by lower compound middle lamella thickness.", "output": "There is no related enetity." }, { "input": "Immunolabelling with JIM5 and JIM7 monoclonal antibodies surprisingly indicated that pectic homogalacturonans were not present in the mature pit membrane regardless of the light treatment.", "output": "There is no related enetity." }, { "input": "Porosity measurements conducted with scanning electron microscopy were significantly affected by the method used for sample dehydration.", "output": "There is no related enetity." }, { "input": "Drying through a gradual ethanol series seems to be a better alternative to drying directly from a hydrated state for pit membrane observations in poplar.", "output": "There is no related enetity." }, { "input": "Scanning electron microscopy based estimates of pit membrane porosity probably overestimated real porosity as suggested by the results from the ' rare pit ' model.", "output": "There is no related enetity." }, { "input": "Sensing embolism in xylem vessels: the role of sucrose as a trigger for refilling.", "output": "There is no related enetity." }, { "input": "Refilling of embolized vessels requires a source of water and the release of energy stored in xylem parenchyma cells.", "output": "There is no related enetity." }, { "input": "Past evidence suggests that embolism presence can trigger a biological response that is switched off upon successful vessel refilling.", "output": "There is no related enetity." }, { "input": "As embolism formation is a purely physical process and most biological triggers rely on chemical sensors, we hypothesized that accumulation of osmotic compounds in walls of embolized vessels are involved in the embolism sensing mechanism.", "output": "There is no related enetity." }, { "input": "Analysis of Populus trichocarpa ' s response to infiltration of sucrose, monosaccharides, polyethylene glycol and potassium chloride into the xylem revealed that only presence of sucrose resulted in a simultaneous physiological and molecular response similar to that induced by embolism.", "output": "Populus trichocarpa." }, { "input": "This response included reduction of the starch pool in xylem parenchyma cells and significant correlation of gene expression from aquaporins, amylases and sugar transporter families.", "output": "There is no related enetity." }, { "input": "The work provides evidence of the ability of plants to sense embolism and suggests that sucrose concentration is the stimulus that allows plants to trigger a biological response to embolism.", "output": "There is no related enetity." }, { "input": "Constrained preferences in nitrogen uptake across plant species and environments.", "output": "There is no related enetity." }, { "input": "Knowledge of determining factors for nitrogen uptake preferences and how they are modified in changing environments are critical to understand ecosystem nitrogen cycling and to predict plant responses to future environmental changes.", "output": "There is no related enetity." }, { "input": "Two ^ 1 ^ 5N tracer experiments utilizing a unique differential labelled nitrogen source were employed in both African savannas and greenhouse settings.", "output": "There is no related enetity." }, { "input": "The results demonstrated that nitrogen uptake preferences were constrained by the climatic conditions.", "output": "There is no related enetity." }, { "input": "As mainly indicated by root delta ^ 1 ^ 5N signatures at 1: 1 ammonium / nitrate ratio, in the drier environments, plants preferred nitrate and in the wetter environments they preferred ammonium.", "output": "There is no related enetity." }, { "input": "Nitrogen uptake preferences were different across different ecosystems ( e. g. from drier to wetter environments ) even for the same species.", "output": "There is no related enetity." }, { "input": "More significantly, our experiments showed that the plant progeny continued to exhibit the same nitrogen preference as the parent plants in the field, even when removed from their native environment and the nitrogen source was changed dramatically.", "output": "There is no related enetity." }, { "input": "The climatic constraint of nitrogen uptake preference is likely influenced by ammonium / nitrate ratios in the native habitats of the plants.", "output": "There is no related enetity." }, { "input": "The constancy in nitrogen preference has important implications in predicting the success of plant communities in their response to climate change, to seed bank use and to reforestation efforts.", "output": "There is no related enetity." }, { "input": "Molecular identification of sequestered diatom chloroplasts and kleptoplastidy in foraminifera.", "output": "There is no related enetity." }, { "input": "Kleptoplastidy is the ability of heterotrophic organisms to preserve chloroplasts of algal preys they eat and partially digest.", "output": "There is no related enetity." }, { "input": "As the sequestered chloroplasts stay functional for months, the \" host \" becomes photosynthetically active.", "output": "There is no related enetity." }, { "input": "Although remaining a marginal process, kleptoplastidy was observed in different protist lineages, including foraminifera.", "output": "There is no related enetity." }, { "input": "Previous studies showed at least eight species of the foraminiferal genera Haynesina and Elphidium grazing on diatoms and husbanding their chloroplasts.", "output": "There is no related enetity." }, { "input": "In order to characterize more precisely the origin of kleptochloroplasts in these genera, we obtained 1027 chloroplastic 16S rDNA sequences from 13 specimens of two Haynesina and five Elphidium species.", "output": "There is no related enetity." }, { "input": "We identified the foraminiferal kleptochloroplasts using a reference phylogeny made of 87 chloroplastic sequences of known species of diatoms and brown algae.", "output": "There is no related enetity." }, { "input": "All the analyzed specimens were performing kleptoplastidy and according to our phylogenetic analyses they seem to retain exclusively chloroplasts of diatom origin.", "output": "There is no related enetity." }, { "input": "There is no apparent specificity for the type of diatom from which chloroplasts originated, however some foraminiferal species seem to accept a wider range of diatoms than others.", "output": "There is no related enetity." }, { "input": "Possibly the diversity of kleptochloroplasts depends on the type of diatoms the foraminiferans feed on.", "output": "There is no related enetity." }, { "input": "Constitutive expression of the maltoporin LamB in the absence of OmpR damages the cell envelope.", "output": "There is no related enetity." }, { "input": "Cells experience multiple environmental stimuli simultaneously.", "output": "There is no related enetity." }, { "input": "To survive, they must respond accordingly.", "output": "There is no related enetity." }, { "input": "Unfortunately, the proper response to one stress easily could make the cell more susceptible to a second coexistent stress.", "output": "There is no related enetity." }, { "input": "To deal with such a problem, a cell must possess a mechanism that balances the need to respond simultaneously to both stresses.", "output": "There is no related enetity." }, { "input": "Our recent studies of ompR malT ( Con ) double mutants show that elevated expression of LamB, the outer membrane porin responsible for maltose uptake, causes cell death when the osmoregulator OmpR is disabled.", "output": "There is no related enetity." }, { "input": "To obtain insight into the nature of the death experienced by ompR malT ( Con ) mutants, we described the death process.", "output": "There is no related enetity." }, { "input": "On the basis of microscopic and biochemical approaches, we conclude that death results from a loss of membrane integrity.", "output": "There is no related enetity." }, { "input": "On the basis of an unbiased genome - wide search for suppressor mutations, we conclude that this loss of membrane integrity results from a LamB - induced envelope stress that the cells do not sufficiently perceive and thus do not adequately accommodate.", "output": "There is no related enetity." }, { "input": "Finally, we conclude that this envelope stress involves an imbalance in the lipopolysaccharide / porin composition of the outer membrane and an increased requirement for inorganic phosphate.", "output": "There is no related enetity." }, { "input": "Regulation of nleA in Shiga toxin - producing Escherichia coli O84: H4 strain 4795 / 97.", "output": "Escherichia coli O84 : H4 strain 4795 / 97." }, { "input": "Many Shiga toxin - producing Escherichia coli ( STEC ) strains express a type III secretion system ( TTSS ) encoded by the locus of enterocyte effacement ( LEE ).", "output": "Escherichia coli, STEC." }, { "input": "Using the TTSS, STEC is able to inject effector proteins directly into eukaryotic host cells, where they cause characteristic attaching and effacing ( A / E ) lesions.", "output": "STEC." }, { "input": "In addition to the LEE - encoded effectors, a number of non - LEE - encoded effectors, located on phage - associated elements, have been described.", "output": "There is no related enetity." }, { "input": "One of them, the non - LEE - encoded effector A ( NleA ), is widely distributed among pathogenic E. coli.", "output": "E . coli." }, { "input": "In this study, we investigated the influence of environmental conditions on the expression of the phage - encoded effector nleA gene ( designated nleA ( 4795 ) ) present in STEC O84: H4 strain 4795 / 97.", "output": "STEC O84 : H4 strain 4795 / 97." }, { "input": "We demonstrated that a particular NaCl concentration and starvation stress increase the activity of the nleA ( 4795 ) promoter.", "output": "There is no related enetity." }, { "input": "Moreover, several regulators that control nleA ( 4795 ) expression were identified.", "output": "There is no related enetity." }, { "input": "The involvement of the LEE regulators Ler, GrlA, and GrlR show that nleA ( 4795 ) is integrated in the LEE regulation circuit.", "output": "There is no related enetity." }, { "input": "Furthermore, the binding of Ler to sequences upstream of nleA ( 4795 ) underlined these findings.", "output": "There is no related enetity." }, { "input": "Bacillus anthracis sin locus and regulation of secreted proteases.", "output": "Bacillus anthracis." }, { "input": "Bacillus anthracis shares many regulatory loci with the nonpathogenic Bacillus species Bacillus subtilis.", "output": "Bacillus anthracis, Bacillus subtilis." }, { "input": "One such locus is sinIR, which in B. subtilis controls sporulation, biofilm formation, motility, and competency.", "output": "B . subtilis." }, { "input": "As B. anthracis is not known to be motile, to be naturally competent, or to readily form biofilms, we hypothesized that the B. anthracis sinIR regulon is distinct from that of B. subtilis.", "output": "B . anthracis, B . anthracis, B . subtilis." }, { "input": "A genome - wide expression microarray analysis of B. anthracis parental and sinR mutant strains indicated limited convergence of the B. anthracis and B. subtilis SinR regulons.", "output": "B . anthracis, B . anthracis, B . subtilis." }, { "input": "The B. anthracis regulon includes homologues of some B. subtilis SinR - regulated genes, including the signal peptidase gene sipW near the sinIR locus and the sporulation gene spoIIE.", "output": "B . anthracis, B . subtilis." }, { "input": "The B. anthracis SinR protein also negatively regulates transcription of genes adjacent to the sinIR locus that are unique to the Bacillus cereus group species.", "output": "B . anthracis, Bacillus cereus group species." }, { "input": "These include calY and inhA1, structural genes for the metalloproteases camelysin and immune inhibitor A1 ( InhA1 ), which have been suggested to be associated with virulence in B. cereus and B. anthracis, respectively.", "output": "B . cereus, B . anthracis." }, { "input": "Electrophoretic mobility shift assays revealed direct binding of B. anthracis SinR to promoter DNA from strongly regulated genes, such as calY and sipW, but not to the weakly regulated inhA1 gene.", "output": "B . anthracis." }, { "input": "Assessment of camelysin and InhA1 levels in culture supernates from sinR -, inhA1 -, and calY - null mutants showed that the concentration of InhA1 in the culture supernatant is inversely proportional to the concentration of camelysin.", "output": "There is no related enetity." }, { "input": "Our data are consistent with a model in which InhA1 protease levels are controlled at the transcriptional level by SinR and at the posttranslational level by camelysin.", "output": "There is no related enetity." }, { "input": "DifA, a methyl - accepting chemoreceptor protein - like sensory protein, uses a novel signaling mechanism to regulate exopolysaccharide production in Myxococcus xanthus.", "output": "Myxococcus xanthus." }, { "input": "DifA is a methyl - accepting chemotaxis protein ( MCP ) - like sensory transducer that regulates exopolysaccharide ( EPS ) production in Myxococcus xanthus.", "output": "Myxococcus xanthus." }, { "input": "Here mutational analysis and molecular biology were used to probe the signaling mechanisms of DifA in EPS regulation.", "output": "There is no related enetity." }, { "input": "We first identified the start codon of DifA experimentally; this identification extended the N terminus of DifA for 45 amino acids ( aa ) from the previous bioinformatics prediction.", "output": "There is no related enetity." }, { "input": "This extension helped to address the outstanding question of how DifA receives input signals from type 4 pili without a prominent periplasmic domain.", "output": "There is no related enetity." }, { "input": "The results suggest that DifA uses its N - terminus extension to sense an upstream signal in EPS regulation.", "output": "There is no related enetity." }, { "input": "We suggest that the perception of the input signal by DifA is mediated by protein - protein interactions with upstream components.", "output": "There is no related enetity." }, { "input": "Subsequent signal transmission likely involves transmembrane signaling instead of direct intramolecular interactions between the input and the output modules in the cytoplasm.", "output": "There is no related enetity." }, { "input": "The basic functional unit of DifA for signal transduction is likely dimeric as mutational alteration of the predicted dimeric interface of DifA significantly affected EPS production.", "output": "There is no related enetity." }, { "input": "Deletions of 14 - aa segments in the C terminus suggest that the newly defined flexible bundle subdomain in MCPs is likely critical for DifA function because shortening of this bundle can lead to constitutively active mutations.", "output": "There is no related enetity." }, { "input": "The SMC - like protein complex SbcCD enhances DNA polymerase IV - dependent spontaneous mutation in Escherichia coli.", "output": "Escherichia coli." }, { "input": "In Escherichia coli, RpoS, the general stress response sigma factor, regulates the activity of the specialized DNA polymerase DNA polymerase IV ( Pol IV ) both in stationary - phase and in exponential - phase cells.", "output": "Escherichia coli." }, { "input": "Because during exponential phase dinB, the gene encoding Pol IV, is transcribed independently of RpoS, RpoS must regulate Pol IV activity in growing cells indirectly via one or more intermediate factors.", "output": "There is no related enetity." }, { "input": "The results presented here show that one of these intermediate factors is SbcCD, an SMC - like protein and an ATP - dependent nuclease.", "output": "There is no related enetity." }, { "input": "By initiating or participating in double - strand break repair, SbcCD may provide DNA substrates for Pol IV polymerase activity.", "output": "There is no related enetity." }, { "input": "Staphylococcus aureus ClpC divergently regulates capsule via sae and codY in strain newman but activates capsule via codY in strain UAMS - 1 and in strain Newman with repaired saeS.", "output": "Staphylococcus aureus, newman, UAMS - 1, Newman." }, { "input": "ClpC is an ATPase chaperone found in most Gram - positive low - GC bacteria.", "output": "There is no related enetity." }, { "input": "It has been recently reported that ClpC affected virulence gene expression in Staphylococcus aureus.", "output": "Staphylococcus aureus." }, { "input": "Here we report that ClpC regulates transcription of the cap operon and accumulation of capsule, a major virulence factor for S. aureus.", "output": "S . aureus." }, { "input": "As virulence genes are regulated by a complex regulatory network in S. aureus, we have used capsule as a model to understand this regulation.", "output": "S . aureus." }, { "input": "By microarray analyses of strain Newman, we found that ClpC strongly activates transcription of the sae operon, whose products are known to negatively regulate capsule synthesis in this strain.", "output": "Newman." }, { "input": "Further studies indicated that ClpC repressed capsule production by activating the sae operon in strain Newman.", "output": "Newman." }, { "input": "Interestingly, the clpC gene cloned into a multiple - copy plasmid vector exhibited an activation phenotype, suggesting that ClpC overexpression has a net positive effect.", "output": "There is no related enetity." }, { "input": "In the absence of sae function, by either deletion or correction of a native mutation within saeS, we found that ClpC had a positive effect on capsule production.", "output": "There is no related enetity." }, { "input": "Indeed, in the UAMS - 1 strain, which does not have the saeS mutation, ClpC functioned as an activator of capsule production.", "output": "UAMS - 1." }, { "input": "Our microarray analyses of strain Newman also revealed that CodY, a repressor of capsule production, was repressed by ClpC.", "output": "Newman." }, { "input": "Using genetic approaches, we showed that CodY functioned downstream of ClpC, leading to capsule activation both in Newman and in UAMS - 1.", "output": "Newman, UAMS - 1." }, { "input": "Thus, ClpC functions in two opposite pathways in capsule regulation in strain Newman but functions as a positive activator in strain UAMS - 1.", "output": "Newman, UAMS - 1." }, { "input": "Flavobacterium johnsoniae sprB is part of an operon spanning the additional gliding motility genes sprC, sprD, and sprF.", "output": "Flavobacterium johnsoniae." }, { "input": "Cells of Flavobacterium johnsoniae move rapidly over surfaces by a process known as gliding motility.", "output": "Flavobacterium johnsoniae." }, { "input": "Gld proteins are thought to comprise the gliding motor that propels cell surface adhesins, such as the 669 - kDa SprB.", "output": "There is no related enetity." }, { "input": "A novel protein secretion apparatus called the Por secretion system ( PorSS ) is required for assembly of SprB on the cell surface.", "output": "There is no related enetity." }, { "input": "Genetic and molecular analyses revealed that sprB is part of a seven - gene operon spanning 29. 3 kbp of DNA.", "output": "There is no related enetity." }, { "input": "In addition to sprB, three other genes of this operon ( sprC, sprD, and sprF ) are involved in gliding.", "output": "There is no related enetity." }, { "input": "Mutations in sprB, sprC, sprD, and sprF resulted in cells that failed to form spreading colonies on agar but that exhibited some motility on glass in wet mounts.", "output": "There is no related enetity." }, { "input": "SprF exhibits some similarity to Porphyromonas gingivalis PorP, which is required for secretion of gingipain protease virulence factors via the P. gingivalis PorSS.", "output": "Porphyromonas gingivalis, P . gingivalis." }, { "input": "F. johnsoniae sprF mutants produced SprB protein but were defective in localization of SprB to the cell surface, suggesting a role for SprF in secretion of SprB.", "output": "F . johnsoniae." }, { "input": "The F. johnsoniae PorSS is involved in secretion of extracellular chitinase in addition to its role in secretion of SprB.", "output": "F . johnsoniae." }, { "input": "SprF was not needed for chitinase secretion and may be specifically required for SprB secretion by the PorSS.", "output": "There is no related enetity." }, { "input": "Cells with nonpolar mutations in sprC or sprD produced and secreted SprB and propelled it rapidly along the cell surface.", "output": "There is no related enetity." }, { "input": "Multiple paralogs of sprB, sprC, sprD, and sprF are present in the genome, which may explain why mutations in sprB, sprC, sprD, and sprF do not result in complete loss of motility and suggests the possibility that semiredundant SprB - like adhesins may allow movement of cells over different surfaces.", "output": "There is no related enetity." }, { "input": "Perithecium morphogenesis in Sordaria macrospora.", "output": "Sordaria macrospora." }, { "input": "The perithecium of the self - fertile ascomycete Sordaria macrospora provides an excellent model in which to analyse fungal multicellular development.", "output": "Sordaria macrospora." }, { "input": "This study provides a detailed analysis of perithecium morphogenesis in the wild type and eight developmental mutants of S. macrospora, using a range of correlative microscopical techniques.", "output": "S . macrospora." }, { "input": "Fundamentally, perithecia and other complex multicellular structures produced by fungi arise by hyphal aggregation and adhesion, and these processes are followed by specialization and septation of hyphal compartments within the aggregates.", "output": "There is no related enetity." }, { "input": "Perithecial morphogenesis can be divided into the ascogonial, protoperithecial, and perithecial stages of development.", "output": "There is no related enetity." }, { "input": "At least 13 specialized, morphologically distinct cell - types are involved in perithecium morphogenesis, and these fall into three basic classes: hyphae, conglutinate cells and spores.", "output": "There is no related enetity." }, { "input": "Conglutinate cells arise from hyphal adhesion and certain perithecial hyphae develop from conglutinate cells.", "output": "There is no related enetity." }, { "input": "Various hypha - conglutinate cell transitions play important roles during the development of the perithecial wall and neck.", "output": "There is no related enetity." }, { "input": "Overexpression of the trichodiene synthase gene tri5 increases trichodermin production and antimicrobial activity in Trichoderma brevicompactum.", "output": "Trichoderma brevicompactum." }, { "input": "Trichoderma brevicompactum produces trichodermin, a simple trichothecene - type toxin that shares the first steps of the sesquiterpene biosynthetic pathway with other phytotoxic trichothecenes from Fusarium spp.", "output": "Trichoderma brevicompactum, Fusarium spp." }, { "input": "Trichodiene synthase catalyses the conversion of farnesyl pyrophosphate to trichodiene and it is encoded by the tri5 gene that was cloned and analysed functionally by homologous overexpression in T. brevicompactum.", "output": "T . brevicompactum." }, { "input": "tri5 expression was up - regulated in media with glucose, H ( 2 ) O ( 2 ) or glycerol.", "output": "There is no related enetity." }, { "input": "tri5 repression was observed in cultures supplemented with the antioxidants ferulic acid and tyrosol.", "output": "There is no related enetity." }, { "input": "Acetone extracts of tri5 - overexpressing transformants displayed higher antifungal activity than those from the wild - type.", "output": "There is no related enetity." }, { "input": "Chromatographic and spectroscopic analyses revealed that tri5 overexpression led to an increased production of trichodermin and tyrosol.", "output": "There is no related enetity." }, { "input": "Agar diffusion assays with these two purified metabolites from the tri5 - overexpressing transformant T. brevicompactum Tb41tri5 showed that only trichodermin had antifungal activity against Saccharomyces cerevisiae, Kluyveromyces marxianus, Candida albicans, Candida glabrata, Candida tropicalis and Aspergillus fumigatus, in most cases such activity being higher than that observed for amphotericin B and hygromycin.", "output": "T . brevicompactum, Saccharomyces cerevisiae, Kluyveromyces marxianus, Candida albicans, Candida glabrata, Candida tropicalis, Aspergillus fumigatus." }, { "input": "Our results point to the significant role of tri5 in the production of trichodermin and in the antifungal activity of T. brevicompactum.", "output": "T . brevicompactum." }, { "input": "Heterotrimeric Galpha protein Pga1 from Penicillium chrysogenum triggers germination in response to carbon sources and affects negatively resistance to different stress conditions.", "output": "Penicillium chrysogenum." }, { "input": "Heterotrimeric Galpha protein Pga1 of Penicillium chrysogenum controls vegetative growth, conidiation and secondary metabolite production.", "output": "Penicillium chrysogenum." }, { "input": "In this work we studied the role of Pga1 in spore germination and resistance to different stress conditions.", "output": "There is no related enetity." }, { "input": "Strains G203R - T ( expressing the dominant inactivating pga1 ( G203R ) allele ) and Deltapga1 ( deleted pga1 ) showed a delayed and asynchronic germination pattern, and a decrease in the percentage of germination, which occurred in only 70 - 80 % of the total conidia.", "output": "Strains G203R - T, Deltapga1." }, { "input": "In contrast, in strains expressing the dominant activating pga1 ( G42R ) allele, germination occurred at earlier times and in 100 % of conidia.", "output": "There is no related enetity." }, { "input": "In addition, strains with the pga1 ( G42R ) allele were able to bypass the carbon source ( glucose or sucrose ) requirement for germination in about 64 % of conidia.", "output": "strains with the pga1 ( G42R ) allele." }, { "input": "Thus Pga1 plays an important, but not essential, role in germination, mediating carbon source sensing.", "output": "There is no related enetity." }, { "input": "Regulation of germination by Pga1 is probably mediated by cAMP, as intracellular levels of this secondary messenger undergo a peak before the onset of germination only in strains with an active Pga1.", "output": "strains with an active Pga1." }, { "input": "Pga1 activity is also a determinant factor in the resistance to different stress conditions.", "output": "There is no related enetity." }, { "input": "Absence or inactivation of Pga1 allow growth on SDS - containing minimal medium, increase resistance of conidia to thermal and oxidative stress, and increase resistance of vegetative mycelium to thermal and osmotic stress.", "output": "There is no related enetity." }, { "input": "In contrast, constitutive activation of Pga1 causes a decrease in the resistance of conidia to thermal stress and of vegetative mycelium to thermal and osmotic stress.", "output": "There is no related enetity." }, { "input": "Together with our previously reported results, we show in this work that Pga1 plays a central role in the regulation of the whole growth - developmental program of this biotechnologically important fungus.", "output": "There is no related enetity." }, { "input": "Systemic therapy in the management of metastatic or locally recurrent adenoid cystic carcinoma of the salivary glands: a systematic review.", "output": "There is no related enetity." }, { "input": "Adenoid cystic carcinomas ( ACC ) are rare cancers usually arising in the salivary glands.", "output": "There is no related enetity." }, { "input": "Once metastatic, the natural history can vary; some patients with indolent cancer remain asymptomatic for long periods, whereas others have rapidly progressive disease.", "output": "There is no related enetity." }, { "input": "Chemotherapy is generally reserved for the palliative treatment of symptomatic locally recurrent or metastatic disease that is not amenable to further surgery or radiation.", "output": "There is no related enetity." }, { "input": "Prospective trials of chemotherapy in advanced ACC are limited, and the optimum regimen is unclear.", "output": "There is no related enetity." }, { "input": "The aim of this systematic review is to summarise and rate the quality of trials assessing chemotherapy for treatment of ACC, by use of the European Lung Cancer Working Party scoring system.", "output": "There is no related enetity." }, { "input": "Endpoints evaluated include tumour response and rates of symptomatic improvement.", "output": "There is no related enetity." }, { "input": "34 trials involving 441 patients are included.", "output": "There is no related enetity." }, { "input": "We give evidence - based recommendations for management of ACC with chemotherapy, along with considerations for the design of future clinical trials in this disease.", "output": "There is no related enetity." }, { "input": "Disrupted energy metabolism and neuronal circuit dysfunction in cognitive impairment and Alzheimer ' s disease.", "output": "There is no related enetity." }, { "input": "Epidemiological, neuropathological, and functional neuroimaging evidence implicates global and regional disruptions in brain metabolism and energetics in the pathogenesis of cognitive impairment.", "output": "There is no related enetity." }, { "input": "Nerve cell microcircuits are modified by excitatory and inhibitory synaptic activity and neurotrophic factors.", "output": "There is no related enetity." }, { "input": "Ageing and Alzheimer ' s disease cause perturbations in cellular energy metabolism, level of excitation or inhibition, and neurotrophic factor release, which overwhelm compensatory mechanisms and result in dysfunction of neuronal microcircuits and brain networks.", "output": "There is no related enetity." }, { "input": "A prolonged positive energy balance impairs the ability of neurons to adapt to oxidative and metabolic stress.", "output": "There is no related enetity." }, { "input": "Results from experimental studies in animals show how disruptions caused by chronic positive energy balance, such as diabetes, lead to accelerated cognitive ageing and Alzheimer ' s disease.", "output": "There is no related enetity." }, { "input": "Therapeutic interventions to allay cognitive dysfunction that target energy metabolism and adaptive stress responses ( such as neurotrophin signalling ) have been effective in animal models and in preliminary studies in humans.", "output": "humans." }, { "input": "Behavioural - variant frontotemporal dementia: diagnosis, clinical staging, and management.", "output": "There is no related enetity." }, { "input": "Patients with behavioural - variant frontotemporal dementia ( bvFTD ) present with insidious changes in personality and interpersonal conduct that indicate progressive disintegration of the neural circuits involved in social cognition, emotion regulation, motivation, and decision making.", "output": "There is no related enetity." }, { "input": "The underlying pathological changes are heterogeneous and are characterised by various intraneuronal inclusions.", "output": "There is no related enetity." }, { "input": "Biomarkers to detect these histopathological changes in life are becoming increasingly important with the development of disease - modifying drugs.", "output": "There is no related enetity." }, { "input": "Gene mutations have been found that collectively account for around 10 - 20 % of cases.", "output": "There is no related enetity." }, { "input": "Recently, criteria proposed for bvFTD define three levels of diagnostic certainty: possible, probable, and definite.", "output": "There is no related enetity." }, { "input": "Detailed history taking from family members to elicit behavioural features underpins the diagnostic process, with support from neuropsychological testing designed to detect impairment in decision making, emotion processing, and social cognition.", "output": "There is no related enetity." }, { "input": "Brain imaging is important for increasing the level of diagnostic certainty.", "output": "There is no related enetity." }, { "input": "A recently developed staging instrument shows much promise for monitoring patients and evaluating therapies, which at present are aimed at symptom amelioration.", "output": "There is no related enetity." }, { "input": "Carer education and support remain of paramount importance.", "output": "There is no related enetity." }, { "input": "Spiral architecture of the nucleoid in Bdellovibrio bacteriovorus.", "output": "Bdellovibrio bacteriovorus." }, { "input": "We present a cryo - electron tomographic analysis of the three - dimensional architecture of a strain of the Gram - negative bacterium Bdellovibrio bacteriovorus in which endogenous MreB2 was replaced with monomeric teal fluorescent protein ( mTFP ) - labeled MreB2.", "output": "Bdellovibrio bacteriovorus." }, { "input": "In contrast to wild - type Bdellovibrio cells that predominantly displayed a compact nucleoid region, cells expressing mTFP - labeled MreB2 displayed a twisted spiral organization of the nucleoid.", "output": "There is no related enetity." }, { "input": "The more open structure of the MreB2 - mTFP nucleoids enabled clear in situ visualization of ribosomes decorating the periphery of the nucleoid.", "output": "There is no related enetity." }, { "input": "Ribosomes also bordered the edges of more compact nucleoids from both wild - type cells and mutant cells.", "output": "There is no related enetity." }, { "input": "Surprisingly, MreB2 - mTFP localized to the interface between the spiral nucleoid and the cytoplasm, suggesting an intimate connection between nucleoid architecture and MreB arrangement.", "output": "There is no related enetity." }, { "input": "Further, in contrast to wild - type cells, where a single tight chemoreceptor cluster localizes close to the single polar flagellum, MreB2 - mTFP cells often displayed extended chemoreceptor arrays present at one or both poles and displayed multiple or inaccurately positioned flagella.", "output": "There is no related enetity." }, { "input": "Our findings provide direct structural evidence for spiral organization of the bacterial nucleoid and suggest a possible role for MreB in regulation of nucleoid architecture and localization of the chemotaxis apparatus.", "output": "There is no related enetity." }, { "input": "A transcriptional regulator and ABC transporters link stress tolerance, ( p ) ppGpp, and genetic competence in Streptococcus mutans.", "output": "There is no related enetity." }, { "input": "Streptococcus mutans, a primary agent of dental caries, has three ( p ) ppGpp synthases: RelA, which is required for a mupirocin - induced stringent response; RelP, which produces ( p ) ppGpp during exponential growth and is regulated by the RelRS two - component system; and RelQ.", "output": "There is no related enetity." }, { "input": "Transcription of relPRS and a gene cluster ( SMu0835 to SMu0837 ) located immediately upstream was activated in cells grown with aeration and during a stringent response, respectively.", "output": "There is no related enetity." }, { "input": "Bioinformatic analysis predicted that SMu0836 and SMu0837 encode ABC exporters, which we designated rcrPQ ( rel competence - related ) genes, respectively.", "output": "There is no related enetity." }, { "input": "SMu0835 ( rcrR ) encodes a MarR family transcriptional regulator.", "output": "There is no related enetity." }, { "input": "Reverse transcriptase PCR ( RT - PCR ) and quantitative RT - PCR analysis showed that RcrR functions as an autogenous negative regulator of the expression of the rcrRPQ operon.", "output": "There is no related enetity." }, { "input": "A mutant in which a polar insertion replaced the SMu836 gene ( Delta836polar ) grew more slowly and had final yields that were lower than those of the wild - type strain.", "output": "There is no related enetity." }, { "input": "Likewise, the Delta836polar strain had an impaired capacity to form biofilms, grew poorly at pH 5. 5, and was more sensitive to oxidative stressors.", "output": "There is no related enetity." }, { "input": "Optimal expression of rcrPQ required RelP and vice versa.", "output": "There is no related enetity." }, { "input": "Replacement of rcrR with a nonpolar antibiotic resistance marker ( Delta835np ), which leads to overexpression of rcrPQ, yielded a strain that was not transformable with exogenous DNA.", "output": "There is no related enetity." }, { "input": "Transcriptional analysis revealed that the expression of comYA and comX was dramatically altered in the Delta835np and Delta836polar mutants.", "output": "There is no related enetity." }, { "input": "Collectively, the data support the suggestion that the rcrRPQ gene products play a critical role in physiologic homeostasis and stress tolerance by linking ( p ) ppGpp metabolism, acid and oxidative stress tolerance, and genetic competence.", "output": "There is no related enetity." }, { "input": "Mapping functional domains of colicin M.", "output": "There is no related enetity." }, { "input": "Colicin M ( Cma ) lyses Escherichia coli cells by inhibiting murein biosynthesis through hydrolysis of the phosphate ester between C ( 55 ) - polyisoprenol and N - acetylmuramyl ( MurNAc ) - pentapeptide - GlcNAc in the periplasm.", "output": "Escherichia coli." }, { "input": "To identify Cma functional domains, we isolated 54 point mutants and small deletion mutants and examined their cytotoxicity levels.", "output": "There is no related enetity." }, { "input": "Activity and uptake mutants were distinguished by osmotic shock, which transfers Cma into the periplasm independent of the specific FhuA receptor and the Ton system.", "output": "There is no related enetity." }, { "input": "Deletion of the hydrophobic helix alpha1, which extends from the compact Cma structure, abolished interference with the antibiotic albomycin, which is transported across the outer membrane by the same system as Cma, thereby identifying alpha1 as the Cma site that binds to FhuA.", "output": "There is no related enetity." }, { "input": "Deletion of the C - terminal Lys - Arg strongly reduced Cma translocation across the outer membrane after binding to FhuA.", "output": "There is no related enetity." }, { "input": "Conversion of Asp226 to Glu, Asn, or Ala inactivated Cma.", "output": "There is no related enetity." }, { "input": "Asp226 is exposed at the Cma surface and is surrounded by Asp225, Asp229, His235, Tyr228, and Arg236; replacement of each with alanine inactivated Cma.", "output": "There is no related enetity." }, { "input": "We propose that Asp226 directly participates in phosphate ester hydrolysis and that the surrounding residues contribute to the active site.", "output": "There is no related enetity." }, { "input": "These residues are strongly conserved in Cma - like proteins of other species.", "output": "There is no related enetity." }, { "input": "Replacement of other conserved residues with alanine inactivated Cma; these mutations probably altered the Cma structure, as particularly apparent for mutants in the unique open Beta - barrel of Cma, which were isolated in lower yields.", "output": "There is no related enetity." }, { "input": "Our results identify regions in Cma responsible for uptake and activity and support the concept of a three - domain arrangement of Cma.", "output": "There is no related enetity." }, { "input": "The recombinase IntA is required for excision of esp - containing ICEEfm1 in Enterococcus faecium.", "output": "Enterococcus faecium." }, { "input": "Comparative genome analysis of Enterococcus faecium recently revealed that a genomic island containing the esp gene, referred to as the esp - containing pathogenicity island ( esp PAI ), can be transferred by conjugation and contains a partial Tn916 - like element and an integrase gene, intA.", "output": "Enterococcus faecium." }, { "input": "Here, we characterize the role of intA in the excision of the esp PAI.", "output": "There is no related enetity." }, { "input": "An intA insertion - deletion mutant in E. faecium E1162 ( E1162DeltaintA ) was constructed and in trans complemented with wild - type intA ( E1162DeltaintA:: pEF30 ).", "output": "E . faecium E1162, E1162DeltaintA, E1162DeltaintA." }, { "input": "Circular intermediates ( CI ) of excised esp PAI were determined using inverse PCR analysis on purified chromosomal DNA from strains E1162, E1162Deltaesp, E1162DeltaintA, and E1162DeltaintA:: pEF30.", "output": "There is no related enetity." }, { "input": "In E1162 and E1162Deltaesp, CI of the esp PAI were detected.", "output": "There is no related enetity." }, { "input": "No CI were detected in E1162DeltaintA, while in the complemented strain E1162DeltaintA:: pEF30 CI formation was restored, indicating that intA is essential for excision and subsequent mobilization of the esp - containing genomic island in E. faecium.", "output": "E . faecium." }, { "input": "Based on the fact that this island can be mobilized and is self - transmissible, we propose to change the name of the esp PAI to ICEEfm1.", "output": "There is no related enetity." }, { "input": "Functional and phylogenetic analysis of ureD in Shiga toxin - producing Escherichia coli.", "output": "Escherichia coli." }, { "input": "Enterohemorrhagic Escherichia coli ( EHEC ) is a food - borne pathogen that can cause severe health complications and utilizes a much lower infectious dose than other E. coli pathotypes.", "output": "Escherichia coli, EHEC, E . coli." }, { "input": "Despite having an intact ure locus, ureDABCEFG, the majority of EHEC strains are phenotypically urease negative under tested conditions.", "output": "EHEC." }, { "input": "Urease activity potentially assists with survival fitness by enhancing acid tolerance during passage through the stomach or by aiding with colonization in either human or animal reservoirs.", "output": "human." }, { "input": "Previously, in the EHEC O157: H7 Sakai strain, a point mutation in ureD, encoding a urease chaperone protein, was identified, resulting in a substitution of an amber stop codon for glutamine.", "output": "EHEC O157 : H7." }, { "input": "This single nucleotide polymorphism ( SNP ) is observed in the majority of EHEC O157: H7 isolates and correlates with a negative urease phenotype in vitro.", "output": "EHEC O157 : H7." }, { "input": "We demonstrate that the lack of urease activity in vitro is not solely due to the amber codon in ureD.", "output": "There is no related enetity." }, { "input": "Our analysis has identified two additional SNPs in ureD affecting amino acid positions 38 and 205, in both cases determining whether the encoded amino acid is leucine or proline.", "output": "There is no related enetity." }, { "input": "Phylogenetic analysis based on Ure protein sequences from a variety of urease - encoding bacteria demonstrates that the proline at position 38 is highly conserved among Gram - negative bacteria.", "output": "There is no related enetity." }, { "input": "Experiments reveal that the L38P substitution enhances urease enzyme activity; however, the L205P substitution does not.", "output": "There is no related enetity." }, { "input": "Multilocus sequence typing analysis for a variety of Shiga toxin - producing E. coli isolates combined with the ureD sequence reveals that except for a subset of the O157: H7 strains, neither the in vitro urease - positive phenotype nor the ureD sequence is phylogenetically restricted.", "output": "E . coli, O157 : H7." }, { "input": "Genome - wide identification of Mycobacterium tuberculosis exported proteins with roles in intracellular growth.", "output": "Mycobacterium tuberculosis." }, { "input": "The exported proteins of Mycobacterium tuberculosis that are localized at the bacterial cell surface or secreted into the environment are ideally situated to interact with host factors and to function in virulence.", "output": "Mycobacterium tuberculosis." }, { "input": "In this study, we constructed a novel Beta - lactamase reporter transposon and used it directly in M. tuberculosis for genome - wide identification of exported proteins.", "output": "M . tuberculosis." }, { "input": "From 177 Beta - lactam - resistant transposon mutants, we identified 111 different exported proteins.", "output": "There is no related enetity." }, { "input": "The majority of these proteins have no known function, and for nearly half of the proteins, our demonstration that they are exported when fused to a Beta - lactamase reporter is the first experimental proof of their extracytoplasmic localization.", "output": "There is no related enetity." }, { "input": "The transposon mutants in our banked library were of further value as a collection of mutants lacking individual exported proteins.", "output": "There is no related enetity." }, { "input": "By individually testing each of 111 mutants for growth in macrophages, six attenuated mutants with insertions in mce1A, mce1B, mce2F, rv0199, ctaC, and lppX were identified.", "output": "There is no related enetity." }, { "input": "Given that much of the M. tuberculosis genome encodes proteins of unknown function, our library of mapped transposon mutants is a valuable resource for efforts in functional genomics.", "output": "M . tuberculosis." }, { "input": "This work also demonstrates the power of a Beta - lactamase reporter transposon that could be applied similarly to other bacterial pathogens.", "output": "There is no related enetity." }, { "input": "Maternal influence on philopatry and space use by juvenile brushtail possums ( Trichosurus vulpecula ).", "output": "Trichosurus vulpecula." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "The causes of juvenile sex - biased philopatry and space use in mammals remain poorly understood, and results of previous research have been conflicting.", "output": "There is no related enetity." }, { "input": "Experimental interventions and manipulations on wild populations are rare, but can play an important role in establishing the factors governing offspring space use.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We experimentally removed mothers of independent juvenile brushtail possums from the maternal home range and examined changes in offspring space use with global positioning system collars.", "output": "There is no related enetity." }, { "input": "We examined the influence of mother absence on philopatric behaviour, and determined whether or not maternal presence affected offspring space use.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We fitted a longitudinal linear mixed effects model to demonstrate a change over time in the home range size of juveniles following experimental treatment by the removal of their mothers.", "output": "There is no related enetity." }, { "input": "When mothers were removed from the natal range, juveniles occupied significantly larger home range areas, with average increases of 175 % in 95 % kernel density estimates and 289 % in minimum convex polygon estimates.", "output": "There is no related enetity." }, { "input": "This increase occurred within the first month following mother absence and was independent of juvenile sex.", "output": "There is no related enetity." }, { "input": "Home ranges of control juveniles did not change during the same time period.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Changes in the spatial structure of mammalian populations in response to removal of individuals have important implications for pest management.", "output": "There is no related enetity." }, { "input": "The impacts of management strategies which target particular individuals in a population may counteract conservation benefits through their effect on the space use of survivors.", "output": "There is no related enetity." }, { "input": "Studies involving experimental removals provide important information on consequences of control and also yield insights into the causes of mammalian space use, philopatric behaviours and ultimately dispersal.", "output": "There is no related enetity." }, { "input": "Competitive interactions shape offspring performance in relation to seasonal timing of emergence in Atlantic salmon.", "output": "Atlantic salmon." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Timing of birth / hatching may have strong effects on offspring fitness.", "output": "There is no related enetity." }, { "input": "Breeding time is generally considered to have evolved to match offspring arrival with optimal seasonal environmental conditions, though this is rarely tested experimentally and factors shaping the relations between timing of birth and reproductive success are often poorly understood.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "By manipulating incubation temperature of Atlantic salmon embryos, and hence controlling for maternal and genetic effects, we obtained offspring emerging from nests prior to ( accelerated ), during and after ( decelerated ) normal emergence times, and accordingly experienced widely different seasonal environmental conditions at emergence ( stream temperature range 4 - 16 ^ 0C ).", "output": "Atlantic salmon." }, { "input": "The accelerated group emerged at temperatures that are generally considered to be highly sub - optimal for growth and likely imposes strong constraints on feeding and activity, and during a peak in water discharge which is expected to negatively influence habitat availability.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "In the wild, overall mortality during the period after emergence was 79 %, and was significantly affected by both release density and emergence timing.", "output": "There is no related enetity." }, { "input": "Accelerated offspring, which emerged earliest and experienced the harshest environmental conditions, had both highest survival and largest final body size.", "output": "There is no related enetity." }, { "input": "The effect was particularly strong at the high density release site, where survival of accelerated offspring was significantly higher than both the normal and decelerated groups.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "In more controlled semi - natural environments, all developmental groups were able to perform well, but accelerated offspring had a relatively better performance than the later emerging offspring when density was high.", "output": "There is no related enetity." }, { "input": "Furthermore, the relative performance of the different groups was not sensitive to water discharge regimes ( temporally stable vs. fluctuating ).", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "These results suggest that the performance of offspring in relation to seasonal timing of emergence is highly affected by competitive interactions in Atlantic salmon.", "output": "Atlantic salmon." }, { "input": "Although a match between phenology and optimal seasonal environmental conditions may be highly important for organisms depending on specific resources that are only available during a limited period of the season, such resources may be available in variable amounts year around for many organisms.", "output": "There is no related enetity." }, { "input": "For these, offspring success may to a larger degree be shaped by the timing of their hatching / birth relative to each other, and particularly so under high population densities.", "output": "There is no related enetity." }, { "input": "Disentangling the effects of predator hunting mode and habitat domain on the top - down control of insect herbivores.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Polyphagous predatory invertebrates play a key role in the top - down control of insect herbivores.", "output": "There is no related enetity." }, { "input": "However, predicting predation risk for herbivores is not a simple function of predator species richness.", "output": "There is no related enetity." }, { "input": "Predation risk may be reduced or enhanced depending on the functional characteristics predator species.", "output": "There is no related enetity." }, { "input": "We predict that where predator species spatially overlap this will reduce predation risk for herbivores by allowing negative inter - specific interaction between predators to occur.", "output": "There is no related enetity." }, { "input": "Where increased predation risk occurs, we also predict that this will have a cascading effect through the food chain reducing plant growth.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We used a substitutive replicated block design to identify the effect of similarity and dissimilarity in predator hunting mode ( e. g. ' sit and wait ', ' sit and pursue ', and ' active ' ) and habitat domain ( e. g. canopy or ground ) on the top - down control of planthoppers in grasslands.", "output": "There is no related enetity." }, { "input": "Predators included within the mesocosms were randomly selected from a pool of 17 local species.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Predation risk was reduced where predators shared the same habitat domain, independent of whether they shared hunting modes.", "output": "There is no related enetity." }, { "input": "Where predators shared the same habitat domains, there was some evidence that this had a cascading negative effect on the re - growth of grass biomass.", "output": "There is no related enetity." }, { "input": "Where predator habitat domains did not overlap, there were substitutable effects on predation risk to planthoppers.", "output": "There is no related enetity." }, { "input": "Predation risk for planthoppers was affected by taxonomic identity of predator species, i. e. whether they were beetles, spiders or true bugs.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Our results indicated that in multi - predator systems, the risk of predation is typically reduced.", "output": "There is no related enetity." }, { "input": "Consideration of functional characteristics of individual species, in particular aspects of habitat domain and hunting mode, are crucial in predicting the effects of multi - predator systems on the top - down control of herbivores.", "output": "There is no related enetity." }, { "input": "Clinical experience and laboratory investigations in patients with anti - NMDAR encephalitis.", "output": "There is no related enetity." }, { "input": "Since its discovery in 2007, the encephalitis associated with antibodies against the N - methyl - D - aspartate receptor ( NMDAR ) has entered the mainstream of neurology and other disciplines.", "output": "There is no related enetity." }, { "input": "Most patients with anti - NMDAR encephalitis develop a multistage illness that progresses from psychosis, memory deficits, seizures, and language disintegration into a state of unresponsiveness with catatonic features often associated with abnormal movements, and autonomic and breathing instability.", "output": "There is no related enetity." }, { "input": "The disorder predominantly affects children and young adults, occurs with or without tumour association, and responds to treatment but can relapse.", "output": "There is no related enetity." }, { "input": "The presence of a tumour ( usually an ovarian teratoma ) is dependent on age, sex, and ethnicity, being more frequent in women older than 18 years, and slightly more predominant in black women than it is in white women.", "output": "There is no related enetity." }, { "input": "Patients treated with tumour resection and immunotherapy ( corticosteroids, intravenous immunoglobulin, or plasma exchange ) respond faster to treatment and less frequently need second - line immunotherapy ( cyclophosphamide or rituximab, or both ) than do patients without a tumour who receive similar initial immunotherapy.", "output": "There is no related enetity." }, { "input": "More than 75 % of all patients have substantial recovery that occurs in inverse order of symptom development and is associated with a decline of antibody titres.", "output": "There is no related enetity." }, { "input": "Patients ' antibodies cause a titre - dependent, reversible decrease of synaptic NMDAR by a mechanism of crosslinking and internalisation.", "output": "There is no related enetity." }, { "input": "On the basis of models of pharmacological or genetic disruption of NMDAR, these antibody effects reveal a probable pathogenic relation between the depletion of receptors and the clinical features of anti - NMDAR encephalitis.", "output": "There is no related enetity." }, { "input": "Acute encephalopathy with inflammation - mediated status epilepticus.", "output": "There is no related enetity." }, { "input": "Fever - induced refractory epileptic encephalopathy in school - aged children ( FIRES ), and idiopathic hemiconvulsion - hemiplegia syndrome ( IHHS ) are both triggered by fever, although evidence for a causal microorganism or an autoimmune phenomenon is lacking.", "output": "There is no related enetity." }, { "input": "FIRES begins in school age with status epilepticus lasting several weeks, involves perisylvian areas including mesial temporal structures, and is followed by pharmacoresistant epilepsy with major cognitive deterioration.", "output": "There is no related enetity." }, { "input": "IHHS begins in infancy with unilateral clonic status epilepticus and is followed by hemiplegia with pharmacoresistant epilepsy.", "output": "There is no related enetity." }, { "input": "The aetiology of FIRES and IHHS remains unknown, although clinical features and experimental models point to a likely vicious cycle involving inflammation and seizure activity that depends on the stage of brain maturation.", "output": "There is no related enetity." }, { "input": "We therefore propose to group these conditions under the concept of acute encephalopathy with inflammation - mediated status epilepticus.", "output": "There is no related enetity." }, { "input": "In addition to preliminary but encouraging clinical observations, there are theoretical reasons to consider the ketogenic diet as an early means to control both seizures and inflammation.", "output": "There is no related enetity." }, { "input": "The ribonucleotide reductase large subunit ( RRM1 ) as a predictive factor in patients with cancer.", "output": "There is no related enetity." }, { "input": "The large subunit of human ribonucleotide reductase, RRM1, is involved in the regulation of cell proliferation, cell migration, tumour and metastasis development, and the synthesis of deoxyribonucleotides for DNA synthesis.", "output": "human." }, { "input": "It is also a cellular target for the chemotherapeutic agent, gemcitabine.", "output": "There is no related enetity." }, { "input": "RRM1 has been studied in a large number of patients with different types of cancer, such as non - small - cell lung cancer, pancreatic cancer, breast cancer, and biliary tract cancer, to establish its prognostic or predictive value when patients were treated with gemcitabine, and mRNA expression and genetic variants as determined by genotyping have in some cases been associated with clinical outcome of patients with cancer.", "output": "There is no related enetity." }, { "input": "Here, we review preclinical and clinical studies of RRM1 assessment and discuss the further steps in the development of this clinically pertinent biomarker.", "output": "There is no related enetity." }, { "input": "KRAS, BRAF, PIK3CA, and PTEN mutations: implications for targeted therapies in metastatic colorectal cancer.", "output": "There is no related enetity." }, { "input": "The discovery of mutant KRAS as a predictor of resistance to epidermal growth - factor receptor ( EGFR ) monoclonal antibodies brought a major change in the treatment of metastatic colorectal cancer.", "output": "There is no related enetity." }, { "input": "This seminal finding also highlighted our sparse knowledge about key signalling pathways in colorectal tumours.", "output": "There is no related enetity." }, { "input": "Drugs that inhibit oncogenic alterations such as phospho - MAP2K ( also called MEK ), phospho - AKT, and mutant B - RAF seem promising as single treatment or when given with EGFR inhibitors.", "output": "There is no related enetity." }, { "input": "However, our understanding of the precise role these potential drug targets have in colorectal tumours, and the oncogenic dependence that tumours might have on these components, has not progressed at the same rate.", "output": "There is no related enetity." }, { "input": "As a result, patient selection and prediction of treatment effects remain problematic.", "output": "There is no related enetity." }, { "input": "We review the role of mutations in genes other than KRAS on the efficacy of anti - EGFR therapy, and discuss strategies to target these oncogenic alterations alone or in combination with receptor tyrosine - kinase inhibition.", "output": "There is no related enetity." }, { "input": "Conserved function of the Kruppel gap gene in the blowfly Lucilia sericata, despite anterior shift of expression.", "output": "Lucilia sericata." }, { "input": "To determine whether expression patterns of segmentation genes found in Drosophila melanogaster can be scaled to pattern larger insects, we studied the expression of the Kruppel ( Kr ) gene in the blowfly Lucilia sericata.", "output": "Drosophila melanogaster, Lucilia sericata." }, { "input": "Compared with Drosophila Kr, L. sericata Kr showed an unexpected 10 % shift of expression towards the anterior pole.", "output": "Drosophila, L . sericata." }, { "input": "Furthermore, expression domains not found in D. melanogaster were present at the blastoderm stage of L. sericata.", "output": "D . melanogaster, L . sericata." }, { "input": "To compare Kr activity and function, we employed RNA interference - mediated gene silencing.", "output": "There is no related enetity." }, { "input": "We found Kr phenotypes in L. sericata comparable with those observed in D. melanogaster, demonstrating that L. sericata Kr functions as a gap gene as it does in Drosophila.", "output": "L . sericata, D . melanogaster, L . sericata, Drosophila." }, { "input": "Our results show that, despite an anterior shift in expression, Kr function has remained conserved during the evolution of the blowflies.", "output": "There is no related enetity." }, { "input": "Antibiotics and UV radiation induce competence for natural transformation in Legionella pneumophila.", "output": "Legionella pneumophila." }, { "input": "Natural transformation by competence is a major mechanism of horizontal gene transfer in bacteria.", "output": "There is no related enetity." }, { "input": "Competence is defined as the genetically programmed physiological state that enables bacteria to actively take up DNA from the environment.", "output": "There is no related enetity." }, { "input": "The conditions that signal competence development are multiple and elusive, complicating the understanding of its evolutionary significance.", "output": "There is no related enetity." }, { "input": "We used expression of the competence gene comEA as a reporter of competence development and screened several hundred molecules for their ability to induce competence in the freshwater living pathogen Legionella pneumophila.", "output": "Legionella pneumophila." }, { "input": "We found that comEA expression is induced by chronic exposure to genotoxic molecules such as mitomycin C and antibiotics of the fluoroquinolone family.", "output": "There is no related enetity." }, { "input": "These results indicated that, in L. pneumophila, competence may be a response to genotoxic stress.", "output": "L . pneumophila." }, { "input": "Sunlight - emitted UV light represents a major source of genotoxic stress in the environment and we found that exposure to UV radiation effectively induces competence development.", "output": "There is no related enetity." }, { "input": "For the first time, we show that genetic exchanges by natural transformation occur within an UV - stressed population.", "output": "There is no related enetity." }, { "input": "Genotoxic stress induces the RecA - dependent SOS response in many bacteria.", "output": "There is no related enetity." }, { "input": "However, genetic and phenotypic evidence suggest that L. pneumophila lacks a prototypic SOS response and competence development in response to genotoxic stress is RecA independent.", "output": "L . pneumophila." }, { "input": "Our results strengthen the hypothesis that competence may have evolved as a DNA damage response in SOS - deficient bacteria.", "output": "There is no related enetity." }, { "input": "This parasexual response to DNA damage may have enabled L. pneumophila to acquire and propagate foreign genes, contributing to the emergence of this human pathogen.", "output": "L . pneumophila, human." }, { "input": "Identification of missing genes and enzymes for autotrophic carbon fixation in crenarchaeota.", "output": "There is no related enetity." }, { "input": "Two autotrophic carbon fixation cycles have been identified in Crenarchaeota.", "output": "There is no related enetity." }, { "input": "The dicarboxylate / 4 - hydroxybutyrate cycle functions in anaerobic or microaerobic autotrophic members of the Thermoproteales and Desulfurococcales.", "output": "There is no related enetity." }, { "input": "The 3 - hydroxypropionate / 4 - hydroxybutyrate cycle occurs in aerobic autotrophic Sulfolobales; a similar cycle may operate in autotrophic aerobic marine Crenarchaeota.", "output": "There is no related enetity." }, { "input": "Both cycles form succinyl - coenzyme A ( CoA ) from acetyl - CoA and two molecules of inorganic carbon, but they use different means.", "output": "There is no related enetity." }, { "input": "Both cycles have in common the ( re ) generation of acetyl - CoA from succinyl - CoA via identical intermediates.", "output": "There is no related enetity." }, { "input": "Here, we identified several missing enzymes / genes involved in the seven - step conversion of succinyl - CoA to two molecules of acetyl - CoA in Thermoproteus neutrophilus ( Thermoproteales ), Ignicoccus hospitalis ( Desulfurococcales ), and Metallosphaera sedula ( Sulfolobales ).", "output": "Thermoproteus neutrophilus, Ignicoccus hospitalis, Metallosphaera sedula." }, { "input": "The identified enzymes / genes include succinyl - CoA reductase, succinic semialdehyde reductase, 4 - hydroxybutyrate - CoA ligase, bifunctional crotonyl - CoA hydratase / ( S ) - 3 - hydroxybutyryl - CoA dehydrogenase, and beta - ketothiolase.", "output": "There is no related enetity." }, { "input": "4 - Hydroxybutyryl - CoA dehydratase, which catalyzes a mechanistically intriguing elimination of water, is well conserved and rightly can be considered the key enzyme of these two cycles.", "output": "There is no related enetity." }, { "input": "In contrast, several of the other enzymes evolved from quite different sources, making functional predictions based solely on genome interpretation difficult, if not questionable.", "output": "There is no related enetity." }, { "input": "Unexpected coregulator range for the global regulator Lrp of Escherichia coli and Proteus mirabilis.", "output": "Escherichia coli, Proteus mirabilis." }, { "input": "The Lrp / AsnC family of transcription factors links gene regulation to metabolism in bacteria and archaea.", "output": "There is no related enetity." }, { "input": "Members of this family, collectively, respond to a wide range of amino acids as coregulators.", "output": "There is no related enetity." }, { "input": "In Escherichia coli, Lrp regulates over 200 genes directly and is well known to respond to leucine and, to a somewhat lesser extent, alanine.", "output": "Escherichia coli." }, { "input": "We focused on Lrp from Proteus mirabilis and E. coli, orthologs with 98 % identity overall and identical helix - turn - helix motifs, for which a previous study nevertheless found functional differences.", "output": "Proteus mirabilis, E . coli." }, { "input": "Sequence differences between these orthologs, within and adjacent to the amino acid - responsive RAM domain, led us to test for differential sensitivity to coregulatory amino acids.", "output": "There is no related enetity." }, { "input": "In the course of this investigation, we found, via in vivo reporter fusion assays and in vitro electrophoretic mobility shift experiments, that E. coli Lrp itself responded to a broader range of amino acids than was previously appreciated.", "output": "E . coli." }, { "input": "In particular, for both the E. coli and P. mirabilis orthologs, Lrp responsiveness to methionine was similar in magnitude to that to leucine.", "output": "E . coli, P . mirabilis." }, { "input": "Both Lrp orthologs are also fairly sensitive to Ile, His, and Thr.", "output": "There is no related enetity." }, { "input": "These observations suggest that Lrp ties gene expression in the Enterobacteriaceae rather extensively to physiological status, as reflected in amino acid pools.", "output": "There is no related enetity." }, { "input": "These findings also have substantial implications for attempts to model regulatory architecture from transcriptome measurements or to infer such architecture from genome sequences, and they suggest that even well - studied regulators deserve ongoing exploration.", "output": "There is no related enetity." }, { "input": "Labeling and enzyme studies of the central carbon metabolism in Metallosphaera sedula.", "output": "Metallosphaera sedula." }, { "input": "Metallosphaera sedula ( Sulfolobales, Crenarchaeota ) uses the 3 - hydroxypropionate / 4 - hydroxybutyrate cycle for autotrophic carbon fixation.", "output": "Metallosphaera sedula." }, { "input": "In this pathway, acetyl - coenzyme A ( CoA ) and succinyl - CoA are the only intermediates that can be considered common to the central carbon metabolism.", "output": "There is no related enetity." }, { "input": "We addressed the question of which intermediate of the cycle most biosynthetic routes branch off.", "output": "There is no related enetity." }, { "input": "We labeled autotrophically growing cells by using 4 - hydroxy [ 1 - ^ 1 ^ 4C ] butyrate and [ 1, 4 - ^ 1 ^ 3C1 ] succinate, respectively, as precursors for biosynthesis.", "output": "There is no related enetity." }, { "input": "The labeling patterns of protein - derived amino acids verified the operation of the proposed carbon fixation cycle, in which 4 - hydroxybutyrate is converted to two molecules of acetyl - CoA.", "output": "There is no related enetity." }, { "input": "The results also showed that major biosynthetic flux does not occur via acetyl - CoA, except for the formation of building blocks that are directly derived from acetyl - CoA.", "output": "There is no related enetity." }, { "input": "Notably, acetyl - CoA is not assimilated via reductive carboxylation to pyruvate.", "output": "There is no related enetity." }, { "input": "Rather, our data suggest that the majority of anabolic precursors are derived from succinyl - CoA, which is removed from the cycle via oxidation to malate and oxaloacetate.", "output": "There is no related enetity." }, { "input": "These C4intermediates yield pyruvate and phosphoenolpyruvate ( PEP ).", "output": "There is no related enetity." }, { "input": "Enzyme activities that are required for forming intermediates from succinyl - CoA were detected, including enzymes catalyzing gluconeogenesis from PEP.", "output": "There is no related enetity." }, { "input": "This study completes the picture of the central carbon metabolism in autotrophic Sulfolobales by connecting the autotrophic carbon fixation cycle to the formation of central carbon precursor metabolites.", "output": "There is no related enetity." }, { "input": "The sensor kinase CbrA is a global regulator that modulates metabolism, virulence, and antibiotic resistance in Pseudomonas aeruginosa.", "output": "Pseudomonas aeruginosa." }, { "input": "Pseudomonas aeruginosa is an opportunistic pathogen that possesses a large arsenal of virulence factors enabling the pathogen to cause serious infections in immunocompromised patients, burn victims, and cystic fibrosis patients.", "output": "Pseudomonas aeruginosa." }, { "input": "CbrA is a sensor kinase that has previously been implied to play a role with its cognate response regulator CbrB in the metabolic regulation of carbon and nitrogen utilization in P. aeruginosa.", "output": "P . aeruginosa." }, { "input": "Here it is demonstrated that CbrA and CbrB play an important role in various virulence and virulence - related processes of the bacteria, including swarming, biofilm formation, cytotoxicity, and antibiotic resistance.", "output": "There is no related enetity." }, { "input": "The cbrA deletion mutant was completely unable to swarm while exhibiting an increase in biofilm formation, supporting the inverse regulation of swarming and biofilm formation in P. aeruginosa.", "output": "P . aeruginosa." }, { "input": "The cbrA mutant also exhibited increased cytotoxicity to human lung epithelial cells as early as 4 and 6 h postinfection.", "output": "human." }, { "input": "Furthermore, the cbrA mutant demonstrated increased resistance toward a variety of clinically important antibiotics, including polymyxin B, ciprofloxacin, and tobramycin.", "output": "There is no related enetity." }, { "input": "Microarray analysis revealed that under swarming conditions, CbrA regulated the expression of many genes, including phoPQ, pmrAB, arnBCADTEF, dnaK, and pvdQ, consistent with the antibiotic resistance and swarming impairment phenotypes of the cbrA mutant.", "output": "There is no related enetity." }, { "input": "Phenotypic and real - time quantitative PCR ( RT - qPCR ) analyses of a PA14 cbrB mutant suggested that CbrA may be modulating swarming, biofilm formation, and cytotoxicity via CbrB and that the CrcZ small RNA is likely downstream of this two - component regulator.", "output": "There is no related enetity." }, { "input": "However, as CbrB did not have a resistance phenotype, CbrA likely modulates antibiotic resistance in a manner independent of CbrB.", "output": "There is no related enetity." }, { "input": "Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene ( DHN ) melanin and naphtho - gamma - pyrone.", "output": "Aspergillus niger." }, { "input": "The genome sequencing of the fungus Aspergillus niger uncovered a large cache of genes encoding enzymes thought to be involved in the production of secondary metabolites yet to be identified.", "output": "Aspergillus niger." }, { "input": "Identification and structural characterization of many of these predicted secondary metabolites are hampered by their low concentration relative to the known A. niger metabolites such as the naphtho - gamma - pyrone family of polyketides.", "output": "A . niger." }, { "input": "We deleted a non - reducing PKS gene in A. niger strain ATCC 11414, a daughter strain of A. niger ATCC strain 1015 whose genome was sequenced by the DOE Joint Genome Institute.", "output": "A . niger strain, A . niger ATCC strain 1015." }, { "input": "This PKS encoding gene we name albA is a predicted ortholog of alb1 from Aspergillus fumigatus which is responsible for production of the naphtho - gamma - pyrone precursor for the 1, 8 - dihydroxynaphthalene ( DHN ) melanin / spore pigment.", "output": "Aspergillus fumigatus." }, { "input": "Our results show that the A. nigeralbA PKS is responsible for both the production of the spore pigment precursor and a family of naphtho - gamma - pyrones commonly found in significant quantity in A. niger culture extracts.", "output": "A . nigeralbA, A . niger." }, { "input": "The generation of an A. niger strain devoid of naphtho - gamma - pyrones will greatly facilitate the elucidation of cryptic biosynthetic pathways in this organism.", "output": "A . niger." }, { "input": "Drivers of age - specific survival in a long - lived seabird: contributions of observed and hidden sources of heterogeneity.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "We assessed the relative influence of variability in recruitment age, dynamic reproductive investment ( time - specific reproductive states ) and frailty ( unobserved differences in survival abilities across individuals ) on survival in the black - legged kittiwake.", "output": "black - legged kittiwake." }, { "input": "Furthermore, we examined whether observed variability in survival trajectories was best explained by immediate reproductive investment, cumulative investment, or both.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Individuals that delayed recruitment ( > = age 7 ) suffered a higher mortality risk than early recruits ( age 3 ), especially later in life, suggesting that recruitment age may be an indicator of individual quality.", "output": "There is no related enetity." }, { "input": "Although recruitment age helped explain variation in survival, time - varying reproductive investment had a more substantial influence.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "The dichotomy of attempting to breed or not explained variability in survival across life better than other parameterizations of reproductive states such as clutch size, brood size or breeding success.", "output": "There is no related enetity." }, { "input": "In the kittiwake, the sinequanon condition to initiate reproduction is to hold a nest site, which is considered a very competitive activity.", "output": "There is no related enetity." }, { "input": "This might explain why attempting to breed is the key level of investment that affects survival, independent of the outcome ( failure or success ).", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Interestingly, the more individuals cumulate reproductive attempts over life, the lower their mortality risk, indicating that breeding experience may be a good indicator of parental quality as well.", "output": "There is no related enetity." }, { "input": "In contrast, attempting to breed at time t increased the risk of mortality between t and t + 1.", "output": "There is no related enetity." }, { "input": "We thus detected an immediate trade - off between attempting to breed and survival in this population; however, the earlier individuals recruited, and the more breeding experience they accumulated, the smaller the cost.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Lastly, unobserved heterogeneity across individuals improved model fit more ( 1 * 3 times ) than fixed and dynamic sources of observed heterogeneity in reproductive investment, demonstrating that it is critical to account for both sources of individual heterogeneity when studying survival trajectories.", "output": "There is no related enetity." }, { "input": "Only after simultaneously accounting for both sources of heterogeneity were we able to detect the ' cost ' of immediate reproductive investment on survival and the ' benefit ' of cumulative breeding attempts ( experience ), a proxy to individual quality.", "output": "There is no related enetity." }, { "input": "Developmental plasticity of immune defence in two life - history ecotypes of the garter snake, Thamnophis elegans - a common - environment experiment.", "output": "garter snake, Thamnophis elegans." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Ecoimmunological theory predicts a link between life - history and immune - defence strategies such that fast - living organisms should rely more on constitutive innate defences compared to slow - living organisms.", "output": "There is no related enetity." }, { "input": "An untested assumption of this hypothesis is that the variation in immune defence associated with variation in life history has a genetic basis.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Replicate populations of two life - history ecotypes of the garter snake Thamnophis elegans provide an ideal system in which to test this assumption.", "output": "garter snake, Thamnophis elegans." }, { "input": "Free - ranging snakes of the fast - living ecotype, which reside in lakeshore habitats, show higher levels of three measures of constitutive innate immunity than those of the slow - living ecotype, which inhabit meadows around the lake.", "output": "There is no related enetity." }, { "input": "Although this pattern is consistent with the ecoimmunological pace - of - life hypothesis, environmental differences between the lakeshore and meadow habitats could also explain the observed differences in immune defence.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We performed a common - environment experiment to distinguish between these alternatives.", "output": "There is no related enetity." }, { "input": "Snakes born and raised in common - environment conditions reflected the immune phenotype of their native habitats when sampled at 4 months of age ( i. e. fast - living lakeshore snakes showed higher levels of natural antibodies, complement activity and bactericidal competence than slow - living meadow snakes ), but no longer showed differences when 19 months old.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "This suggests that the differences in innate immunity observed between the two ecotypes have an important - and likely age - specific - environmental influence, with these immune components showing developmental plasticity.", "output": "There is no related enetity." }, { "input": "A genetic effect in early life may also be present, but further research is needed to confirm this possibility and therefore provide a more definitive test of the ecoimmunological pace - of - life hypothesis in this system.", "output": "There is no related enetity." }, { "input": "Prey, predators, parasites: intraguild predation or simpler community modules in disguise?", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Competition and predation are at the heart of community ecology.", "output": "There is no related enetity." }, { "input": "The theoretical concept of intraguild predation ( IGP ) combines these key interactions in a single community module.", "output": "There is no related enetity." }, { "input": "Because IGP is believed to be ubiquitous in nature, it has been subject to extensive research, and there exists a well - developed theoretical framework.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We show that a general class of IGP models can be transformed to simpler, but equivalent community structures.", "output": "There is no related enetity." }, { "input": "This rather unexpected simplification depends critically on the property of ' indiscriminate predation ', which we define broadly as the top - predator not distinguishing between its two different prey species.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "In a broader context, the great importance of IGP and of the simplifying transformation we report here is enhanced by the recent insight that the basic IGP structure extends naturally to host - parasitoid and host - pathogen communities.", "output": "There is no related enetity." }, { "input": "We show that parasites infecting prey ( predators ) tend to render IGP effectively into exploitative competition ( tritrophic food chain, respectively ).", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "The equivalence between the original and simplified community module makes it possible to take advantage from already existing insights.", "output": "There is no related enetity." }, { "input": "We illustrate this by means of an eco - epidemiological IGP model that is strikingly similar to a classical exploitative competition model.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "The change of perspective on certain community modules may contribute to a better understanding of food web dynamics.", "output": "There is no related enetity." }, { "input": "In particular, it may help explain the interactions in food webs that include parasites.", "output": "There is no related enetity." }, { "input": "Given the ubiquity of parasitism, food webs may appear in a different light when they are transformed to their simplified analogue.", "output": "There is no related enetity." }, { "input": "Individual differences in reproductive costs examined using multi - state methods.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Trade - offs among life - history traits are common because individuals have to partition limited resources between multiple traits.", "output": "There is no related enetity." }, { "input": "Reproductive costs are generally assumed to be high, resulting in reduced survival and fecundity in the following year.", "output": "There is no related enetity." }, { "input": "However, it is common to find positive rather than negative correlations between life - history traits.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Here, we use a data set from the individual - based study of red deer on the Isle of Rum to examine how these costs vary between individuals and at different ages, using multi - state mark - recapture methodology.", "output": "red deer." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Females that had reproduced frequently in the past incurred lower costs of reproduction in terms of survival in the following year and were more likely to reproduce in two consecutive years.", "output": "There is no related enetity." }, { "input": "Older individuals and those that had not reproduced frequently exhibited higher costs.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "These results highlight the importance of considering heterogeneity and individual quality when examining trade - offs and demonstrate the effectiveness of using detailed long - term data sets to explore life - history strategies using multi - state mark - recapture models.", "output": "There is no related enetity." }, { "input": "Functional analysis of the fungal / plant class chitinase family in Aspergillus fumigatus.", "output": "Aspergillus fumigatus." }, { "input": "A quintuple mutant was constructed to delete the entire family of the fungal / plant ( class III ) chitinases of Aspergillus fumigatus.", "output": "Aspergillus fumigatus." }, { "input": "Only a limited reduction in the total chitinolytic activity was seen for the different chitinase mutants including the quintuple mutant.", "output": "There is no related enetity." }, { "input": "In spite of this reduction in chitinolytic activity, no growth or germination defects were observed in these chitinase mutants.", "output": "There is no related enetity." }, { "input": "This result demonstrated that the fungal / plant chitinases do not have an essential role in the morphogenesis of A. fumigatus.", "output": "A . fumigatus." }, { "input": "A slight diminution of the growth during autolysis was seen for the quintuple mutant suggesting that class III chitinases may play only a nutritional role during this phase of the cycle, retarding fungal death.", "output": "There is no related enetity." }, { "input": "Early - onset versus late - onset Alzheimer ' s disease: the case of the missing APOE epsilo4 allele.", "output": "There is no related enetity." }, { "input": "Some patients with early - onset Alzheimer ' s disease ( AD ) present with a distinct phenotype.", "output": "There is no related enetity." }, { "input": "Typically, the first and most salient characteristic of AD is episodic memory impairment.", "output": "There is no related enetity." }, { "input": "A few patients, however, present with focal cortical, non - memory symptoms, such as difficulties with language, visuospatial, or executive functions.", "output": "There is no related enetity." }, { "input": "These presentations are associated with specific patterns of atrophy and frequently with a young age at onset.", "output": "There is no related enetity." }, { "input": "Age is not, however, the only determinant of phenotype; underlying factors, especially genetic factors, seem also to affect phenotype and predispose patients to younger or older age at onset.", "output": "There is no related enetity." }, { "input": "Importantly, patients with atypical early - onset disease seldom carry the APOE epsilo4 allele, which is the most important risk factor for lowering the age of onset in patients with AD.", "output": "There is no related enetity." }, { "input": "Additionally, theAPOE epsilo4 genotype seems to predispose patients to vulnerability in the medial temporal areas, which leads to memory loss.", "output": "There is no related enetity." }, { "input": "Conversely, patients negative for the APOE epsilo4 allele and with early - onset AD are more likely to be predisposed to vulnerability of cerebral networks beyond the medial temporal lobes.", "output": "There is no related enetity." }, { "input": "Other factors are probably involved in determining the pattern of atrophy, but these are currently unknown.", "output": "There is no related enetity." }, { "input": "Breathing some air into the single - species vacuum: multi - species responses to environmental change.", "output": "There is no related enetity." }, { "input": "Studies of ecological responses to climate change have often analysed species independently of each other, yet interactions between species are fundamental aspects of ecology.", "output": "There is no related enetity." }, { "input": "Mutshinda, O ' Hara & amp; Woiwod ( 2011 ) used light - trapping data for Lepidoptera ( moths ) to examine population responses to intraspecific effects and effects of winter rainfall and temperature.", "output": "There is no related enetity." }, { "input": "They show how Bayesian hierarchical models can analyse residual correlations among species ' responses, illustrating an approach to account for and measure dependencies that are not fully explained by the candidate explanatory variables.", "output": "There is no related enetity." }, { "input": "A key result is that the responses of the different moth species did not appear to have strong residual correlation ( Mutshinda, O ' Hara & amp; Woiwod 2011 ).", "output": "There is no related enetity." }, { "input": "These analyses provide an approach for synthesising across species and can better inform ecological responses to environmental change.", "output": "There is no related enetity." }, { "input": "Functional analysis of a mitochondrial phosphopantetheinyl transferase ( PPTase ) gene pptB in Aspergillus fumigatus.", "output": "Aspergillus fumigatus." }, { "input": "The mitochondrial phosphopantetheinyl transferase gene pptB of the opportunistic pathogen Aspergillus fumigatus has been identified and characterised.", "output": "Aspergillus fumigatus." }, { "input": "Unlike pptA, which is required for lysine biosynthesis, secondary metabolism, and iron assimilation, pptB is essential for viability.", "output": "There is no related enetity." }, { "input": "PptB is located in the mitochondria.", "output": "There is no related enetity." }, { "input": "In vitro expression of pptA and pptB has shown that PptB is specific for the mitochondrial acyl carrier protein AcpA.", "output": "There is no related enetity." }, { "input": "Borderline personality disorder.", "output": "There is no related enetity." }, { "input": "Recent research findings have contributed to an improved understanding and treatment of borderline personality disorder.", "output": "There is no related enetity." }, { "input": "This disorder is characterised by severe functional impairments, a high risk of suicide, a negative effect on the course of depressive disorders, extensive use of treatment, and high costs to society.", "output": "There is no related enetity." }, { "input": "The course of this disorder is less stable than expected for personality disorders.", "output": "There is no related enetity." }, { "input": "The causes are not yet clear, but genetic factors and adverse life events seem to interact to lead to the disorder.", "output": "There is no related enetity." }, { "input": "Neurobiological research suggests that abnormalities in the frontolimbic networks are associated with many of the symptoms.", "output": "There is no related enetity." }, { "input": "Data for the effectiveness of pharmacotherapy vary and evidence is not yet robust.", "output": "There is no related enetity." }, { "input": "Specific forms of psychotherapy seem to be beneficial for at least some of the problems frequently reported in patients with borderline personality disorder.", "output": "There is no related enetity." }, { "input": "At present, there is no evidence to suggest that one specific form of psychotherapy is more effective than another.", "output": "There is no related enetity." }, { "input": "Further research is needed on the diagnosis, neurobiology, and treatment of borderline personality disorder.", "output": "There is no related enetity." }, { "input": "Spatio - temporal variation in territory quality and oxidative status: a natural experiment in the Seychelles warbler ( Acrocephalus sechellensis ).", "output": "Seychelles warbler, Acrocephalus sechellensis." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Fluctuations in the quality of the habitat in which an animal lives can have major consequences for its behaviour and physiological state.", "output": "There is no related enetity." }, { "input": "In poor - quality habitat with low food availability, metabolically intensive foraging activity is likely to result in increased generation of reactive oxygen species, while scarcity of food can lead to a weakening of exogenously derived antioxidant defences.", "output": "There is no related enetity." }, { "input": "The consequent oxidant / antioxidant imbalance may lead to elevated oxidative stress.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Although the link between food availability and oxidative stress has been studied in the laboratory, very little is known about this relationship in the wild.", "output": "There is no related enetity." }, { "input": "Here, we investigate the association between territory quality ( measured through food availability ) and oxidative stress in the Seychelles warbler ( Acrocephalus sechellensis ).", "output": "Seychelles warbler, Acrocephalus sechellensis." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Seychelles warblers are insectivorous birds that inhabit a fixed feeding territory year round.", "output": "Seychelles warblers." }, { "input": "Individuals experience profound and rapid local fluctuations in territory quality within these territories, owing to changing patterns of vegetation defoliation resulting from seasonal changes in prevailing wind direction and wind - borne salt spray.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "As expected, oxidant generation ( measured as reactive oxygen metabolites; ROMs ) was higher when territory quality was low, but there was no correlation between territory quality and antioxidant capacity ( OXY ).", "output": "There is no related enetity." }, { "input": "The negative correlation between territory quality and ROMs was significant between individuals and approached significance within individuals, indicating that the pattern resulted from individual responses to environmental variation.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "ROMs and OXY levels within individuals were positively correlated, but the relationship between territory quality and ROMs persisted after including OXY as a covariate, implying that oxidative stress occurs in low territory quality conditions.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "Our results indicate that the oxidative stress balance of an individual is sensitive to relatively short - term changes in territory quality, which may have consequences for the birds ' fitness.", "output": "There is no related enetity." }, { "input": "Ice - cover effects on competitive interactions between two fish species.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Variations in the strength of ecological interactions between seasons have received little attention, despite an increased focus on climate alterations on ecosystems.", "output": "There is no related enetity." }, { "input": "Particularly, the winter situation is often neglected when studying competitive interactions.", "output": "There is no related enetity." }, { "input": "In northern temperate freshwaters, winter implies low temperatures and reduced food availability, but also strong reduction in ambient light because of ice and snow cover.", "output": "There is no related enetity." }, { "input": "Here, we study how brown trout [ Salmo trutta ( L. ) ] respond to variations in ice - cover duration and competition with Arctic charr [ Salvelinus alpinus ( L. ) ], by linking laboratory - derived physiological performance and field data on variation in abundance among and within natural brown trout populations.", "output": "brown trout, Salmo trutta, Arctic charr, Salvelinus alpinus, brown trout." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Both Arctic charr and brown trout reduced resting metabolic rate under simulated ice - cover ( darkness ) in the laboratory, compared to no ice ( 6 - h daylight ).", "output": "Arctic charr, brown trout." }, { "input": "However, in contrast to brown trout, Arctic charr was able to obtain positive growth rate in darkness and had higher food intake in tank experiments than brown trout.", "output": "brown trout, Arctic charr, brown trout." }, { "input": "Arctic charr also performed better ( lower energy loss ) under simulated ice - cover in a semi - natural environment with natural food supply.", "output": "Arctic charr." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "When comparing brown trout biomass across 190 Norwegian lakes along a climate gradient, longer ice - covered duration decreased the biomass only in lakes where brown trout lived together with Arctic charr.", "output": "brown trout, brown trout, Arctic charr." }, { "input": "We were not able to detect any effect of ice - cover on brown trout biomass in lakes where brown trout was the only fish species.", "output": "brown trout, brown trout." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Similarly, a 25 - year time series from a lake with both brown trout and Arctic charr showed that brown trout population growth rate depended on the interaction between ice breakup date and Arctic charr abundance.", "output": "brown trout, Arctic charr, brown trout, Arctic charr." }, { "input": "High charr abundance was correlated with low trout population growth rate only in combination with long winters.", "output": "charr." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "In conclusion, the two species differed in performance under ice, and the observed outcome of competition in natural populations was strongly dependent on duration of the ice - covered period.", "output": "There is no related enetity." }, { "input": "Our study shows that changes in ice phenology may alter species interactions in Northern aquatic systems.", "output": "There is no related enetity." }, { "input": "Increased knowledge of how adaptations to winter conditions differ among coexisting species is therefore vital for our understanding of ecological impacts of climate change.", "output": "There is no related enetity." }, { "input": "Predicting the post - fire responses of animal assemblages: testing a trait - based approach using spiders.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Developing a predictive understanding of how species assemblages respond to fire is a key conservation goal.", "output": "There is no related enetity." }, { "input": "In moving from solely describing patterns following fire to predicting changes, plant ecologists have successfully elucidated generalizations based on functional traits.", "output": "There is no related enetity." }, { "input": "Using species traits might also allow better predictions for fauna, but there are few empirical tests of this approach.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We examined whether species traits changed with post - fire age for spiders in 27 sites, representing a chronosequence of 0 - 20 years post - fire.", "output": "There is no related enetity." }, { "input": "We predicted a priori whether spiders with ten traits associated with survival, dispersal, reproduction, resource - utilization and microhabitat occupation would increase or decrease with post - fire age.", "output": "There is no related enetity." }, { "input": "We then tested these predictions using a direct ( fourth - corner on individual traits and composite traits ) and an indirect ( emergent groups ) approach, comparing the benefits of each and also examining the degree to which traits were intercorrelated.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "For the seven individual traits that were significant, three followed predictions ( body size, abundance of burrow ambushers and burrowers was greater in recently burnt sites ); two were opposite ( species with heavy sclerotisation of the cephalothorax and longer time to maturity were in greater abundance in long unburnt and recently burnt sites respectively ); and two displayed response patterns more complex than predicted ( abdominal scutes displayed a U - shaped response and dispersal ability a hump shaped curve ).", "output": "There is no related enetity." }, { "input": "However, within a given trait, there were few significant differences among post - fire ages.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Several traits were intercorrelated and scores based on composite traits used in a fourth - corner analysis found significant patterns, but slightly different to those using individual traits.", "output": "There is no related enetity." }, { "input": "Changes in abundance with post - fire age were significant for three of the five emergent groups.", "output": "There is no related enetity." }, { "input": "The fourth - corner analysis yielded more detailed results, but overall we consider the two approaches complementary.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "While we found significant differences in traits with post - fire age, our results suggest that a trait - based approach may not increase predictive power, at least for the assemblages of spiders we studied.", "output": "There is no related enetity." }, { "input": "That said, there are many refinements to faunal traits that could increase predictive power.", "output": "There is no related enetity." }, { "input": "Analysis of expressed sequence tags from Maize mosaic rhabdovirus - infected gut tissues of Peregrinus maidis reveals the presence of key components of insect innate immunity.", "output": "Maize mosaic rhabdovirus, Peregrinus maidis." }, { "input": "The corn planthopper, Peregrinus maidis, causes direct feeding damage to plants and transmits Maize mosaic rhabdovirus ( MMV ) in a persistent - propagative manner.", "output": "corn planthopper, Peregrinus maidis, Maize mosaic rhabdovirus ( MMV )." }, { "input": "MMV must cross several insect tissue layers for successful transmission to occur, and the gut serves as an important barrier for rhabdovirus transmission.", "output": "MMV." }, { "input": "In order to facilitate the identification of proteins that may interact with MMV either by facilitating acquisition or responding to virus infection, we generated and analysed the gut transcriptome of P. maidis.", "output": "MMV, P . maidis." }, { "input": "From two normalized cDNA libraries, we generated a P. maidis gut transcriptome composed of 20, 771 expressed sequence tags ( ESTs ).", "output": "P . maidis." }, { "input": "Assembly of the sequences yielded 1860 contigs and 14, 032 singletons, and biological roles were assigned to 5793 ( 36 % ).", "output": "There is no related enetity." }, { "input": "Comparison of P. maidis ESTs with other insect amino acid sequences revealed that P. maidis shares greatest sequence similarity with another hemipteran, the brown planthopper Nilaparvata lugens.", "output": "P . maidis, P . maidis, brown planthopper, Nilaparvata lugens." }, { "input": "We identified 202 P. maidis transcripts with putative homology to proteins associated with insect innate immunity, including those implicated in the Toll, Imd, JAK / STAT, Jnk and the small - interfering RNA - mediated pathways.", "output": "P . maidis." }, { "input": "Sequence comparisons between our P. maidis gut EST collection and the currently available National Center for Biotechnology Information EST database collection for Ni. lugens revealed that a pathogen recognition receptor in the Imd pathway, peptidoglycan recognition protein - long class ( PGRP - LC ), is present in these two members of the family Delphacidae; however, these recognition receptors are lacking in the model hemipteran Acyrthosiphon pisum.", "output": "P . maidis, Ni . lugens, Acyrthosiphon pisum." }, { "input": "In addition, we identified sequences in the P. maidis gut transcriptome that share significant amino acid sequence similarities with the rhabdovirus receptor molecule, acetylcholine receptor ( AChR ), found in other hosts.", "output": "P . maidis." }, { "input": "This EST analysis sheds new light on immune response pathways in hemipteran guts that will be useful for further dissecting innate defence response pathways to rhabdovirus infection.", "output": "There is no related enetity." }, { "input": "Genetic analysis of the xenobiotic resistance - associated ABC gene subfamilies of the Lepidoptera.", "output": "There is no related enetity." }, { "input": "Some ATP - binding cassette ( ABC ) transporters of subfamilies B, C and G confer resistance to xenobiotics including insecticides.", "output": "There is no related enetity." }, { "input": "We identified genes of these subfamilies expressed by the lepidopterans Trichoplusia ni and Bombyx mori.", "output": "Trichoplusia ni, Bombyx mori." }, { "input": "The B. mori genome includes eight, six and 13 ABC - B, - C and - G genes, respectively, which encode P - glycoprotein, multidrug resistance protein, MRP, and breast cancer resistance protein, BCRP, homologues.", "output": "B . mori." }, { "input": "Among the ABC - C and - G subfamilies, gene duplication contributes to protein diversity.", "output": "There is no related enetity." }, { "input": "We have identified three ABC - B and two ABC - C T. ni genes.", "output": "T . ni." }, { "input": "Analyses of the T. ni MRP ( TrnMRP ) revealed unique features, including the potential for TrnMRP4 hyperglycosylation and the alternative splicing of TrnMRP1.", "output": "T . ni." }, { "input": "Taken together, these attributes of moth multidrug resistance - associated ABCs may confer distinct functional capacities to xenobiotic efflux.", "output": "There is no related enetity." }, { "input": "Effects of Wolbachia on mtDNA variation and evolution in natural populations of Tetranychus urticae Koch.", "output": "Tetranychus urticae." }, { "input": "We investigated the effects of Wolbachia infection on mtDNA variation in spider mites by sequencing a portion of the mitochondrial cytochrome oxidase I ( COI ) gene from 198 individuals of known infection status.", "output": "There is no related enetity." }, { "input": "Four Wolbachia strains were described in the current study, namely wUrtOri1, wUrtOri2, wUrtOri3 and wUrtCon1.", "output": "There is no related enetity." }, { "input": "As predicted, the haplotype and nucleotide diversity were lower in infected individuals than in uninfected individuals.", "output": "There is no related enetity." }, { "input": "However, these mtDNA haplotype data are not entirely concordant with the surface protein of wolbachia ( wsp ) sequence data and both infected and uninfected individuals were found of the same haplotype.", "output": "There is no related enetity." }, { "input": "Although values of Tajima ' s D and Fu & amp; Li ' s F were consistently less than zero for most infected groups, McDonald - Kreitman tests suggested that the patterns of variation were different from those expected under neutrality in only the uninfected group.", "output": "There is no related enetity." }, { "input": "Thus, the neutrality tests do not show a clear effect of Wolbachia infection on patterns of mtDNA variation and substitution in spider mites.", "output": "There is no related enetity." }, { "input": "Decompression illness.", "output": "There is no related enetity." }, { "input": "Decompression illness is caused by intravascular or extravascular bubbles that are formed as a result of reduction in environmental pressure ( decompression ).", "output": "There is no related enetity." }, { "input": "The term covers both arterial gas embolism, in which alveolar gas or venous gas emboli ( via cardiac shunts or via pulmonary vessels ) are introduced into the arterial circulation, and decompression sickness, which is caused by in - situ bubble formation from dissolved inert gas.", "output": "There is no related enetity." }, { "input": "Both syndromes can occur in divers, compressed air workers, aviators, and astronauts, but arterial gas embolism also arises from iatrogenic causes unrelated to decompression.", "output": "There is no related enetity." }, { "input": "Risk of decompression illness is affected by immersion, exercise, and heat or cold.", "output": "There is no related enetity." }, { "input": "Manifestations range from itching and minor pain to neurological symptoms, cardiac collapse, and death.", "output": "There is no related enetity." }, { "input": "First - aid treatment is 100 % oxygen and definitive treatment is recompression to increased pressure, breathing 100 % oxygen.", "output": "There is no related enetity." }, { "input": "Adjunctive treatment, including fluid administration and prophylaxis against venous thromboembolism in paralysed patients, is also recommended.", "output": "There is no related enetity." }, { "input": "Treatment is, in most cases, effective although residual deficits can remain in serious cases, even after several recompressions.", "output": "There is no related enetity." }, { "input": "The genetic basis for 3 - ADON and 15 - ADON trichothecene chemotypes in Fusarium.", "output": "There is no related enetity." }, { "input": "Certain Fusarium species cause head blight of wheat and other small grains worldwide and produce trichothecene mycotoxins.", "output": "wheat." }, { "input": "These mycotoxins can induce toxicoses in animals and humans and can contribute to the ability of some fusaria to cause plant disease.", "output": "humans." }, { "input": "Production of the trichothecene 3 - acetyldeoxynivalenol ( 3 - ADON ) versus 15 - acetyldeoxynivalenol ( 15 - ADON ) is an important phenotypic difference within and among some Fusarium species.", "output": "There is no related enetity." }, { "input": "However, until now, the genetic basis for this difference in chemotype has not been identified.", "output": "There is no related enetity." }, { "input": "Here, we identified consistent DNA sequence differences in the coding region of the trichothecene biosynthetic gene TRI8 in 3 - ADON and 15 - ADON strains.", "output": "There is no related enetity." }, { "input": "Functional analyses of the TRI8 enzyme ( Tri8 ) in F. graminearum, the predominant cause of wheat head blight in North America and Europe, revealed that Tri8 from 3 - ADON strains catalyzes deacetylation of the trichothecene biosynthetic intermediate 3, 15 - diacetyldeoxynivalenol at carbon 15 to yield 3 - ADON, whereas Tri8 from 15 - ADON strains catalyzes deacetylation of 3, 15 - diacetyldeoxynivalenol at carbon 3 to yield 15 - ADON.", "output": "F . graminearum." }, { "input": "Fusarium strains that produce the trichothecene nivalenol have a Tri8 that functions like that in 15 - ADON strains.", "output": "There is no related enetity." }, { "input": "TRI3, which encodes a trichothecene carbon 15 acetyltransferase, was found to be functional in all three chemotypes.", "output": "There is no related enetity." }, { "input": "Together, our data indicate that differential activity of Tri8 determines the 3 - ADON and 15 - ADON chemotypes in Fusarium.", "output": "There is no related enetity." }, { "input": "Influence of proximity to a geographical range limit on the physiology of a tropical bird.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Species ' geographical ranges can be limited by a variety of biotic and abiotic factors.", "output": "There is no related enetity." }, { "input": "Physiological challenge in response to unsuitable environmental conditions can establish limits to geographical ranges.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We studied the physiology of Song Wrens ( Cyphorhinus phaeocephalus ) across their geographical range on the isthmus of Panama, an area characterized by a strong rainfall gradient.", "output": "Song Wrens, Cyphorhinus phaeocephalus." }, { "input": "Wrens are common on the Caribbean slope of the isthmus where annual rainfall is greatest, but wren abundance declines towards the south as annual rainfall declines.", "output": "There is no related enetity." }, { "input": "Song Wrens are completely absent from the driest third of the isthmus.", "output": "Song Wrens." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We searched for the existence of a physiologically induced distribution limit by measuring body condition ( an integrative measure of energy balance ), hematocrit ( % packed red blood cells in a given blood sample ), and corticosterone levels ( CORT, a steroid hormone that regulates the availability of energy and the endocrine stress response ) in males and females.", "output": "There is no related enetity." }, { "input": "We caught birds by luring them into nets when they responded to playback of conspecific song.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Wrens living in drier habitat near the geographical range edge were significantly more likely to have abnormally low hematocrit scores.", "output": "There is no related enetity." }, { "input": "Baseline CORT levels were negatively associated with rainfall in one of our three best - fit path models, indicating potential energetic challenge in some individuals.", "output": "There is no related enetity." }, { "input": "Maximum CORT levels during a 60 - min period of restraint correlated significantly only with sex, being higher in females.", "output": "There is no related enetity." }, { "input": "Birds with the poorest body condition lived at the dry end of the gradient.", "output": "There is no related enetity." }, { "input": "Birds on the wet end of the gradient responded fastest to conspecific song.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Environmental conditions vary across geographical ranges and may influence the physiological conditions of organisms, thereby enforcing limits to species ' distributions.", "output": "There is no related enetity." }, { "input": "Highly specialized species, such as birds of the rain forest understory, may be especially susceptible to environmental variation associated with changing climatic conditions.", "output": "There is no related enetity." }, { "input": "New insights into the mechanism of light modulated signaling by heterotrimeric G - proteins: ENVOY acts on gna1 and gna3 and adjusts cAMP levels in Trichoderma reesei ( Hypocrea jecorina ).", "output": "Trichoderma reesei, Hypocrea jecorina." }, { "input": "Sensing of environmental signals is often mediated by G - protein coupled receptors and their cognate heterotrimeric G - proteins.", "output": "There is no related enetity." }, { "input": "In Trichoderma reesei ( Hypocrea jecorina ) the signals transmitted via the G - protein alpha subunits GNA1 and GNA3 cause considerable modulation of cellulase transcript levels and the extent of this adjustment is dependent on the light status.", "output": "Trichoderma reesei, Hypocrea jecorina." }, { "input": "We therefore intended to elucidate the underlying mechanism connecting light response and heterotrimeric G - protein signaling.", "output": "There is no related enetity." }, { "input": "Analysis of double mutant strains showed that constitutive activation of GNA1 or GNA3 in the absence of the PAS / LOV domain protein ENVOY ( ENV1 ) leads to the phenotype of constitutive G - alpha activation in darkness.", "output": "There is no related enetity." }, { "input": "In light, however the deletion - phenotype of Deltaenv1 was observed with respect to growth, conidiation and cellulase gene transcription.", "output": "There is no related enetity." }, { "input": "Additionally deletion of env1 causes decreased intracellular cAMP accumulation, even upon constitutive activation of GNA1 or GNA3.", "output": "There is no related enetity." }, { "input": "While supplementation of cAMP caused an even more severe growth phenotype of all strains lacking env1 in light, addition of the phosphodiesterase inhibitor caffeine rescued the growth phenotype of these strains.", "output": "There is no related enetity." }, { "input": "ENV1 is consequently suggested to connect the light response pathway with nutrient signaling by the heterotrimeric G - protein cascade by adjusting transcript levels of gna1 and gna3 and action on cAMP levels - presumably through inhibition of a phosphodiesterase.", "output": "There is no related enetity." }, { "input": "Chronic diseases and injuries in India.", "output": "There is no related enetity." }, { "input": "Chronic diseases ( eg, cardiovascular diseases, mental health disorders, diabetes, and cancer ) and injuries are the leading causes of death and disability in India, and we project pronounced increases in their contribution to the burden of disease during the next 25 years.", "output": "There is no related enetity." }, { "input": "Most chronic diseases are equally prevalent in poor and rural populations and often occur together.", "output": "There is no related enetity." }, { "input": "Although a wide range of cost - effective primary and secondary prevention strategies are available, their coverage is generally low, especially in poor and rural populations.", "output": "There is no related enetity." }, { "input": "Much of the care for chronic diseases and injuries is provided in the private sector and can be very expensive.", "output": "There is no related enetity." }, { "input": "Sufficient evidence exists to warrant immediate action to scale up interventions for chronic diseases and injuries through private and public sectors; improved public health and primary health - care systems are essential for the implementation of cost - effective interventions.", "output": "There is no related enetity." }, { "input": "We strongly advocate the need to strengthen social and policy frameworks to enable the implementation of interventions such as taxation on bidis ( small hand - rolled cigarettes ), smokeless tobacco, and locally brewed alcohols.", "output": "tobacco." }, { "input": "We also advocate the integration of national programmes for various chronic diseases and injuries with one another and with national health agendas.", "output": "There is no related enetity." }, { "input": "India has already passed the early stages of a chronic disease and injury epidemic; in view of the implications for future disease burden and the demographic transition that is in progress in India, the rate at which effective prevention and control is implemented should be substantially increased.", "output": "There is no related enetity." }, { "input": "The emerging agenda of chronic diseases and injuries should be a political priority and central to national consciousness, if universal health care is to be achieved.", "output": "There is no related enetity." }, { "input": "Health care and equity in India.", "output": "There is no related enetity." }, { "input": "In India, despite improvements in access to health care, inequalities are related to socioeconomic status, geography, and gender, and are compounded by high out - of - pocket expenditures, with more than three - quarters of the increasing financial burden of health care being met by households.", "output": "There is no related enetity." }, { "input": "Health - care expenditures exacerbate poverty, with about 39 million additional people falling into poverty every year as a result of such expenditures.", "output": "There is no related enetity." }, { "input": "We identify key challenges for the achievement of equity in service provision, and equity in financing and financial risk protection in India.", "output": "There is no related enetity." }, { "input": "These challenges include an imbalance in resource allocation, inadequate physical access to high - quality health services and human resources for health, high out - of - pocket health expenditures, inflation in health spending, and behavioural factors that affect the demand for appropriate health care.", "output": "human." }, { "input": "Use of equity metrics in monitoring, assessment, and strategic planning; investment in development of a rigorous knowledge base of health - systems research; development of a refined equity - focused process of deliberative decision making in health reform; and redefinition of the specific responsibilities and accountabilities of key actors are needed to try to achieve equity in health care in India.", "output": "There is no related enetity." }, { "input": "The implementation of these principles with strengthened public health and primary - care services will help to ensure a more equitable health care for India ' s population.", "output": "There is no related enetity." }, { "input": "Reproductive health, and child health and nutrition in India: meeting the challenge.", "output": "There is no related enetity." }, { "input": "India, with a population of more than 1 billion people, has many challenges in improving the health and nutrition of its citizens.", "output": "There is no related enetity." }, { "input": "Steady declines have been noted in fertility, maternal, infant and child mortalities, and the prevalence of severe manifestations of nutritional deficiencies, but the pace has been slow and falls short of national and Millennium Development Goal targets.", "output": "There is no related enetity." }, { "input": "The likely explanations include social inequities, disparities in health systems between and within states, and consequences of urbanisation and demographic transition.", "output": "There is no related enetity." }, { "input": "In 2005, India embarked on the National Rural Health Mission, an extraordinary effort to strengthen the health systems.", "output": "There is no related enetity." }, { "input": "However, coverage of priority interventions remains insufficient, and the content and quality of existing interventions are suboptimum.", "output": "There is no related enetity." }, { "input": "Substantial unmet need for contraception remains, adolescent pregnancies are common, and access to safe abortion is inadequate.", "output": "There is no related enetity." }, { "input": "Increases in the numbers of deliveries in institutions have not been matched by improvements in the quality of intrapartum and neonatal care.", "output": "There is no related enetity." }, { "input": "Infants and young children do not get the health care they need; access to effective treatment for neonatal illness, diarrhoea, and pneumonia shows little improvement; and the coverage of nutrition programmes is inadequate.", "output": "There is no related enetity." }, { "input": "Absence of well functioning health systems is indicated by the inadequacies related to planning, financing, human resources, infrastructure, supply systems, governance, information, and monitoring.", "output": "human." }, { "input": "We provide a case for transformation of health systems through effective stewardship, decentralised planning in districts, a reasoned approach to financing that affects demand for health care, a campaign to create awareness and change health and nutrition behaviour, and revision of programmes for child nutrition on the basis of evidence.", "output": "There is no related enetity." }, { "input": "This agenda needs political commitment of the highest order and the development of a people ' s movement.", "output": "There is no related enetity." }, { "input": "Human resources for health in India.", "output": "Human." }, { "input": "India has a severe shortage of human resources for health.", "output": "human." }, { "input": "It has a shortage of qualified health workers and the workforce is concentrated in urban areas.", "output": "There is no related enetity." }, { "input": "Bringing qualified health workers to rural, remote, and underserved areas is very challenging.", "output": "There is no related enetity." }, { "input": "Many Indians, especially those living in rural areas, receive care from unqualified providers.", "output": "There is no related enetity." }, { "input": "The migration of qualified allopathic doctors and nurses is substantial and further strains the system.", "output": "There is no related enetity." }, { "input": "Nurses do not have much authority or say within the health system, and the resources to train them are still inadequate.", "output": "There is no related enetity." }, { "input": "Little attention is paid during medical education to the medical and public health needs of the population, and the rapid privatisation of medical and nursing education has implications for its quality and governance.", "output": "There is no related enetity." }, { "input": "Such issues are a result of underinvestment in and poor governance of the health sector - - two issues that the government urgently needs to address.", "output": "There is no related enetity." }, { "input": "A comprehensive national policy for human resources is needed to achieve universal health care in India.", "output": "human." }, { "input": "The public sector will need to redesign appropriate packages of monetary and non - monetary incentives to encourage qualified health workers to work in rural and remote areas.", "output": "There is no related enetity." }, { "input": "Such a policy might also encourage task - shifting and mainstreaming doctors and practitioners who practice traditional Indian medicine ( ayurveda, yoga and naturopathy, unani, and siddha ) and homoeopathy to work in these areas while adopting other innovative ways of augmenting human resources for health.", "output": "human." }, { "input": "At the same time, additional investments will be needed to improve the relevance, quantity, and quality of nursing, medical, and public health education in the country.", "output": "There is no related enetity." }, { "input": "Emerging diversity within chrysophytes, choanoflagellates and bicosoecids based on molecular surveys.", "output": "There is no related enetity." }, { "input": "In recent years, a substantial amount of data on aquatic protists has been obtained from culture - independent molecular approaches, unveiling a large diversity and the existence of new lineages.", "output": "There is no related enetity." }, { "input": "However, sequences affiliated with minor groups ( in terms of clonal abundance ) have often been under - analyzed, and this hides a potentially relevant source of phylogenetic information.", "output": "There is no related enetity." }, { "input": "Here we have searched public databases for 18S rDNA sequences of chrysophytes, choanoflagellates and bicosoecids retrieved from molecular surveys of protists.", "output": "There is no related enetity." }, { "input": "These three groups are often considered to account for most of the heterotrophic flagellates, an important functional component in microbial food webs.", "output": "There is no related enetity." }, { "input": "They represented a significant fraction of clones in freshwater studies, whereas their relative clonal abundance was low in marine studies.", "output": "There is no related enetity." }, { "input": "The novelty displayed by this dataset was notable.", "output": "There is no related enetity." }, { "input": "Most environmental sequences were distant to sequences of cultured organisms, indicating a significant bias in the representation of taxa in culture.", "output": "There is no related enetity." }, { "input": "Moreover, they were often distant to sequences from other molecular surveys, suggesting an insufficient sequencing effort to characterize the in situ diversity of these groups.", "output": "There is no related enetity." }, { "input": "Phylogenetic trees with complete sequences present the most accurate representation of the diversity of these groups, with the emergence of several new clades formed exclusively by environmental sequences.", "output": "There is no related enetity." }, { "input": "Exhaustive data mining in sequence databases allowed the identification of new diversity hidden inside chrysophytes, choanoflagellates and bicosoecids.", "output": "There is no related enetity." }, { "input": "Gene expression analysis of wounding - induced root - to - shoot communication in Arabidopsis thaliana.", "output": "Arabidopsis thaliana." }, { "input": "Root - to - shoot communication plays an important role in the adaptation to environmental stress.", "output": "There is no related enetity." }, { "input": "In this study, we established a model system for root - to - shoot signalling to observe global gene expression in Arabidopsis thaliana.", "output": "Arabidopsis thaliana." }, { "input": "The roots of Arabidopsis seedlings were wounded and the expression in the shoots of 68 and 5 genes was up - regulated threefold at 30 min and 6 h post - injury, respectively.", "output": "Arabidopsis." }, { "input": "These genes were designated early and late Root - to - Shoot responsive ( RtS ) genes, respectively.", "output": "There is no related enetity." }, { "input": "Many of the early RtS genes were found to encode transcription factors such as AtERFs, whereas others were associated with jasmonic acid ( JA ) and ethylene ( ET ).", "output": "There is no related enetity." }, { "input": "Some of the late RtS genes were shown to be regulated by 12 - oxo - phytodienoic acid ( OPDA ).", "output": "There is no related enetity." }, { "input": "In fact, elevated levels of JA and OPDA were detected in the shoots of seedlings 30 min and 6 h, respectively, after wounding of the roots.", "output": "There is no related enetity." }, { "input": "A mutant analysis revealed that JA and ET are involved in the expression of the early RtS genes.", "output": "There is no related enetity." }, { "input": "Thus, root - to - shoot communication for many RtS genes is associated with the systemic production of JA, OPDA and possibly ET.", "output": "There is no related enetity." }, { "input": "Effects of the hydraulic coupling between xylem and phloem on diurnal phloem diameter variation.", "output": "There is no related enetity." }, { "input": "Measurements of diurnal diameter variations of the xylem and phloem are a promising tool for studying plant hydraulics and xylem - phloem interactions in field conditions.", "output": "There is no related enetity." }, { "input": "However, both the theoretical framework and the experimental verification needed to interpret phloem diameter data are incomplete.", "output": "There is no related enetity." }, { "input": "In this study, we analytically evaluate the effects of changing the radial conductance between the xylem and the phloem on phloem diameter variations and test the theory using simple manipulation experiments.", "output": "There is no related enetity." }, { "input": "Our results show that phloem diameter variations are mainly caused by changes in the radial flow rate of water between the xylem and the phloem.", "output": "There is no related enetity." }, { "input": "Reducing the hydraulic conductance between these tissues decreases the amplitude of phloem diameter variation and increases the time lag between xylem and phloem diameter variation in a predictable manner.", "output": "There is no related enetity." }, { "input": "Variation in the amplitude and timing of diameter variations that cannot be explained by changes in the hydraulic conductance, could be related to changes in the osmotic concentration in the phloem.", "output": "There is no related enetity." }, { "input": "Light exerts multiple levels of influence on the Arabidopsis wound response.", "output": "Arabidopsis." }, { "input": "Light plays important roles in modulating plant responses to attack by pests and pathogens.", "output": "There is no related enetity." }, { "input": "Here, we test the hypothesis that darkness modifies the response to wounding, and examine possible mechanisms for such an effect.", "output": "There is no related enetity." }, { "input": "We investigated changes in the Arabidopsis transcriptome following a light - dark transition and the response to wounding either in the light or in the dark.", "output": "Arabidopsis." }, { "input": "The transcriptional response to the light - dark transition strongly resembles responses associated with carbon depletion.", "output": "There is no related enetity." }, { "input": "The dark shift and wound responses acted largely independently, but more complex interactions were identified at a number of levels.", "output": "There is no related enetity." }, { "input": "Darkness attenuates the overall transcriptional response to wounding, and we identified genes and physiological processes, such as anthocyanin accumulation, that exhibit light - dependent wound responses.", "output": "There is no related enetity." }, { "input": "Transcriptional activation of light - dependent wound - induced genes requires a chloroplast - derived signal originating from photosynthetic electron transport.", "output": "There is no related enetity." }, { "input": "We also present evidence of a role for the circadian clock in modifying wound responses.", "output": "There is no related enetity." }, { "input": "Our results show that darkness impacts on the wound response at a number of levels, which may imply differences in induced herbivore defences during the day and night.", "output": "There is no related enetity." }, { "input": "The effect of competition from neighbours on stomatal conductance in lettuce and tomato plants.", "output": "lettuce, tomato." }, { "input": "Competition decreased transpiration from young lettuce plants after 2 days, before any reductions in leaf area became apparent, and stomatal conductance ( g ( s ) ) of lettuce and tomato plants was also reduced.", "output": "lettuce, lettuce, tomato." }, { "input": "Stomatal closure was not due to hydraulic signals or competition for nutrients, as soil water content, leaf water status and leaf nitrate concentrations were unaffected by neighbours.", "output": "There is no related enetity." }, { "input": "Competition - induced stomatal closure was absent in an abscisic acid ( ABA ) - deficient tomato mutant, flacca, indicating a fundamental involvement of ABA.", "output": "tomato." }, { "input": "Although tomato xylem sap ABA concentrations were unaffected by the presence of neighbours, ABA / pH - based stomatal modulation is still likely to underlie the response to competition, as soil and xylem sap alkalization was observed in competing plants.", "output": "tomato." }, { "input": "Competition also modulated leaf ethylene production, and treatment of lettuce plants with an ethylene perception inhibitor ( 1 - methylcyclopropene ) diminished the difference in g ( s ) between single and competing plants grown in a controlled environment room, but increased it in plants grown in the greenhouse: ethylene altered the extent of the stomatal response to competition.", "output": "lettuce." }, { "input": "Effects of competition on g ( s ) are discussed in terms of the detection of the absence of neighbours: increases in g ( s ) and carbon fixation may allow faster initial space occupancy within an emerging community / crop.", "output": "There is no related enetity." }, { "input": "The role of class A1 heat shock factors ( HSFA1s ) in response to heat and other stresses in Arabidopsis.", "output": "Arabidopsis." }, { "input": "In Arabidopsis, there are four homologs of class A1 heat shock factor ( HSFA1 ) genes, which likely encode the master regulators of heat shock response ( HSR ).", "output": "Arabidopsis." }, { "input": "However, previous studies with double knockout ( KO ) mutants were unable to confirm this point probably due to functional redundancy.", "output": "There is no related enetity." }, { "input": "Here, we generated a quadruple KO ( QK ) and four triple KO mutants to dissect their functions.", "output": "There is no related enetity." }, { "input": "Our data show that members of the HSFA1 group not only play a pivotal role in HSR but also are involved in growth and development.", "output": "There is no related enetity." }, { "input": "Alterations in morphology and retardation in growth were observed in the quadruple but not in triple KO mutants.", "output": "There is no related enetity." }, { "input": "The basal and acquired thermotolerance capacity was dramatically decreased in the QK mutant but varied in triple KO mutants at different developmental stages.", "output": "There is no related enetity." }, { "input": "The transcriptomics profiles suggested that more than 65 % of the heat stress ( HS ) - up - regulated genes were HSFA1 dependent.", "output": "There is no related enetity." }, { "input": "HSFA1s were also involved in the expression of several HS genes induced by H ( 2 ) O ( 2 ), salt and mannitol, which is consistent with the increased sensitive phenotype of the QK mutant to the stress factors.", "output": "There is no related enetity." }, { "input": "In conclusion, the Arabidopsis HSFA1s function as the master regulators of HSR and participate as important components in other abiotic stress responses as well.", "output": "Arabidopsis." }, { "input": "Predicting the optimal prey group size from predator hunting behaviour.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "How group size affects predator attack and success rate, and so prey vulnerability, is important in determining the nonlethal consequences of predation risk on animal populations and communities.", "output": "There is no related enetity." }, { "input": "Theory predicts that both predator attack success rate and the dilution effect decline exponentially with group size and that selection generates optimal group sizes at a ' risk threshold ' above which antipredation benefits are outweighed by costs, such as those owing to higher attack rates.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We examined whether flock size risk thresholds for attack rate, success rate or dilution differed, and therefore whether the strength of selection for group size differed for these three factors, using a system of redshank Tringa totanus flocks being hunted by Eurasian sparrowhawks Accipiter nisus.", "output": "redshank, Tringa totanus, Eurasian sparrowhawks, Accipiter nisus." }, { "input": "We also asked which of the three thresholds, on their own or in combination, predicted the most commonly observed group size.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Mean redshank flock size increased with a very gradual quadratic function ( i. e. approximately linearly ) with population size, although at a rate half that possible; when population size was not limiting, individuals almost always avoided flocks of less than 30 and birds were frequently in flocks up to at least 80.", "output": "redshank." }, { "input": "Sparrowhawk attack rate showed a quadratic relationship with flock size and peaked at 55 redshanks.", "output": "Sparrowhawk, redshanks." }, { "input": "Sparrowhawk attack success rate, however, declined exponentially, becoming less steep at flock sizes of about 40 and remaining uniformly low ( a 95 % decrease ) by 70.", "output": "Sparrowhawk." }, { "input": "Combined with dilution, individual risk of death per attack decreased by 95 % when group size reached 30 ( 20 for the dilution effect alone ).", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Redshanks most commonly formed group sizes that gained the maximum individual predation risk reduction.", "output": "Redshanks." }, { "input": "They also commonly formed group sizes far above any further substantial advantages from the dilution effect or from reducing attack rate, but that continued to reduce predation risk by lowering attack success rate.", "output": "There is no related enetity." }, { "input": "Individuals did not always form the largest groups possible which we suggest is because individual variation in risk - taking subdivides the population.", "output": "There is no related enetity." }, { "input": "This places a constraint on the ability of individuals to compensate for predation risk and will have a variety of important effects on animal populations.", "output": "There is no related enetity." }, { "input": "Ecosystem engineering and predation: the multi - trophic impact of two ant species.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Ants are ubiquitous ecosystem engineers and generalist predators and are able to affect ecological communities via both pathways.", "output": "There is no related enetity." }, { "input": "They are likely to influence any other terrestrial arthropod group either directly or indirectly caused by their high abundance and territoriality.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We studied the impact of two ant species common in Central Europe, Myrmica rubra and Lasius niger, on an arthropod community.", "output": "Myrmica rubra, Lasius niger." }, { "input": "Colony presence and density of these two ant species were manipulated in a field experiment from the start of ant activity in spring to late summer.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "The experiment revealed a positive influence of the presence of one ant colony on densities of decomposers, herbivores and parasitoids.", "output": "There is no related enetity." }, { "input": "However, in the case of herbivores and parasitoids, this effect was reversed in the presence of two colonies.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Generally, effects of the two ant species were similar with the exception of their effect on Braconidae parasitoid densities that responded positively to one colony of M. rubra but not of L. niger.", "output": "M . rubra, L . niger." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Spider density was not affected by ant colony manipulation, but species richness of spiders responded positively to ant presence.", "output": "There is no related enetity." }, { "input": "This effect was independent of ant colony density, but where two colonies were present, spider richness was significantly greater in plots with two M. rubra colonies than in plots with one colony of each ant species.", "output": "M . rubra." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "To test whether the positive ecosystem engineering effects were purely caused by modified properties of the soil, we added in an additional experiment ( i ) the soil from ant nests ( without ants ) or ( ii ) unmodified soil or ( iii ) ant nests ( including ants ) to experimental plots.", "output": "There is no related enetity." }, { "input": "Ant nest soil on its own did not have a significant impact on densities of decomposers, herbivores or predators, which were significantly, and positively, affected by the addition of an intact nest.", "output": "There is no related enetity." }, { "input": "7.", "output": "There is no related enetity." }, { "input": "The results suggest an important role of both ant species in the grassland food web, strongly affecting the densities of decomposers, herbivores and higher trophic levels.", "output": "There is no related enetity." }, { "input": "We discuss how the relative impact via bottom - up and top - down effects of ants depends on nest density, with a relatively greater top - down predatory impact at higher densities.", "output": "There is no related enetity." }, { "input": "Constraints on host choice: why do parasitic birds rarely exploit some common potential hosts?", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Why are some common and apparently suitable resources avoided by potential users?", "output": "There is no related enetity." }, { "input": "This interesting ecological and evolutionary conundrum is vividly illustrated by obligate brood parasites.", "output": "There is no related enetity." }, { "input": "Parasitic birds lay their eggs into nests of a wide range of host species, including many rare ones, but do not parasitize some commonly co - occurring potential hosts.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Attempts to explain the absence of parasitism in common potential hosts are limited and typically focused on single - factor explanations while ignoring other potential factors.", "output": "There is no related enetity." }, { "input": "We tested why thrushes Turdus spp. are extremely rarely parasitized by common cuckoos Cuculus canorus despite breeding commonly in sympatry and building the most conspicuous nests among forest - breeding passerines.", "output": "common cuckoos, Cuculus canorus." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "No single examined factor explained cuckoo avoidance of thrushes.", "output": "cuckoo." }, { "input": "Life - history traits of all six European thrush species and the 10 most frequently used cuckoo hosts in Europe were similar except body / egg size, nest design and nestling diet.", "output": "cuckoo." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Experiments ( n = 1211 ) in several populations across Europe showed that host defences at egg - laying and incubation stages did not account for the lack of cuckoo parasitism in thrushes.", "output": "cuckoo." }, { "input": "However, cross - fostering experiments disclosed that various factors during the nestling period prevent cuckoos from successfully parasitizing thrushes.", "output": "cuckoos." }, { "input": "Specifically, in some thrush species, the nest cup design forced cuckoo chicks to compete with host chicks with fatal consequences for the parasite.", "output": "cuckoo." }, { "input": "Other species were reluctant to care even for lone cuckoo chicks.", "output": "cuckoo." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Importantly, in an apparently phylogenetically homogenous group of hosts, there were interspecific differences in factors responsible for the absence of cuckoo parasitism.", "output": "cuckoo." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "This study highlights the importance of considering multiple potential factors and their interactions for understanding absence of parasitism in potential hosts of parasitic birds.", "output": "There is no related enetity." }, { "input": "In the present study, comparative and experimental procedures are integrated, which represent a novel approach that should prove useful for the understanding of interspecific ecological relationships in general.", "output": "There is no related enetity." }, { "input": "Neurological complications of acute ischaemic stroke.", "output": "There is no related enetity." }, { "input": "Complications after ischaemic stroke, including both neurological and medical complications, are a major cause of morbidity and mortality.", "output": "There is no related enetity." }, { "input": "Neurological complications, such as brain oedema or haemorrhagic transformation, occur earlier than do medical complications and can affect outcomes with potential serious short - term and long - term consequences.", "output": "There is no related enetity." }, { "input": "Some of these complications could be prevented or, when this is not possible, early detection and proper management could be effective in reducing the adverse effects.", "output": "There is no related enetity." }, { "input": "However, there is little evidence - based data to guide the management of these neurological complications.", "output": "There is no related enetity." }, { "input": "There is a clear need for improved surveillance and specific interventions for the prevention, early diagnosis, and proper management of neurological complications during the acute phase of stroke to reduce stroke morbidity and mortality.", "output": "There is no related enetity." }, { "input": "The decoupling of abundance and species richness in lizard communities.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Patterns of species richness often correlate strongly with measures of energy.", "output": "There is no related enetity." }, { "input": "The more individuals hypothesis ( MIH ) proposes that this relationship is facilitated by greater resources supporting larger populations, which are less likely to become extinct.", "output": "There is no related enetity." }, { "input": "Hence, the MIH predicts that community abundance and species richness will be positively related.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Recently, Buckley & amp; Jetz ( 2010, Journal of Animal Ecology, 79, 358 - 365 ) documented a decoupling of community abundance and species richness in lizard communities in south - west United States, such that richer communities did not contain more individuals.", "output": "There is no related enetity." }, { "input": "They predicted, as a consequence of the mechanisms driving the decoupling, a more even distribution of species abundances in species - rich communities, evidenced by a positive relationship between species evenness and species richness.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We found a similar decoupling of the relationship between abundance and species richness for lizard communities in semi - arid south - eastern Australia.", "output": "There is no related enetity." }, { "input": "However, we note that a positive relationship between evenness and richness is expected because of the nature of the indices used.", "output": "There is no related enetity." }, { "input": "We illustrate this mathematically and empirically using data from both sets of lizard communities.", "output": "There is no related enetity." }, { "input": "When we used a measure of evenness, which is robust to species richness, there was no relationship between evenness and richness in either data set.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "For lizard communities in both Australia and the United States, species dominance decreased as species richness increased.", "output": "There is no related enetity." }, { "input": "Further, with the iterative removal of the first, second and third most dominant species from each community, the relationship between abundance and species richness became increasingly more positive.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Our data support the contention that species richness in lizard communities is not directly related to the number of individuals an environment can support.", "output": "There is no related enetity." }, { "input": "We propose an alternative hypothesis regarding how the decoupling of abundance and richness is accommodated; namely, an inverse relationship between species dominance and species richness, possibly because of ecological release.", "output": "There is no related enetity." }, { "input": "Food chain length and omnivory determine the stability of a marine subtidal food web.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Using a subtidal marine food web as a model system, we examined how food chain length ( predators present or absent ) and the prevalence of omnivory influenced temporal stability ( and its components ) of herbivores and plants.", "output": "There is no related enetity." }, { "input": "We held the density of top predators constant but manipulated their identity to generate a gradient in omnivory prevalence.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We measured temporal stability as the inverse of the coefficient of variation of abundance over time.", "output": "There is no related enetity." }, { "input": "Predators and omnivory could influence temporal stability through effects on abundance ( the ' abundance ' effect ), summed variance across taxa ( the ' portfolio effect ' ) or summed covariances among taxa ( the ' covariance effect ' ).", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We found that increasing food chain length by predator addition destabilized aggregate herbivore abundance through their cascading effects on abundances.", "output": "There is no related enetity." }, { "input": "Thus, predators destabilized herbivores through the overyielding effect.", "output": "There is no related enetity." }, { "input": "We also found that the stability of herbivore abundance and microalgae declined with increasing prevalence of omnivory among top predators.", "output": "There is no related enetity." }, { "input": "Aggregate macroalgae was not affected, but the stability of one algal taxon increased with the prevalence of omnivory.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Our results suggest that herbivores are more sensitive than plants to changes in food web structure because of predator additions by invasion or deletions such as might occur via harvesting and habitat loss.", "output": "There is no related enetity." }, { "input": "Are numbers enough?", "output": "There is no related enetity." }, { "input": "Colonizer phenotype and abundance interact to affect population dynamics.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Ecologists have long recognized that the number of colonizers entering a population can be a major driver of population dynamics, but still struggle to explain why the importance of colonizer supply varies so dramatically.", "output": "There is no related enetity." }, { "input": "While there are indications that differences in the phenotype among dispersing individuals could also be important to populations, the role of phenotypic variation relative to the number of individuals, and the extent to which they interact, remains unknown.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We simultaneously manipulated the phenotype ( dispersal duration ) and abundance of settlers of a marine bryozoan and measured subsequent population structure in the field.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Increases in the number of colonizing individuals increased the subsequent recruitment and biomass of populations, regardless of colonizer phenotype.", "output": "There is no related enetity." }, { "input": "However, the relationship between colonizer abundance and the subsequent reproductive yield of the population was strongly reduced in populations containing individuals that had long dispersal durations.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "The interactive effects of colonizer phenotype and abundance on the reproductive yield of populations occurred because longer dispersal durations decreased the proportion of individuals that reproduced.", "output": "There is no related enetity." }, { "input": "In fact, populations established from a few individuals with short dispersal durations had similar reproductive yield to populations c.", "output": "There is no related enetity." }, { "input": "30 times larger established from individuals with long dispersal durations.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Interactions between colonizer phenotype and abundance have important implications for predicting population dynamics beyond those previously provided by numerical abundance or recruit phenotype alone.", "output": "There is no related enetity." }, { "input": "A bicistronic, Ubiquitin - 10 promoter - based vector cassette for transient transformation and functional analysis of membrane transport demonstrates the utility of quantitative voltage clamp studies on intact Arabidopsis root epidermis.", "output": "There is no related enetity." }, { "input": "To date the use of fluorescent reporter constructs in analysing membrane transport has been limited primarily to cell lines expressing stably either the tagged transporter protein ( s ) or markers to identify lineages of interest.", "output": "There is no related enetity." }, { "input": "Strategies for transient expression have yet to be exploited in transport analysis, despite their wide application in cellular imaging studies.", "output": "There is no related enetity." }, { "input": "Here we describe a Gateway - compatible, bicistronic vector, incorporating the constitutive Ubiqutin - 10 gene promoter of Arabidopsis that gives prolonged expression after transient transformation and enables fluorescence marking of cells without a fusion construct.", "output": "There is no related enetity." }, { "input": "We show that Arabidopsis root epidermal cells are readily transformed by co - cultivation with Agrobacterium and are tractable for quantitative electrophysiological analysis.", "output": "There is no related enetity." }, { "input": "As a proof of principle, we transiently transformed Arabidopsis with the bicistronic vector carrying GFP as the fluorescent marker and, separately, the integral plasma membrane protein SYP121 essential for the inward K + channel current.", "output": "There is no related enetity." }, { "input": "We demonstrate that transient expression of SYP121 in syp121 mutant plants is sufficient to rescue the K + current in vivo.", "output": "There is no related enetity." }, { "input": "The combination of transient expression and use of the bicistronic vector promises significant advantages for studies of membrane transport and nutrient acquisition in roots.", "output": "There is no related enetity." }, { "input": "Treatment of patients with essential tremor.", "output": "There is no related enetity." }, { "input": "Essential tremor is a common movement disorder.", "output": "There is no related enetity." }, { "input": "Tremor severity and handicap vary widely, but most patients with essential tremor do not receive a diagnosis and hence are never treated.", "output": "There is no related enetity." }, { "input": "Furthermore, many patients abandon treatment because of side - effects or poor efficacy.", "output": "There is no related enetity." }, { "input": "A newly developed algorithm, based on the logarithmic relation between tremor amplitude and clinical tremor ratings, can be used to compare the magnitude of effect of available treatments.", "output": "There is no related enetity." }, { "input": "Drugs with established efficacy ( propranolol and primidone ) produce a mean tremor reduction of about 50 %.", "output": "There is no related enetity." }, { "input": "Deep brain stimulation ( DBS ) in the thalamic nucleus ventrointermedius or neighbouring subthalamic structures reduces tremor by about 90 %.", "output": "There is no related enetity." }, { "input": "However, no controlled trials of DBS have been done, and the best target is still uncertain.", "output": "There is no related enetity." }, { "input": "Better drugs are needed, and controlled trials are required to determine the safety and efficacy of DBS in the nucleus ventrointermedius and neighbouring subthalamic structures.", "output": "There is no related enetity." }, { "input": "Mechanisms of epileptogenesis and potential treatment targets.", "output": "There is no related enetity." }, { "input": "Prevention of epileptogenesis after brain trauma is an unmet medical challenge.", "output": "There is no related enetity." }, { "input": "Recent molecular profiling studies have provided an insight into molecular changes that contribute to formation of ictogenic neuronal networks, including genes regulating synaptic or neuronal plasticity, cell death, proliferation, and inflammatory or immune responses.", "output": "There is no related enetity." }, { "input": "These mechanisms have been targeted to prevent epileptogenesis in animal models.", "output": "There is no related enetity." }, { "input": "Favourable effects have been obtained using immunosuppressants, antibodies blocking adhesion of leucocytes to endothelial cells, gene therapy driving expression of neurotrophic factors, pharmacological neurostimulation, or even with conventional antiepileptic drugs by administering them before the appearance of genetic epilepsy.", "output": "There is no related enetity." }, { "input": "Further studies are needed to clarify the optimum time window and aetiological specificity of treatments.", "output": "There is no related enetity." }, { "input": "Questions related to adverse events also need further consideration.", "output": "There is no related enetity." }, { "input": "Encouragingly, the recent experimental studies emphasise that the complicated process of epileptogenesis can be favourably modified, and that antiepileptogenesis as a treatment indication might not be an impossible mission.", "output": "There is no related enetity." }, { "input": "Pterin - based ornamental coloration predicts yolk antioxidant levels in female striped plateau lizards ( Sceloporus virgatus ).", "output": "striped plateau lizards, Sceloporus virgatus." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Maternal investment in egg quality can have important consequences for offspring fitness.", "output": "There is no related enetity." }, { "input": "For example, yolk antioxidants can affect embryonic development as well as juvenile and adult phenotype.", "output": "There is no related enetity." }, { "input": "Thus, females may be selected to advertise their yolk antioxidant deposition to discriminatory males via ornamental signals, perhaps depending on the reproductive costs associated with signal production.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Female striped plateau lizards ( Sceloporus virgatus ) develop pterin - based orange colour patches during the reproductive season that influence male behaviour and that are positively associated with the phenotypic quality of the female and her offspring.", "output": "striped plateau lizards, Sceloporus virgatus." }, { "input": "Here, we assessed one potential developmental mechanism underlying the relationship between offspring quality and female ornamentation in S. virgatus, by examining the relationship between ornament expression and yolk antioxidant levels.", "output": "S . virgatus." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "As expected, concentrations of the yolk antioxidants vitamin A, vitamin E and carotenoids ( lutein and zeaxanthin ) were strongly positively intercorrelated.", "output": "There is no related enetity." }, { "input": "Eggs from larger clutches had fewer antioxidants than eggs from smaller clutches, suggesting that females may be limited in antioxidant availability or use.", "output": "There is no related enetity." }, { "input": "Fertilized and unfertilized eggs did not differ in yolk antioxidant levels.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "The size of a female ' s ornament was positively related to both the concentration and total amount of yolk antioxidants, and ornament colour was positively related to yolk antioxidant concentration.", "output": "There is no related enetity." }, { "input": "Thus, in S. virgatus, female ornaments may advertise egg quality.", "output": "S . virgatus." }, { "input": "In addition, these data suggest that more ornamented females may produce higher - quality offspring, in part because their eggs contain more antioxidants.", "output": "There is no related enetity." }, { "input": "As the colour ornament of interest is derived from pterins, not carotenoids, direct resource trade - offs between ornaments and eggs may be eliminated, reducing reproductive costs associated with signalling.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "This is the first example of a positive relationship between female ornamentation and yolk antioxidants in reptiles and may indicate the general importance of these patterns in oviparous vertebrates.", "output": "There is no related enetity." }, { "input": "Human resources for health in southeast Asia: shortages, distributional challenges, and international trade in health services.", "output": "Human." }, { "input": "In this paper, we address the issues of shortage and maldistribution of health personnel in southeast Asia in the context of the international trade in health services.", "output": "There is no related enetity." }, { "input": "Although there is no shortage of health workers in the region overall, when analysed separately, five low - income countries have some deficit.", "output": "There is no related enetity." }, { "input": "All countries in southeast Asia face problems of maldistribution of health workers, and rural areas are often understaffed.", "output": "There is no related enetity." }, { "input": "Despite a high capacity for medical and nursing training in both public and private facilities, there is weak coordination between production of health workers and capacity for employment.", "output": "There is no related enetity." }, { "input": "Regional experiences and policy responses to address these challenges can be used to inform future policy in the region and elsewhere.", "output": "There is no related enetity." }, { "input": "A distinctive feature of southeast Asia is its engagement in international trade in health services.", "output": "There is no related enetity." }, { "input": "Singapore and Malaysia import health workers to meet domestic demand and to provide services to international patients.", "output": "There is no related enetity." }, { "input": "Thailand attracts many foreign patients for health services.", "output": "There is no related enetity." }, { "input": "This situation has resulted in the so - called brain drain of highly specialised staff from public medical schools to the private hospitals.", "output": "There is no related enetity." }, { "input": "The Philippines and Indonesia are the main exporters of doctors and nurses in the region.", "output": "There is no related enetity." }, { "input": "Agreements about mutual recognition of professional qualifications for three groups of health workers under the Association of Southeast Asian Nations Framework Agreement on Services could result in increased movement within the region in the future.", "output": "There is no related enetity." }, { "input": "To ensure that vital human resources for health are available to meet the needs of the populations that they serve, migration management and retention strategies need to be integrated into ongoing efforts to strengthen health systems in southeast Asia.", "output": "human." }, { "input": "There is also a need for improved dialogue between the health and trade sectors on how to balance economic opportunities associated with trade in health services with domestic health needs and equity issues.", "output": "There is no related enetity." }, { "input": "Emerging infectious diseases in southeast Asia: regional challenges to control.", "output": "There is no related enetity." }, { "input": "Southeast Asia is a hotspot for emerging infectious diseases, including those with pandemic potential.", "output": "There is no related enetity." }, { "input": "Emerging infectious diseases have exacted heavy public health and economic tolls.", "output": "There is no related enetity." }, { "input": "Severe acute respiratory syndrome rapidly decimated the region ' s tourist industry.", "output": "There is no related enetity." }, { "input": "Influenza A H5N1 has had a profound effect on the poultry industry.", "output": "There is no related enetity." }, { "input": "The reasons why southeast Asia is at risk from emerging infectious diseases are complex.", "output": "There is no related enetity." }, { "input": "The region is home to dynamic systems in which biological, social, ecological, and technological processes interconnect in ways that enable microbes to exploit new ecological niches.", "output": "There is no related enetity." }, { "input": "These processes include population growth and movement, urbanisation, changes in food production, agriculture and land use, water and sanitation, and the effect of health systems through generation of drug resistance.", "output": "There is no related enetity." }, { "input": "Southeast Asia is home to about 600 million people residing in countries as diverse as Singapore, a city state with a gross domestic product ( GDP ) of US $ 37, 500 per head, and Laos, until recently an overwhelmingly rural economy, with a GDP of US $ 890 per head.", "output": "There is no related enetity." }, { "input": "The regional challenges in control of emerging infectious diseases are formidable and range from influencing the factors that drive disease emergence, to making surveillance systems fit for purpose, and ensuring that regional governance mechanisms work effectively to improve control interventions.", "output": "There is no related enetity." }, { "input": "Health - financing reforms in southeast Asia: challenges in achieving universal coverage.", "output": "There is no related enetity." }, { "input": "In this sixth paper of the Series, we review health - financing reforms in seven countries in southeast Asia that have sought to reduce dependence on out - of - pocket payments, increase pooled health finance, and expand service use as steps towards universal coverage.", "output": "There is no related enetity." }, { "input": "Laos and Cambodia, both resource - poor countries, have mostly relied on donor - supported health equity funds to reach the poor, and reliable funding and appropriate identification of the eligible poor are two major challenges for nationwide expansion.", "output": "There is no related enetity." }, { "input": "For Thailand, the Philippines, Indonesia, and Vietnam, social health insurance financed by payroll tax is commonly used for formal sector employees ( excluding Malaysia ), with varying outcomes in terms of financial protection.", "output": "There is no related enetity." }, { "input": "Alternative payment methods have different implications for provider behaviour and financial protection.", "output": "There is no related enetity." }, { "input": "Two alternative approaches for financial protection of the non - poor outside the formal sector have emerged - contributory arrangements and tax - financed schemes - with different abilities to achieve high population coverage rapidly.", "output": "There is no related enetity." }, { "input": "Fiscal space and mobilisation of payroll contributions are both important in accelerating financial protection.", "output": "There is no related enetity." }, { "input": "Expanding coverage of good - quality services and ensuring adequate human resources are also important to achieve universal coverage.", "output": "human." }, { "input": "As health - financing reform is complex, institutional capacity to generate evidence and inform policy is essential and should be strengthened.", "output": "There is no related enetity." }, { "input": "Health and health - care systems in southeast Asia: diversity and transitions.", "output": "There is no related enetity." }, { "input": "Southeast Asia is a region of enormous social, economic, and political diversity, both across and within countries, shaped by its history, geography, and position as a major crossroad of trade and the movement of goods and services.", "output": "There is no related enetity." }, { "input": "These factors have not only contributed to the disparate health status of the region ' s diverse populations, but also to the diverse nature of its health systems, which are at varying stages of evolution.", "output": "There is no related enetity." }, { "input": "Rapid but inequitable socioeconomic development, coupled with differing rates of demographic and epidemiological transitions, have accentuated health disparities and posed great public health challenges for national health systems, particularly the control of emerging infectious diseases and the rise of non - communicable diseases within ageing populations.", "output": "There is no related enetity." }, { "input": "While novel forms of health care are evolving in the region, such as corporatised public health - care systems ( government owned, but operating according to corporate principles and with private - sector participation ) and financing mechanisms to achieve universal coverage, there are key lessons for health reforms and decentralisation.", "output": "There is no related enetity." }, { "input": "New challenges have emerged with rising trade in health services, migration of the health workforce, and medical tourism.", "output": "There is no related enetity." }, { "input": "Juxtaposed between the emerging giant economies of China and India, countries of the region are attempting to forge a common regional identity, despite their diversity, to seek mutually acceptable and effective solutions to key regional health challenges.", "output": "There is no related enetity." }, { "input": "In this first paper in the Lancet Series on health in southeast Asia, we present an overview of key demographic and epidemiological changes in the region, explore challenges facing health systems, and draw attention to the potential for regional collaboration in health.", "output": "There is no related enetity." }, { "input": "Field tests of interspecific competition in ant assemblages: revisiting the dominant red wood ants.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "There has been considerable debate on the importance of competition in ecological communities, but its importance in structuring ant assemblages has often been uncritically accepted.", "output": "There is no related enetity." }, { "input": "Here, we briefly review field experiments examining competition in ant assemblages and use a removal experiment to test the effect of the classical territorial dominant ant, Formica aquilonia.", "output": "Formica aquilonia." }, { "input": "Ants of this species group are thought to structure communities through a dominance hierarchy.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "First, we used pitfall traps to compare the abundance of other ants in replicated sites with low and high densities of F. aquilonia.", "output": "F . aquilonia." }, { "input": "We found differences in community composition, in particular, Camponotus herculeanus was more common in low - density sites, in accordance with predictions.", "output": "Camponotus herculeanus." }, { "input": "Differences in ant assemblages were not owing to differences in measured habitat variables.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We removed F. aquilonia from a set of high - density sites, using physical and chemical methods, and repeated these procedures at procedural control sites.", "output": "F . aquilonia." }, { "input": "One year after removal, abundances of F. aquilonia at removal sites were similar to those at low - density sites.", "output": "F . aquilonia." }, { "input": "However, the composition of other species did not change in response to F. aquilonia removal.", "output": "F . aquilonia." }, { "input": "Replication rates were identical in the mensurative and experimental components of this study, so this is unlikely to be owing to the analysis being insufficiently powerful.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "We suggest three possibilities for the lack of difference.", "output": "There is no related enetity." }, { "input": "First, the study may have been too short term or small scale to detect differences.", "output": "There is no related enetity." }, { "input": "However, previous studies have shown effects on smaller spatial - and temporal - scales.", "output": "There is no related enetity." }, { "input": "Second, priority effects may be important in the successful colonisation by F. aquilonia.", "output": "F . aquilonia." }, { "input": "Thirdly, boreal ant assemblages may be too depauperate for redundancy in ecological roles and for competition to play an important structuring role.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "We thus recommend that long - term large - scale experiments be considered essential if we are to distinguish between competing hypotheses in community ecology.", "output": "There is no related enetity." }, { "input": "Effective management in clusters of pneumococcal disease: a systematic review.", "output": "pneumococcal." }, { "input": "Outbreaks of serious pneumococcal disease can occur with high attack rates in certain settings.", "output": "pneumococcal." }, { "input": "We systematically reviewed studies of interventions implemented in pneumococcal clusters and those reporting the effect of antibiotics on carriage reduction to assess the effectiveness of interventions.", "output": "pneumococcal." }, { "input": "Evidence was graded according to the Scottish Intercollegiate Guidelines Network system.", "output": "There is no related enetity." }, { "input": "Of 28 identified cluster reports, one showed that administration of antibiotics to close contacts reduced risk of pneumococcal disease.", "output": "pneumococcal." }, { "input": "In three of four clusters where rifampicin chemoprophylaxis was used and in four of five clusters where penicillin was used no further cases were seen after intervention.", "output": "There is no related enetity." }, { "input": "In clusters where pneumococcal polysaccharide vaccine was used, subsequent cases occurred, all within around 2 weeks of vaccination, which suggests delayed benefit with this approach ( evidence grade D ).", "output": "pneumococcal." }, { "input": "Use of infection control measures alone was reported in eight clusters, with no further cases being reported in seven ( grade D ).", "output": "There is no related enetity." }, { "input": "From 21 selected carriage studies, large carriage reductions were observed consistently with use of penicillin and azithromycin, with median values being 90 % and 73 %, respectively ( grade C ).", "output": "There is no related enetity." }, { "input": "The findings were presented to a working group for pneumococcal cluster guidelines and used to develop key recommendations on the management of clusters that supported prompt use of amoxicillin or azithromycin chemoprophylaxis, pneumococcal vaccination for close contacts, and implementation of infection control measures.", "output": "pneumococcal, pneumococcal." }, { "input": "Urbanisation and infectious diseases in a globalised world.", "output": "There is no related enetity." }, { "input": "The world is becoming urban.", "output": "There is no related enetity." }, { "input": "The UN predicts that the world ' s urban population will almost double from 3 * 3 billion in 2007 to 6 * 3 billion in 2050.", "output": "There is no related enetity." }, { "input": "Most of this increase will be in developing countries.", "output": "There is no related enetity." }, { "input": "Exponential urban growth is having a profound effect on global health.", "output": "There is no related enetity." }, { "input": "Because of international travel and migration, cities are becoming important hubs for the transmission of infectious diseases, as shown by recent pandemics.", "output": "There is no related enetity." }, { "input": "Physicians in urban environments in developing and developed countries need to be aware of the changes in infectious diseases associated with urbanisation.", "output": "There is no related enetity." }, { "input": "Furthermore, health should be a major consideration in town planning to ensure urbanisation works to reduce the burden of infectious diseases in the future.", "output": "There is no related enetity." }, { "input": "Emerging opportunistic yeast infections.", "output": "There is no related enetity." }, { "input": "A growing population of immunosuppressed patients has resulted in increasingly frequent diagnoses of invasive fungal infections, including those caused by unusual yeasts.", "output": "There is no related enetity." }, { "input": "The incidence of non - albicans species of Candida is increasing compared with that of Candida albicans, and several species, such as Candida glabrata and Candida krusei, may be resistant to azole antifungal therapy.", "output": "Candida albicans, Candida glabrata, Candida krusei." }, { "input": "Trichosporon species are the second most common cause of fungaemia in patients with haematological malignant disease and are characterised by resistance to amphotericin and echinocandins and poor prognosis.", "output": "There is no related enetity." }, { "input": "Rhodotorula species belong to the family Cryptococcaceae, and are a cause of catheter - related fungaemia, sepsis, and invasive disease in severely immunosuppressed patients.", "output": "There is no related enetity." }, { "input": "An increasing number of sporadic cases of invasive fungal infections by non - neoformans cryptococci have been reported in immunocompromised hosts, especially for patients with advanced HIV infection or cancer who are undergoing transplant.", "output": "HIV." }, { "input": "Other uncommon yeasts that can cause invasive disease in severely immunosuppressed patients include Geotrichum, Hansenula, Malassezia, and Saccharomyces.", "output": "There is no related enetity." }, { "input": "Host immune status is a crucial determinant of the type of invasive fungal infection a patient is at risk for.", "output": "There is no related enetity." }, { "input": "Diagnosis can be challenging and relies heavily on traditional cultures of blood and other sterile sites, although serum ( 1, 3 ) - Beta - D - glucan testing might have an adjunctive role.", "output": "There is no related enetity." }, { "input": "Although rare yeasts are emerging as opportunistic human pathogens, diagnosis remains challenging and treatment suboptimal.", "output": "human." }, { "input": "Protist - like inclusions in amber, as evidenced by Charentes amber.", "output": "There is no related enetity." }, { "input": "The mid - Cretaceous amber of France contains thousands of protist - like inclusions similar in shape to some ciliates, flagellates and amoebae.", "output": "There is no related enetity." }, { "input": "The sheer abundance of these inclusions and their size variation within a single amber piece are not concordant with true fossil protists.", "output": "There is no related enetity." }, { "input": "French amber is coniferous in origin, which generally does not preserve well protists without cell walls.", "output": "There is no related enetity." }, { "input": "Thus, it would be surprising if French Cretaceous amber had preserved millions of protists.", "output": "There is no related enetity." }, { "input": "Here, we present a survey of the protist - like inclusions from French amber and attempt to elucidate their origins.", "output": "There is no related enetity." }, { "input": "Diverse Cretaceous ambers ( from Spain, Germany and Lebanon ), also derived from conifer resins, contain thousands of protist - like inclusions.", "output": "There is no related enetity." }, { "input": "In contrast, Tertiary ambers and modern resins are poor in protist - like fossils.", "output": "There is no related enetity." }, { "input": "This suggests these inclusions originated from early Cretaceous plant resins, probably secreted with the resin by trees that did not survive after the Cretaceous ( such as the Cheirolepidiaceae ).", "output": "There is no related enetity." }, { "input": "A review of the recent literature on amber microfossils indicates several protist - like inclusions that are unlikely to have a biological origin have already been described as real fossil protists.", "output": "There is no related enetity." }, { "input": "This is problematic in that it will bias our understanding of protist evolution.", "output": "There is no related enetity." }, { "input": "Management of uncommon chemotherapy - induced emergencies.", "output": "There is no related enetity." }, { "input": "Chemotherapy can induce various clinical emergencies.", "output": "There is no related enetity." }, { "input": "Prompt recognition and management of these adverse events are important for avoiding further morbidity and mortality.", "output": "There is no related enetity." }, { "input": "Some events such as hypersensitivity and extravasation are quite common, whereas emergencies such as neutropenic typhlitis, pancreatitis, and acute haemolysis are very rare.", "output": "There is no related enetity." }, { "input": "Little information exists on the management of rare chemotherapy - induced emergencies that affect fewer than 1 % of patients.", "output": "There is no related enetity." }, { "input": "We review these uncommon chemotherapy - induced life - threatening emergencies, their pathogenesis and management, and recommendations for rechallenge with the offending chemotherapy.", "output": "There is no related enetity." }, { "input": "New driver mutations in non - small - cell lung cancer.", "output": "There is no related enetity." }, { "input": "Treatment decisions for patients with lung cancer have historically been based on tumour histology.", "output": "There is no related enetity." }, { "input": "Some understanding of the molecular composition of tumours has led to the development of targeted agents, for which initial findings are promising.", "output": "There is no related enetity." }, { "input": "Clearer understanding of mutations in relevant genes and their effects on cancer cell proliferation and survival, is, therefore, of substantial interest.", "output": "There is no related enetity." }, { "input": "We review current knowledge about molecular subsets in non - small - cell lung cancer that have been identified as potentially having clinical relevance to targeted therapies.", "output": "There is no related enetity." }, { "input": "Since mutations in EGFR and KRAS have been extensively reviewed elsewhere, here, we discuss subsets defined by so - called driver mutations in ALK, HER2 ( also known as ERBB2 ), BRAF, PIK3CA, AKT1, MAP2K1, and MET.", "output": "There is no related enetity." }, { "input": "The adoption of treatment tailored according to the genetic make - up of individual tumours would involve a paradigm shift, but might lead to substantial therapeutic improvements.", "output": "There is no related enetity." }, { "input": "Thermal performance curves of Paramecium caudatum: a model selection approach.", "output": "Paramecium caudatum." }, { "input": "The ongoing climate change has motivated numerous studies investigating the temperature response of various organisms, especially that of ectotherms.", "output": "There is no related enetity." }, { "input": "To correctly describe the thermal performance of these organisms, functions are needed which sufficiently fit to the complete optimum curve.", "output": "There is no related enetity." }, { "input": "Surprisingly, model - comparisons for the temperature - dependence of population growth rates of an important ectothermic group, the protozoa, are still missing.", "output": "There is no related enetity." }, { "input": "In this study, temperature reaction norms of natural isolates of the freshwater protist Paramecium caudatum were investigated, considering nearly the entire temperature range.", "output": "Paramecium caudatum." }, { "input": "These reaction norms were used to estimate thermal performance curves by applying a set of commonly used model functions.", "output": "There is no related enetity." }, { "input": "An information theory approach was used to compare models and to identify the best ones for describing these data.", "output": "There is no related enetity." }, { "input": "Our results indicate that the models which can describe negative growth at the high - and low - temperature branch of an optimum curve are preferable.", "output": "There is no related enetity." }, { "input": "This is a prerequisite for accurately calculating the critical upper and lower thermal limits.", "output": "There is no related enetity." }, { "input": "While we detected a temperature optimum of around 29 ^ 0C for all investigated clonal strains, the critical thermal limits were considerably different between individual clones.", "output": "There is no related enetity." }, { "input": "Here, the tropical clone showed the narrowest thermal tolerance, with a shift of its critical thermal limits to higher temperatures.", "output": "There is no related enetity." }, { "input": "The molecular and genetic basis of conidial pigmentation in Aspergillus niger.", "output": "Aspergillus niger." }, { "input": "A characteristic hallmark of Aspergillus niger is the formation of black conidiospores.", "output": "Aspergillus niger." }, { "input": "We have identified four loci involved in spore pigmentation of A. niger by using a combined genomic and classical complementation approach.", "output": "A . niger." }, { "input": "First, we characterized a newly isolated color mutant, colA, which lacked pigmentation resulting in white or colorless conidia.", "output": "There is no related enetity." }, { "input": "Pigmentation of the colA mutant was restored by a gene ( An12g03950 ) which encodes a putative 4 ' phosphopantetheinyl transferase protein ( PptA ).", "output": "There is no related enetity." }, { "input": "4 ' Phosphopantetheinyl transferase activity is required for the activation of Polyketide Synthases ( PKSs ) and / or Non - Ribosomal Peptide Synthases ( NRPSs ).", "output": "There is no related enetity." }, { "input": "The loci whose mutation resulted in fawn, olive, and brown color phenotypes were identified by complementation.", "output": "There is no related enetity." }, { "input": "The fawn phenotype was complemented by a PKS protein ( FwnA, An09g05730 ), the ovlA mutant by An14g05350 ( OlvA ) and the brnA mutant by An14g05370 ( BrnA ), the respective homologs of alb1 / pksP, ayg1 and abr1 in A. fumigatus.", "output": "A . fumigatus." }, { "input": "Targeted disruption of the pptA, fwnA, olvA and brnA genes confirmed the complementation results.", "output": "There is no related enetity." }, { "input": "Disruption of the pptA gene abolished synthesis of all polyketides and non - ribosomal peptides, while the naphtho - gamma - pyrone subclass of polyketides were specifically dependent on fwnA, and funalenone on fwnA, olvA and brnA.", "output": "There is no related enetity." }, { "input": "Thus, secondary metabolite profiling of the color mutants revealed a close relationship between polyketide synthesis and conidial pigmentation in A. niger.", "output": "A . niger." }, { "input": "Identification and characterization of putative osmosensors, HwSho1A and HwSho1B, from the extremely halotolerant black yeast Hortaea werneckii.", "output": "Hortaea werneckii." }, { "input": "In Saccharomyces cerevisiae, the Sho1 protein is one of two potential osmosensors that can activate the kinase cascade of the HOG pathway in response to increased extracellular osmolarity.", "output": "Saccharomyces cerevisiae." }, { "input": "Two novel SHO1 - like genes, HwSHO1A and HwSHO1B, have been cloned from the saltern - inhabiting, extremely halotolerant black yeast Hortaea werneckii.", "output": "Hortaea werneckii." }, { "input": "The HwSho1 protein isoforms are 93. 8 % identical in their amino - acid sequences, and have a conserved SH3 domain.", "output": "There is no related enetity." }, { "input": "When the HwSHO1 genes were transferred into S. cerevisae cells lacking the SHO1 gene, both of the HwSho1 isoforms fully complemented the function of the native S. cerevisiae Sho1 protein.", "output": "S . cerevisae, S . cerevisiae." }, { "input": "Through microscopic and biochemical validation, we demonstrate that in S. cerevisiae, both of the HwSho1 proteins have characteristic subcellular localizations similar to the S. cerevisiae Sho1 protein, and they can both activate the HOG pathway under conditions of osmotic stress.", "output": "S . cerevisiae, S . cerevisiae." }, { "input": "To a lower extent, crosstalk to the mating pathway expressing HwSho1 proteins is conserved in the PBS2 deleted S. cerevisiae strain.", "output": "S . cerevisiae." }, { "input": "These data show that the HwSho1 proteins from H. werneckii are true functional homologs of the Sho1 protein of S. cerevisiae.", "output": "H . werneckii, S . cerevisiae." }, { "input": "Polymorphism of Paramecium pentaurelia ( Ciliophora, Oligohymenophorea ) strains revealed by rDNA and mtDNA sequences.", "output": "Paramecium pentaurelia." }, { "input": "Paramecium pentaurelia is one of 15 known sibling species of the Paramecium aurelia complex.", "output": "Paramecium pentaurelia." }, { "input": "It is recognized as a species showing no intra - specific differentiation on the basis of molecular fingerprint analyses, whereas the majority of other species are polymorphic.", "output": "There is no related enetity." }, { "input": "This study aimed at assessing genetic polymorphism within P. pentaurelia including new strains recently found in Poland ( originating from two water bodies, different years, seasons, and clones of one strain ) as well as strains collected from distant habitats ( USA, Europe, Asia ), and strains representing other species of the complex.", "output": "P . pentaurelia." }, { "input": "We compared two DNA fragments: partial sequences ( 349 bp ) of the LSU rDNA and partial sequences ( 618 bp ) of cytochrome B gene.", "output": "There is no related enetity." }, { "input": "A correlation between the geographical origin of the strains and the genetic characteristics of their genotypes was not observed.", "output": "There is no related enetity." }, { "input": "Different genotypes were found in Kraksigmaw in two types of water bodies ( Opatkowice - natural pond; Jordan ' s Park - artificial pond ).", "output": "There is no related enetity." }, { "input": "Haplotype diversity within a single water body was not recorded.", "output": "There is no related enetity." }, { "input": "Likewise, seasonal haplotype differences between the strains within the artificial water body, as well as differences between clones originating from one strain, were not detected.", "output": "There is no related enetity." }, { "input": "The clustering of some strains belonging to different species was observed in the phylogenies.", "output": "There is no related enetity." }, { "input": "Determinants of reproductive success in dominant pairs of clownfish: a boosted regression tree analysis.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Central questions of behavioural and evolutionary ecology are what factors influence the reproductive success of dominant breeders and subordinate nonbreeders within animal societies?", "output": "There is no related enetity." }, { "input": "A complete understanding of any society requires that these questions be answered for all individuals.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "The clown anemonefish, Amphiprion percula, forms simple societies that live in close association with sea anemones, Heteractis magnifica.", "output": "Amphiprion percula, Heteractis magnifica." }, { "input": "Here, we use data from a well - studied population of A. percula to determine the major predictors of reproductive success of dominant pairs in this species.", "output": "A . percula." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We analyse the effect of multiple predictors on four components of reproductive success, using a relatively new technique from the field of statistical learning: boosted regression trees ( BRTs ).", "output": "There is no related enetity." }, { "input": "BRTs have the potential to model complex relationships in ways that give powerful insight.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "We show that the reproductive success of dominant pairs is unrelated to the presence, number or phenotype of nonbreeders.", "output": "There is no related enetity." }, { "input": "This is consistent with the observation that nonbreeders do not help or hinder breeders in any way, confirming and extending the results of a previous study.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Primarily, reproductive success is negatively related to male growth and positively related to breeding experience.", "output": "There is no related enetity." }, { "input": "It is likely that these effects are interrelated because males that grow a lot have little breeding experience.", "output": "There is no related enetity." }, { "input": "These effects are indicative of a trade - off between male growth and parental investment.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "Secondarily, reproductive success is positively related to female growth and size.", "output": "There is no related enetity." }, { "input": "In this population, female size is positively related to group size and anemone size, also.", "output": "There is no related enetity." }, { "input": "These positive correlations among traits likely are caused by variation in site quality and are suggestive of a silver - spoon effect.", "output": "There is no related enetity." }, { "input": "7.", "output": "There is no related enetity." }, { "input": "Noteworthily, whereas reproductive success is positively related to female size, it is unrelated to male size.", "output": "There is no related enetity." }, { "input": "This observation provides support for the size advantage hypothesis for sex change: both individuals maximize their reproductive success when the larger individual adopts the female tactic.", "output": "There is no related enetity." }, { "input": "8.", "output": "There is no related enetity." }, { "input": "This study provides the most complete picture to date of the factors that predict the reproductive success of dominant pairs of clown anemonefish and illustrates the utility of BRTs for analysis of complex behavioural and evolutionary ecology data.", "output": "There is no related enetity." }, { "input": "Novel cultured protists identify deep - branching environmental DNA clades of cercozoa: New Genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrinia.", "output": "There is no related enetity." }, { "input": "We describe three new orders of filosan Cercozoa, five new deep - branching genera, eight new species of Thaumatomonas, Reckertia, Spongomonas, Rhogostoma, Agitata, Neoheteromita and Paracercomonas, sequence their 18S rDNA, and construct 18S rDNA trees for 148 Cercozoa.", "output": "There is no related enetity." }, { "input": "Our phylogeny indicates that Filosa were ancestrally gliding flagellates; non - flagellate filose amoebae evolved from them five times independently.", "output": "There is no related enetity." }, { "input": "The new genera are more closely related to environmental DNA sequences than cultured organisms.", "output": "There is no related enetity." }, { "input": "Tremula longifila, a zooflagellate glider on both flagella ( unlike other Cercozoa ), is the most divergent filosan ( Tremulida ord. n. ).", "output": "Tremula longifila." }, { "input": "Micrometopion nutans is a eukaryote - eating gliding zooflagellate like Metopion and Metromonas.", "output": "Micrometopion nutans." }, { "input": "Minimassisteria diva is a widespread trimorphic marine amoeboflagellate granofilosan.", "output": "Minimassisteria diva." }, { "input": "Peregrinia clavideferens, a non - testate, scale - bearing, filose amoeba, branches deeply in Thaumatomonadida, which are probably sisters to Spongomonadida.", "output": "Peregrinia clavideferens." }, { "input": "Nudifila producta is a filose amoeboflagellate related to Clautriavia and Marimonadida ( ord. n., e. g. Pseudopirsonia, Auranticordis ).", "output": "Nudifila producta." }, { "input": "We substantially revise Imbricatea, now including Spongomonadida, and Thecofilosea to include Phaeodaria.", "output": "There is no related enetity." }, { "input": "Thecofilosea and Imbricatea and Thecofilosea are sisters, both arguably ancestrally rigid gliding flagellates with ventral pseudopod - emitting grooves.", "output": "There is no related enetity." }, { "input": "Scale - free Ovulinata parva is sister to Paulinella, so imbricate silica scales can be lost.", "output": "Ovulinata parva." }, { "input": "Internal hollow silica skeletons evolved twice in Thecofilosea ( Ebriida, Phaeodaria ) or were multiply lost.", "output": "There is no related enetity." }, { "input": "Protaspa replaces preoccupied ' Protaspis '.", "output": "There is no related enetity." }, { "input": "Amyotrophic lateral sclerosis.", "output": "There is no related enetity." }, { "input": "Amyotrophic lateral sclerosis ( ALS ) is an idiopathic, fatal neurodegenerative disease of the human motor system.", "output": "human." }, { "input": "In this Seminar, we summarise current concepts about the origin of the disease, what predisposes patients to develop the disorder, and discuss why all cases of ALS are not the same.", "output": "There is no related enetity." }, { "input": "In the 150 years since Charcot originally described ALS, painfully slow progress has been made towards answering these questions.", "output": "There is no related enetity." }, { "input": "We focus on what is known about ALS and where research is heading - from the small steps of extending longevity, improving therapies, undertaking clinical trials, and compiling population registries to the overarching goals of establishing the measures that guard against onset and finding the triggers for this neurodegenerative disorder.", "output": "There is no related enetity." }, { "input": "Tyrosine phosphorylation of actin during microcyst formation and germination in Polysphondylium pallidum.", "output": "Polysphondylium pallidum." }, { "input": "High osmolarity causes amoebae of the cellular slime mould Polysphondylium pallidum to individually encyst, forming microcysts.", "output": "Polysphondylium pallidum." }, { "input": "During microcyst differentiation, actin is tyrosine phosphorylated.", "output": "There is no related enetity." }, { "input": "Tyrosine phosphorylation of actin is independent of encystment conditions and occurs during the final stages of microcyst formation.", "output": "There is no related enetity." }, { "input": "During microcyst germination, actin undergoes dephosphorylation prior to amoebal emergence.", "output": "There is no related enetity." }, { "input": "Renewed phosphorylation of actin in germinating microcysts can be triggered by increasing the osmolarity of the medium which inhibits emergence.", "output": "There is no related enetity." }, { "input": "Immunofluorescence reveals that actin is dispersed throughout the cytoplasm in dormant microcysts.", "output": "There is no related enetity." }, { "input": "Following the onset of germination, actin is observed around vesicles where it co - localizes with phosphotyrosine.", "output": "There is no related enetity." }, { "input": "Prior to emergence, actin localizes to patches near the cell surface.", "output": "There is no related enetity." }, { "input": "Increasing osmolarity disrupts this localization and causes actin to redistribute throughout the cytoplasm, a situation similar to that observed in dormant microcysts.", "output": "There is no related enetity." }, { "input": "The tyrosine phosphorylation state of actin does not appear to influence the long - term viability of dormant microcysts.", "output": "There is no related enetity." }, { "input": "Together, these results indicate an association between actin tyrosine phosphorylation, organization of the actin cytoskeleton, and microcyst dormancy.", "output": "There is no related enetity." }, { "input": "Mechanisms of unisexual mating in Cryptococcus neoformans.", "output": "Cryptococcus neoformans." }, { "input": "Sex serves a pivotal role in genetic exchange and it contributes to the fitness and genetic diversity for eukaryotic populations.", "output": "There is no related enetity." }, { "input": "Although the importance of the canonical bisexual mating has been widely accepted, the significance of the evolution and maintenance of unisexual mating observed in some eukaryotes is unclear.", "output": "There is no related enetity." }, { "input": "The recent discovery of same - sex mating in the human fungal pathogen Cryptococcus neoformans and the revelation of its impact on the Cryptococcus global population structure provide a platform to elucidate the molecular mechanisms and significance of unisexual mating.", "output": "human, Cryptococcus neoformans." }, { "input": "Here, we review the evidence of unisexual mating in Cryptococcus and provide some perspective on the biological significance of this life style on the survival of this important fungal pathogen in the environment and in animal hosts.", "output": "There is no related enetity." }, { "input": "We also summarize our current understanding of the molecular mechanisms governing this unconventional mode of reproduction.", "output": "There is no related enetity." }, { "input": "Patchy bed disturbance and fish predation independently influence the distribution of stream invertebrates and algae.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "The identification of factors determining the patchy distribution of organisms in space and time is a central concern of ecology.", "output": "There is no related enetity." }, { "input": "Predation and abiotic disturbance are both well - known drivers of this patchiness, but their interplay is still poorly understood, especially for communities dominated by mobile organisms in frequently disturbed ecosystems.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We investigated the separate and interactive influences of bed disturbance by floods and predation by fish on the benthic community in a flood - prone stream.", "output": "There is no related enetity." }, { "input": "Electric fields excluded fish predators from half of 48 stream bed patches ( area 0 * 49 m ( 2 ) ) with contrasting disturbance treatments.", "output": "There is no related enetity." }, { "input": "Three types of bed disturbance were created by either scouring or filling patches to a depth of 15 - 20 cm or by leaving the patches undisturbed, thus mimicking the mosaic of scour and fill caused by a moderate flood.", "output": "There is no related enetity." }, { "input": "Benthic invertebrates and algae were sampled repeatedly until 57 days after the disturbance.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Disturbance influenced all ten investigated biological response variables, whereas predation affected four variables.", "output": "There is no related enetity." }, { "input": "Averaged across time, invertebrate taxon richness and total abundance were highest in stable patches.", "output": "There is no related enetity." }, { "input": "Algal biomass and densities of five of the seven most common invertebrate taxa ( most of which were highly mobile ) were higher in fill than in scour patches, whereas two taxa were more abundant in scour and stable than in fill patches.", "output": "There is no related enetity." }, { "input": "Furthermore, two common invertebrate grazers were more abundant and algal biomass tended to be reduced in fish exclusion patches, suggesting a patch - scale trophic cascade from fish to algae.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Our results highlight the importance of patchy physical disturbance for the microdistribution of mobile stream organisms and indicate a notable, but less prevalent, influence of fish predation at the patch scale in this frequently disturbed environment.", "output": "There is no related enetity." }, { "input": "Disturbance and predation treatments interacted only once, suggesting that the observed predation effects were largely independent of local bed disturbance patterns.", "output": "There is no related enetity." }, { "input": "Contrasting cascade effects of carnivores on plant fitness: a meta - analysis.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Although carnivores indirectly improve plant fitness by decreasing herbivory, they may also decrease plant reproduction by disrupting plant - pollinator mutualism.", "output": "There is no related enetity." }, { "input": "The overall magnitude of the resulting net effect of carnivores on plant fitness and the factors responsible for the variations in strength and direction of this effect have not been explored quantitatively to date.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We performed a meta - analysis of 67 studies containing 163 estimates of the effects of carnivores on plant fitness and examined the relative importance of several potential sources of variation in carnivore effects.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Carnivores significantly increased plant fitness via suppression of herbivores and decreased fitness by consuming pollinators.", "output": "There is no related enetity." }, { "input": "The overall net effect of carnivores on plant fitness was positive ( 32 % increase ), indicating that effects via herbivores were stronger than effects via pollinators.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Parasitoids had stronger positive effect on plant fitness than predators.", "output": "There is no related enetity." }, { "input": "Active hunters increased plant fitness, whereas stationary predators had no significant effect, presumably because they were more prone to disrupt plant - pollinator mutualism.", "output": "There is no related enetity." }, { "input": "Carnivores with broader habitat domain had negative effects on plant fitness, whereas those with narrow habitat domain had positive effects.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Predator effects were positive for plants which offered rewards ( e. g. extrafloral nectaries ) and negative for plants which lacked any attractors.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "This study adds new knowledge on the factors that determine the strength of terrestrial trophic cascades and highlights the importance of considering simultaneous contrasting interactions in the same study system.", "output": "There is no related enetity." }, { "input": "Shrinking by numbers: landscape context affects the species composition but not the quantitative structure of local food webs.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "With habitat fragmentation spreading around the world, there is a pressing need to understand its impacts on local food webs.", "output": "There is no related enetity." }, { "input": "To date, few studies have examined the effects of landscape context on multiple local communities in a quantitative, spatially realistic setting.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "To examine how the isolation of a food web affects its structure, we construct local food webs of specialist herbivores and their natural enemies on 82 individual oaks ( Quercus robur ) growing in different landscape contexts.", "output": "oaks, Quercus robur." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Across this set of webs, we find that communities in isolated habitat patches not only contained fewer species than did well - connected ones, but also differed in species composition.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Surprisingly, the effects observed in terms of species composition were not reflected in the quantitative interaction structure of local food webs: landscape context had no detectable effect on either the interaction evenness, linkage density, connectance, generality or vulnerability of local webs.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "We conclude that the quantitative structure of food webs may be stable in the face of habitat fragmentation, despite clear - cut impacts on individual species.", "output": "There is no related enetity." }, { "input": "This finding offers hope - inspiring news for conservation, but should clearly be verified by empirical studies across both naturally and more recently fragmented systems.", "output": "There is no related enetity." }, { "input": "Comparative immunofluorescence and ultrastructural analysis of microtubule organization in Uronema sp., Klebsormidium flaccidum, K. subtilissimum, Stichococcus bacillaris and S. chloranthus ( Chlorophyta ).", "output": "Klebsormidium flaccidum, K . subtilissimum, Stichococcus bacillaris, S . chloranthus." }, { "input": "A detailed comparative examination of microtubule ( MT ) organization in interphase and dividing cells of Uronema sp., Klebsormidium flaccidum, K. subtilissimum, Stichococcus bacillaris and S. chloranthus was made using tubulin immunofluorescence and transmission electron microscopy ( TEM ).", "output": "Klebsormidium flaccidum, K . subtilissimum, Stichococcus bacillaris, S . chloranthus." }, { "input": "During interphase all the species bear a well - organized cortical MT system, consisting of parallel bundles with different orientations.", "output": "There is no related enetity." }, { "input": "In Uronema sp. the cortical MT bundles are longitudinally oriented, whereas in the other species they are in transverse orientation to the axis of the cells.", "output": "There is no related enetity." }, { "input": "Considerable differences in MT organization were also observed during stages of mitosis, mainly preprophase, as well as cytokinesis.", "output": "There is no related enetity." }, { "input": "In Uronema sp., a particular radial MT assembly is organized during preprophase - early prophase, which was not observed in the other species.", "output": "There is no related enetity." }, { "input": "In Stichococcus a fine MT ring surrounded the nucleus during preprophase and prophase.", "output": "There is no related enetity." }, { "input": "An MT ring, together with single cytoplasmic MTs, was also found associated with the developing diaphragm during cytokinesis in Stichococcus.", "output": "There is no related enetity." }, { "input": "A phycoplast participates in cytokinesis in Uronema sp., but not in the other species.", "output": "There is no related enetity." }, { "input": "In Uronema sp. the centrosome functions as a microtubule organizing center ( MTOC ) during mitosis, but not during interphase and cytokinesis.", "output": "There is no related enetity." }, { "input": "The phylogenetic significance of these differences is discussed in combination with SSU / ITS sequencing and other, existing molecular data.", "output": "There is no related enetity." }, { "input": "Intentional genetic introgression influences survival of adults and subadults in a small, inbred felid population.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Inbreeding and low genetic diversity can cause reductions in individual fitness and increase extinction risk in animal populations.", "output": "There is no related enetity." }, { "input": "Intentional introgression, achieved by releasing genetically diverse individuals into inbred populations, has been used as a conservation tool to improve demographic performance in endangered populations.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "By the 1980s, Florida panthers ( Puma concolor coryi ) had been reduced to a small, inbred population that appeared to be on the brink of extinction.", "output": "Florida panthers, Puma concolor coryi." }, { "input": "In 1995, female pumas from Texas ( P. c. stanleyana ) were released in occupied panther range as part of an intentional introgression programme to restore genetic variability and improve demographic performance of panthers.", "output": "P . c . stanleyana." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We used 25 years ( 1981 - 2006 ) of continuous radiotelemetry and genetic data to estimate and model subadult and adult panther survival and cause - specific mortality to provide rigorous sex and age class - specific survival estimates and evaluate the effect of the introgression programme on these parameters.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Genetic ancestry influenced annual survival of subadults and adults after introgression, as F ( 1 ) generation admixed panthers ( = 0 * 98 ) survived better than pre - introgression type panthers ( = 0 * 77 ) and other admixed individuals ( = 0 * 82 ).", "output": "There is no related enetity." }, { "input": "Furthermore, heterozygosity was higher for admixed panthers relative to pre - introgression type panthers and positively influenced survival.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Our results are consistent with hybrid vigour; however, extrinsic factors such as low density of males in some areas of panther range may also have contributed to higher survival of F ( 1 ) panthers.", "output": "There is no related enetity." }, { "input": "Regardless, improved survival of F ( 1 ) subadults and adults likely contributed to the numerical increase in panthers following introgression, and our results indicate that intentional admixture, achieved here by releasing individuals from another population, appears to have been successful in improving demographic performance in this highly endangered population.", "output": "There is no related enetity." }, { "input": "Projectin PEVK domain, splicing variants and domain structure in basal and derived insects.", "output": "There is no related enetity." }, { "input": "The third elastic filament of striated muscles consists of giant proteins: titin ( in vertebrates ) and kettin / projectin ( in insects ).", "output": "There is no related enetity." }, { "input": "In all three proteins, elasticity is at least partly associated with the so - called PEVK domain.", "output": "There is no related enetity." }, { "input": "The projectin PEVK domains of diverse insects are highly divergent compared with an otherwise conserved protein organization.", "output": "There is no related enetity." }, { "input": "We present the characterization of the PEVK domain in two dragonflies and in human lice.", "output": "human lice." }, { "input": "A conserved segment at the end of the PEVK, the NH ( 2 ) - terminal conserved segment - 1 ( NTCS - 1 ), may serve as an anchor point for projectin to either myosin or actin, providing a mechanical link.", "output": "There is no related enetity." }, { "input": "The analysis of alternative splicing variants identifies the shortest PEVK isoform as the predominant form in the flight muscles of several insects, possibly contributing to myofibrillar stiffness.", "output": "There is no related enetity." }, { "input": "Paediatric stroke: genetic insights into disease mechanisms and treatment targets.", "output": "There is no related enetity." }, { "input": "In children, stroke is as common as brain tumour and causes substantial mortality and long - term morbidity, with recurrence in up to 20 %.", "output": "There is no related enetity." }, { "input": "There are three sets of international clinical guidelines relating to childhood stroke; however, acute and preventive treatment recommendations are based on interventions effective in adults, rather than data regarding efficacy in children.", "output": "There is no related enetity." }, { "input": "A wide spectrum of risk factors underlies childhood stroke, and these risk factors vary from those encountered in adults.", "output": "There is no related enetity." }, { "input": "Specific disease mechanisms implicated in childhood arterial ischaemic stroke have received little attention, but an increased understanding of disease pathogenesis could lead to novel targeted treatment approaches.", "output": "There is no related enetity." }, { "input": "Here, we consider insights into the pathogenesis of childhood arterial ischaemic stroke and cerebral arteriopathy, provided by current knowledge of Mendelian diseases that are associated with an increased risk of these conditions.", "output": "There is no related enetity." }, { "input": "We give particular attention to aspects of vascular development, homoeostasis, and response to environmental effects.", "output": "There is no related enetity." }, { "input": "Our analysis highlights a potential role for interventions already licensed for pharmaceutical use, as well as new therapeutic targets and avenues for further research.", "output": "There is no related enetity." }, { "input": "The sirtuin pathway in ageing and Alzheimer disease: mechanistic and therapeutic considerations.", "output": "There is no related enetity." }, { "input": "BACKGROUND: Advances in gerontology have yielded crucial insights into the molecular and biochemical aspects of the ageing process.", "output": "There is no related enetity." }, { "input": "The sirtuin pathway, which is most notable for its association with the anti - ageing effects of calorie restriction, has received particular attention, and pharmacological or transgenic upregulation of the sirtuin pathway has shown promising results in laboratory models of ageing.", "output": "There is no related enetity." }, { "input": "Alzheimer ' s disease is a neurodegenerative disease that is imposing an increasing burden on society, and is the leading cause of senile dementia worldwide.", "output": "There is no related enetity." }, { "input": "The lack of therapies for Alzheimer ' s disease provides a strong incentive for the development of an effective treatment strategy and, interestingly, research has uncovered a mechanism of action of the sirtuin pathway that might have therapeutic potential for Alzheimer ' s disease.", "output": "There is no related enetity." }, { "input": "RECENT DEVELOPMENTS: SIRT1, one of the seven mammalian proteins of the sirtuin family of NAD ( + ) - dependent deacetylases, has recently been shown to attenuate amyloidogenic processing of amyloid - Beta protein precursor ( APP ) in cell culture studies in vitro and in transgenic mouse models of Alzheimer ' s disease.", "output": "mouse." }, { "input": "Mechanistically, SIRT1 increases alpha - secretase production and activity through activation of the alpha - secretase gene ADAM10.", "output": "There is no related enetity." }, { "input": "Because alpha - secretase is the enzyme responsible for the non - amyloidogenic cleavage of APP, upregulation of alpha - secretase shifts APP processing to reduce the pathological accumulation of the presumptive toxic ABeta species that results from Beta - secretase and gamma - secretase activity.", "output": "There is no related enetity." }, { "input": "Interestingly, the spatial patterns of ABeta deposition in the brain might correlate with increased aerobic glycolysis in those regions.", "output": "There is no related enetity." }, { "input": "Because aerobic glycolysis depletes cellular levels of NAD ( + ) ( through a decreased NAD ( + ) / NADH ratio ), it is possible that a corresponding downregulation of the NAD ( + ) - dependent sirtuin pathway contributes to the amyloidogenic processing of APP.", "output": "There is no related enetity." }, { "input": "WHERE NEXT?: The specific inhibition of ABeta generation by SIRT1 coupled with the potential link between aerobic glycolysis, NAD ( + ) depletion, and amyloidogenesis through the sirtuin pathway has translational implications.", "output": "There is no related enetity." }, { "input": "On the one hand, the possible underlying role of the sirtuin pathway in Alzheimer ' s disease onset and development might increase our understanding of this devastating condition.", "output": "There is no related enetity." }, { "input": "On the other hand, therapeutic upregulation of SIRT1 might provide opportunities for the amelioration of Alzheimer ' s - disease - type neuropathology through inhibition of amyloidogenesis.", "output": "There is no related enetity." }, { "input": "Ultimately, further analysis into both aspects is necessary if any progress is to be made.", "output": "There is no related enetity." }, { "input": "Ventricular septal defect.", "output": "There is no related enetity." }, { "input": "Ventricular septal defects account for up to 40 % of all congenital cardiac malformations.", "output": "There is no related enetity." }, { "input": "The diagnosis encompasses a broad range of anomalies, including isolated defects and those associated with other congenital cardiac malformations.", "output": "There is no related enetity." }, { "input": "Presentation, symptoms, natural history, and management of ventricular septal defects depend on size and anatomical associations of the anomaly, patient ' s age, and local diagnostic and interventional expertise.", "output": "There is no related enetity." }, { "input": "In this Seminar, we describe the anatomical range of ventricular septal defects and discuss present management of these malformations.", "output": "There is no related enetity." }, { "input": "Genetic determinants, diagnostic techniques, physiological considerations, and management challenges are examined in detail.", "output": "There is no related enetity." }, { "input": "Unfortunately, in many circumstances, evidence on which to guide optimum management is scarce.", "output": "There is no related enetity." }, { "input": "We present some longer term considerations of ventricular septal defects in adolescents and adults, with particular emphasis on patients with raised pulmonary vascular resistance and Eisenmenger ' s syndrome.", "output": "There is no related enetity." }, { "input": "Interplay between the parasite Amoebophrya sp.", "output": "Amoebophrya sp .." }, { "input": "( Alveolata ) and the cyst formation of the red tide dinoflagellate Scrippsiella trochoidea.", "output": "Scrippsiella trochoidea." }, { "input": "Syndiniales ( Alveolata ) are marine parasites of a wide range of hosts, from unicellular organisms to Metazoa.", "output": "There is no related enetity." }, { "input": "Many Syndiniales obligatorily kill their hosts to accomplish their life cycle.", "output": "There is no related enetity." }, { "input": "This is the case for Amoebophrya spp. infecting dinoflagellates.", "output": "Amoebophrya spp .." }, { "input": "However, several dinoflagellate species known to be infected by these parasites produce diploid resting cysts as part of their life history.", "output": "There is no related enetity." }, { "input": "These resting cysts may survive several seasons in the sediment before germinating.", "output": "There is no related enetity." }, { "input": "How these parasites survive during the dormancy of their host remained an open question.", "output": "There is no related enetity." }, { "input": "We successfully established infections by Amoebophrya sp. in the red tide dinoflagellate Scrippsiella trochoidea.", "output": "Amoebophrya sp ., Scrippsiella trochoidea." }, { "input": "This host strain was homothallic and able to continuously produce typical calcified cysts covered by calcareous spines.", "output": "There is no related enetity." }, { "input": "Presence of the parasite significantly speeded up the host cyst production, and cysts produced were the only cells to resist infections.", "output": "There is no related enetity." }, { "input": "However, some of them were clearly infected, probably earlier in their formation.", "output": "There is no related enetity." }, { "input": "After 10 months, cysts produced in presence of the parasite were able to germinate and new infective cycles of the parasite were rapidly observed.", "output": "There is no related enetity." }, { "input": "Thus, a very novel relationship for protists is demonstrated, one in which parasite and host simultaneously enter dormancy, emerging months later to propagate both species.", "output": "There is no related enetity." }, { "input": "Treatment implications of the emerging molecular classification system for melanoma.", "output": "There is no related enetity." }, { "input": "Melanoma is an aggressive disease with few standard treatment options.", "output": "There is no related enetity." }, { "input": "The conventional classification system for this disease is based on histological growth patterns, with division into four subtypes: superficial spreading, lentigo maligna, nodular, and acral lentiginous.", "output": "There is no related enetity." }, { "input": "Major limitations of this classification system are absence of prognostic importance and little correlation with treatment outcomes.", "output": "There is no related enetity." }, { "input": "Recent preclinical and clinical findings support the notion that melanoma is not one malignant disorder but rather a family of distinct molecular diseases.", "output": "There is no related enetity." }, { "input": "Incorporation of genetic signatures into the conventional histopathological classification of melanoma has great implications for development of new and effective treatments.", "output": "There is no related enetity." }, { "input": "Genes of the mitogen - associated protein kinase ( MAPK ) pathway harbour alterations sometimes identified in people with melanoma.", "output": "There is no related enetity." }, { "input": "The mutation Val600Glu in the BRAF oncogene ( designated BRAF ( V600E ) ) has been associated with sensitivity in vitro and in vivo to agents that inhibit BRAF ( V600E ) or MEK ( a kinase in the MAPK pathway ).", "output": "There is no related enetity." }, { "input": "Melanomas arising from mucosal, acral, chronically sun - damaged surfaces sometimes have oncogenic mutations in KIT, against which several inhibitors have shown clinical efficacy.", "output": "There is no related enetity." }, { "input": "Some uveal melanomas have activating mutations in GNAQ and GNA11, rendering them potentially susceptible to MEK inhibition.", "output": "There is no related enetity." }, { "input": "These findings suggest that prospective genotyping of patients with melanoma should be used increasingly as we work to develop new and effective treatments for this disease.", "output": "There is no related enetity." }, { "input": "Ciliate community associated with aquatic macrophyte roots: effects of nutrient enrichment on the community composition and species richness.", "output": "There is no related enetity." }, { "input": "The objective of this study was to identify the impact of nutrient enrichment on the diversity of the ciliate community associated with the roots of the aquatic macrophyte Eichhornia crassipes.", "output": "Eichhornia crassipes." }, { "input": "The experiment was performed in the Garsigmaas Lake, located in the Upper Parana River floodplain, Brazil.", "output": "There is no related enetity." }, { "input": "We conducted two treatments ( fertilized and control ) with three replicates each.", "output": "There is no related enetity." }, { "input": "To increase the initial nutrient concentrations in each mesocosm of the fertilized treatment, we added 1000 mugL ( - 1 ) of KNO ( 3 ) and 200 mugL ( - 1 ) of KH ( 2 ) PO ( 4 ) during each sampling date.", "output": "There is no related enetity." }, { "input": "We found a relative high number of ciliate species ( 85 species ) and a predominance of hypotrichs.", "output": "There is no related enetity." }, { "input": "Among the recorded species, about 25 % occurred exclusively in the fertilized treatment.", "output": "There is no related enetity." }, { "input": "Moreover, detrended correspondence analysis demonstrated that the ciliate community associated with E. crassipes roots changed significantly in response to the nutrient input in such a way that the species composition of the fertilized treatment was remarkably different from that of the control.", "output": "E . crassipes." }, { "input": "In contrast to our expectations, species richness in the fertilized treatment was significantly higher than that in the control, refuting our hypothesis that species richness decreases under eutrophic conditions.", "output": "There is no related enetity." }, { "input": "International Cognition and Cancer Task Force recommendations to harmonise studies of cognitive function in patients with cancer.", "output": "There is no related enetity." }, { "input": "It has become increasingly apparent that cytotoxic drugs given systemically for non - CNS tumours might have cognitive side - effects, but many fundamental questions require further elucidation, and large samples from several institutions are needed.", "output": "There is no related enetity." }, { "input": "Two working groups brought together by the International Cognition and Cancer Task Force ( ICCTF ) developed recommendations for a core set of neuropsychological tests, common criterion for defining cognitive impairment and cognitive changes, and common approaches to improve the homogeneity of study methods.", "output": "There is no related enetity." }, { "input": "These recommendations will improve research design and facilitate study combinations, between - study comparisons, and meta - analyses, which will allow more accurate estimates of incidence, severity, individual risk factors, and causes of cognitive problems associated with chemotherapy for non - CNS tumours.", "output": "There is no related enetity." }, { "input": "Low functional richness and redundancy of a predator assemblage in native forest fragments of Chiloe island, Chile.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Changes in land use and habitat fragmentation are major drivers of global change, and studying their effects on biodiversity constitutes a major research programme.", "output": "There is no related enetity." }, { "input": "However, biodiversity is a multifaceted concept, with a functional component linking species richness to ecosystem function.", "output": "There is no related enetity." }, { "input": "Currently, the interaction between functional and taxonomic components of biodiversity under realistic scenarios of habitat degradation is poorly understood.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "The expected functional richness ( FR ) - species richness relationship ( FRSR ) is positive, and attenuated for functional redundancy in species - rich assemblages.", "output": "There is no related enetity." }, { "input": "Further, environmental filters are expected to flatten that association by sorting species with similar traits.", "output": "There is no related enetity." }, { "input": "Thus, analysing FRSR can inform about the response of biodiversity to environmental gradients and habitat fragmentation, and its expected functional consequences.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Top predators affect ecosystem functioning through prey consumption and are particularly vulnerable to changes in land use and habitat fragmentation, being good indicators of ecosystem health and suitable models for assessing the effects of habitat fragmentation on their FR.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Thus, this study analyses the functional redundancy of a vertebrate predator assemblage at temperate forest fragments in a rural landscape of Chiloe island ( Chile ), testing the existence of environmental filters by contrasting an empirically derived FRSR against those predicted from null models, and testing the association between biodiversity components and the structure of forest fragments.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Overall, contrasts against null models indicate that regional factors determine low levels of FR and redundancy for the vertebrate predator assemblage studied, while recorded linear FRSR indicates proportional responses of the two biodiversity components to the structure of forest fragments.", "output": "There is no related enetity." }, { "input": "Further, most species were positively associated with either fragment size or shape complexity, which are highly correlated.", "output": "There is no related enetity." }, { "input": "This, and the absence of ecological filters at the single - fragment scale, rendered taxonomically and functionally richer predator assemblages at large complex - shaped fragments.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "These results predict strong effects of deforestation on both components of biodiversity, potentially affecting the functioning of remnants of native temperate forest ecosystems.", "output": "There is no related enetity." }, { "input": "Thus, the present study assesses general responses of functional and taxonomic components of biodiversity to a specific human - driven process.", "output": "human." }, { "input": "Fluorescent proteins illuminate the structure and function of the hyphal tip apparatus.", "output": "There is no related enetity." }, { "input": "Fungal hyphae show extreme polarized growth at the tip.", "output": "There is no related enetity." }, { "input": "Electron microscope studies have revealed a apical body called the Spitzenkorper that is thought to drive polarized growth.", "output": "There is no related enetity." }, { "input": "Studies of polarized growth in S. cerevisiae have identified the protein components of the polarized growth machinery, that are conserved in other fungi.", "output": "S . cerevisiae." }, { "input": "Fusion of these proteins to GFP and its variants has for the first time allowed the localization of these proteins in real time to the hyphal tip without the need for drastic fixation procedures.", "output": "There is no related enetity." }, { "input": "Such studies showed that vesicle - associated proteins localize to the Spitzenkorper and identified a second compartment located at the tip surface composed of exocyst and other proteins that mediate the fusion of secretory vesicles with the plasma membrane.", "output": "There is no related enetity." }, { "input": "One step construction of Agrobacterium - Recombination - ready - plasmids ( OSCAR ), an efficient and robust tool for ATMT based gene deletion construction in fungi.", "output": "There is no related enetity." }, { "input": "Increasing availability of genomic data and sophistication of analytical methodology in fungi has elevated the need for functional genomics tools in these organisms.", "output": "There is no related enetity." }, { "input": "Previously we reported a method called DelsGate for rapid preparation of deletion constructs for protoplast - mediated fungal transformation systems, which is based on Gateway ( R ) technology.", "output": "There is no related enetity." }, { "input": "However, over the past several years Agrobacteriumtumefaciens - mediated transformation ( ATMT ) has become the preferred genetic transformation method for an increasing number of fungi.", "output": "Agrobacteriumtumefaciens." }, { "input": "Therefore, we developed a method for One Step Construction of Agrobacterium - Recombination - ready - plasmids ( OSCAR ), to rapidly create deletion constructs for ATMT systems.", "output": "There is no related enetity." }, { "input": "The OSCAR methodology involves PCR amplification of the upstream and downstream flanks of the gene of interest, using gene specific primers each with a 5 ' extension containing one of four different attB recombination sites, modified from the Invitrogen MultiSite Gateway ( R ) system.", "output": "There is no related enetity." }, { "input": "Amplified gene flanks are then mixed with specifically designed marker and binary vectors and treated with BP clonase, generating the deletion construct in a single cloning step.", "output": "There is no related enetity." }, { "input": "The entire process of deletion construct preparation can be accomplished in just 2days.", "output": "There is no related enetity." }, { "input": "Using OSCAR we generated eight targeted deletion constructs and used two of them to generate deletion mutants in Verticillium dahliae by ATMT.", "output": "Verticillium dahliae." }, { "input": "In summary, OSCAR methodology combines PCR and Gateway ( R ) technology to rapidly and robustly generate precise deletion constructs for fungal ATMT and homologous gene replacement.", "output": "There is no related enetity." }, { "input": "Scales of orientation, directed walks and movement path structure in sharks.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Animal search patterns reflect sensory perception ranges combined with memory and knowledge of the surrounding environment.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Random walks are used when the locations of resources are unknown, whereas directed walks should be optimal when the location of favourable habitats is known.", "output": "There is no related enetity." }, { "input": "However, directed walks have been quantified for very few species.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We re - analysed tracking data from three shark species to determine whether they were using directed walks, and if so, over which spatial scales.", "output": "There is no related enetity." }, { "input": "Fractal analysis was used to quantify how movement structure varied with spatial scale and determine whether the sharks were using patches.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Tiger sharks performed directed walks at large spatial scales ( at least 6 - 8 km ).", "output": "There is no related enetity." }, { "input": "Thresher sharks also showed directed movement ( at scales of 400 - 1900 m ), and adult threshers were able to orient at greater scales than juveniles, which may suggest that learning improves the ability to perform directed walks.", "output": "threshers." }, { "input": "Blacktip reef sharks had small home ranges, high site fidelity and showed no evidence of oriented movements at large scales.", "output": "Blacktip reef sharks." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "There were inter - and intraspecific differences in path structure and patch size, although most individuals showed scale - dependent movements.", "output": "There is no related enetity." }, { "input": "Furthermore, some individuals of each species performed movements similar to a correlated random walk.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "Sharks can perform directed walks over large spatial scales, with scales of movements reflecting site fidelity and home range size.", "output": "There is no related enetity." }, { "input": "Understanding when and where directed walks occur is crucial for developing more accurate population - level dispersal models.", "output": "There is no related enetity." }, { "input": "El Nino in the warm tropics: local sea temperature predicts breeding parameters and growth of blue - footed boobies.", "output": "blue - footed boobies." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "There is increasing interest in the impacts of El Nino Southern Oscillation ( ENSO ) on reproduction of apical predators such as seabirds and marine mammals.", "output": "There is no related enetity." }, { "input": "Long - term studies documenting ENSO effects on reproduction of seabirds in the warm tropics are scarce, and differential sensitivity of breeding parameters to ENSO has rarely been explored.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Analysis of 18 years of breeding data from a colony of the blue - footed booby Sula nebouxii ( Milne - Edwards ) showed a delay in onset of breeding when the global Southern Oscillation Index was negative; each unit of the atmospheric pressure differential ( hPa ) across the Pacific Ocean meant a delay of 7 days.", "output": "blue - footed booby, Sula nebouxii." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "ENSO conditions also produced declines in breeding participation, clutch size, brood size, hatching success and fledging success, especially when surface waters surrounding the colony were warmer during winter and spring.", "output": "There is no related enetity." }, { "input": "Each additional degree ( ^ 0C ) of water temperature produced a reduction of 0. 45 fledglings per nest.", "output": "There is no related enetity." }, { "input": "Different breeding parameters were sensitive to ENSO indices in different blocks of months.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Warming of local waters during the winter was associated with decline in ocean productivity in the current year and the following year, consistent with ENSO impacts on breeding parameters being mediated by effects on local productivity and prey availability.", "output": "There is no related enetity." }, { "input": "However, there was no evidence of lagged effects of ENSO on any breeding parameter.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Comparison of 5 years revealed that when local surface waters were warm, chicks grew more slowly, but no effects of ENSO on weight and size of eggs were evident in data of 9 and 7 years, respectively.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "Our findings extend evidence of impacts of ENSO on seabird reproduction to the eastern tropical Pacific and indicate that several breeding parameters of blue - footed boobies ( but not egg size ) are affected in the short term by ENSO conditions, particularly by local anomalies in sea surface temperature associated with decline in ocean productivity.", "output": "blue - footed boobies." }, { "input": "Partial diel vertical migrations in pelagic fish.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Field studies on diel vertical migration ( DVM ) usually report uniform behaviour with population - wide ascents and descents during crepuscular periods.", "output": "There is no related enetity." }, { "input": "This contrasts partial seasonal migrations of many animal populations, where individuals choose either the resident or the migrant strategy depending on population density, feeding opportunity and predation risk in the resident and migrant habitats.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We tested whether DVM of freshwater zooplanktivorous fish ( Coregonus spp. ) resembles partial migrations.", "output": "There is no related enetity." }, { "input": "Twenty - eight hydroacoustic surveys were performed in the deep Lake Stechlin ( Germany ) between 2000 and 2010, with samplings encompassing all months between March and December.", "output": "There is no related enetity." }, { "input": "Zooplankton samples were simultaneously taken in epilimnetic and hypolimnetic layers.", "output": "There is no related enetity." }, { "input": "Fish obtained from depth - stratified samplings by a midwater trawl were used to test for individual differences between residents and migrants.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We show for the first time that DVMs of freshwater fish resemble patterns of partial migrations often found in seasonal environments.", "output": "There is no related enetity." }, { "input": "Across all samplings, 7 - 33 % of fish did not ascend at dusk, but exhibited the resident strategy.", "output": "There is no related enetity." }, { "input": "The proportion or residents increased at low zooplankton feeding rates in the daytime habitat and during months when the temperature difference between daytime and night - time habitats was minor.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Slightly larger size and higher caloric density of migrants over residents in one of the coexisting Coregonus species suggested that individual differences contributed to the migration strategy performed.", "output": "There is no related enetity." }, { "input": "However, these results were based on one sample only, and extrapolation to the entire data set is not possible.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Our results are indirect evidence that the balance between migrants and residents may primarily depend on the trade - off between feeding gains and metabolic and predation costs of migration.", "output": "There is no related enetity." }, { "input": "However, the results also suggest that the global fitness consequences for the resident and migrant strategies may not be identical, rendering the importance of individual traits in the ' decision to migrate ' likely.", "output": "There is no related enetity." }, { "input": "Clinical management of Staphylococcus aureus bacteraemia.", "output": "Staphylococcus aureus." }, { "input": "Staphylococcus aureus bacteraemia is one of the most common serious bacterial infections worldwide.", "output": "Staphylococcus aureus." }, { "input": "In the UK alone, around 12, 500 cases each year are reported, with an associated mortality of about 30 %, yet the evidence guiding optimum management is poor.", "output": "There is no related enetity." }, { "input": "To date, fewer than 1500 patients with S aureus bacteraemia have been recruited to 16 controlled trials of antimicrobial therapy.", "output": "S aureus." }, { "input": "Consequently, clinical practice is driven by the results of observational studies and anecdote.", "output": "There is no related enetity." }, { "input": "Here, we propose and review ten unanswered clinical questions commonly posed by those managing S aureus bacteraemia.", "output": "S aureus." }, { "input": "Our findings define the major areas of uncertainty in the management of S aureus bacteraemia and highlight just two key principles.", "output": "S aureus." }, { "input": "First, all infective foci must be identified and removed as soon as possible.", "output": "There is no related enetity." }, { "input": "Second, long - term antimicrobial therapy is required for those with persistent bacteraemia or a deep, irremovable focus.", "output": "There is no related enetity." }, { "input": "Beyond this, the best drugs, dose, mode of delivery, and duration of therapy are uncertain, a situation compounded by emerging S aureus strains that are resistant to old and new antibiotics.", "output": "S aureus." }, { "input": "We discuss the consequences on clinical practice, and how these findings define the agenda for future clinical research.", "output": "There is no related enetity." }, { "input": "Seasonal influenza epidemiology in sub - Saharan Africa: a systematic review.", "output": "There is no related enetity." }, { "input": "Acute respiratory infection ( ARI ) is a leading cause of mortality worldwide, of which influenza is an important cause that can be prevented with vaccination.", "output": "There is no related enetity." }, { "input": "We did a systematic review of research published from 1980 to 2009 on seasonal influenza epidemiology in sub - Saharan Africa to identify data strengths and weaknesses that might affect policy decisions, to assess the state of knowledge on influenza disease burden, and to ascertain unique features of influenza epidemiology in the region.", "output": "There is no related enetity." }, { "input": "We assessed 1203 papers, reviewed 104, and included 49 articles.", "output": "There is no related enetity." }, { "input": "1 - 25 % of outpatient ARI visits were caused by influenza ( 11 studies; mean 9 * 5 %; median 10 % ), whereas 0 * 6 - 15 * 6 % of children admitted to hospital for ARI had influenza identified ( 15 studies; mean 6 * 6 %; median 6 * 3 % ).", "output": "There is no related enetity." }, { "input": "Influenza was highly seasonal in southern Africa.", "output": "There is no related enetity." }, { "input": "Other data were often absent, particularly direct measurement of influenza incidence rates for all ages, within different patient settings ( outpatient, inpatient, community ), and for all countries.", "output": "There is no related enetity." }, { "input": "Data from sub - Saharan Africa are insufficient to allow most countries to prioritise strategies for influenza prevention and control.", "output": "There is no related enetity." }, { "input": "Key data gaps include incidence and case - fatality ratios for all ages, the contribution of influenza towards admission of adults to hospital for ARI, representative seasonality data, economic burden, and the interaction of influenza with prevalent disorders in Africa, such as malaria, HIV, and malnutrition.", "output": "HIV." }, { "input": "Population biological principles of drug - resistance evolution in infectious diseases.", "output": "There is no related enetity." }, { "input": "The emergence of resistant pathogens in response to selection pressure by drugs and their possible disappearance when drug use is discontinued are evolutionary processes common to many pathogens.", "output": "There is no related enetity." }, { "input": "Population biological models have been used to study the dynamics of resistance in viruses, bacteria, and eukaryotic microparasites both at the level of the individual treated host and of the treated host population.", "output": "There is no related enetity." }, { "input": "Despite the existence of generic features that underlie such evolutionary dynamics, different conclusions have been reached about the key factors affecting the rate of resistance evolution and how to best use drugs to minimise the risk of generating high levels of resistance.", "output": "There is no related enetity." }, { "input": "Improved understanding of generic versus specific population biological aspects will help to translate results between different studies, and allow development of a more rational basis for sustainable drug use than exists at present.", "output": "There is no related enetity." }, { "input": "Guidelines for hospital - acquired pneumonia and health - care - associated pneumonia: a vulnerability, a pitfall, and a fatal flaw.", "output": "There is no related enetity." }, { "input": "The 2005 American Thoracic Society and Infectious Disease Society of America ' s guidelines for pneumonia introduced the new category of health - care - associated pneumonia, which increased the number of people to whom the guidelines for multidrug - resistant pathogens applied.", "output": "There is no related enetity." }, { "input": "Three fundamental issues inherent in the definition of hospital - acquired pneumonia and health - care - associated pneumonia undermined the credibility of these guidelines and the applicability of their recommendations: a vulnerability, a pitfall, and a fatal flaw.", "output": "There is no related enetity." }, { "input": "The vulnerability is the extreme heterogeneity of the population of patients.", "output": "There is no related enetity." }, { "input": "The fatal flaw is the failure to accurately diagnose hospital - acquired pneumonia and ventilator - associated pneumonia; inability to distinguish colonisation from infection in respiratory - tract cultures renders the guidelines inherently unstable.", "output": "There is no related enetity." }, { "input": "The pitfall is spiralling empiricism of antibiotic use for severely ill patients in whom infection might not be present.", "output": "There is no related enetity." }, { "input": "A vicious circle of antibiotic overuse leading to emergence of resistant microflora can become established, leading to unnecessary use of empirical broad - spectrum combination antibiotics and increased mortality.", "output": "There is no related enetity." }, { "input": "Controlled studies now show that administration of broad - spectrum combination antibiotic therapy can lead to increased mortality in uninfected patients.", "output": "There is no related enetity." }, { "input": "Proposed solutions include the use of individualised assessment of patients.", "output": "There is no related enetity." }, { "input": "Health - care - associated pneumonia should be broken down into several distinct subgroups so narrow - spectrum antibiotic therapy can be used.", "output": "There is no related enetity." }, { "input": "Emphasis should be placed on defining the microbial cause of the pneumonia rather than reflex administration of empirical combination therapy.", "output": "There is no related enetity." }, { "input": "Alzheimer ' s disease.", "output": "There is no related enetity." }, { "input": "An estimated 24 million people worldwide have dementia, the majority of whom are thought to have Alzheimer ' s disease.", "output": "There is no related enetity." }, { "input": "Thus, Alzheimer ' s disease represents a major public health concern and has been identified as a research priority.", "output": "There is no related enetity." }, { "input": "Although there are licensed treatments that can alleviate symptoms of Alzheimer ' s disease, there is a pressing need to improve our understanding of pathogenesis to enable development of disease - modifying treatments.", "output": "There is no related enetity." }, { "input": "Methods for improving diagnosis are also moving forward, but a better consensus is needed for development of a panel of biological and neuroimaging biomarkers that support clinical diagnosis.", "output": "There is no related enetity." }, { "input": "There is now strong evidence of potential risk and protective factors for Alzheimer ' s disease, dementia, and cognitive decline, but further work is needed to understand these better and to establish whether interventions can substantially lower these risks.", "output": "There is no related enetity." }, { "input": "In this Seminar, we provide an overview of recent evidence regarding the epidemiology, pathogenesis, diagnosis, and treatment of Alzheimer ' s disease, and discuss potential ways to reduce the risk of developing the disease.", "output": "There is no related enetity." }, { "input": "Serum c testing in patients with HER2 - positive breast cancer: the death knell tolls.", "output": "There is no related enetity." }, { "input": "Determination of the human epidermal growth factor receptor 2 ( HER2; also known as ERBB2 ) status of breast tumours is emphasised in various national guidelines as a necessary step for the diagnosis of breast cancer.", "output": "There is no related enetity." }, { "input": "As an alternative to tissue - based diagnostic methods, there has been substantial interest in the establishment of an easily accessible serum - based alternative that could be used for prognosis and diagnosis.", "output": "There is no related enetity." }, { "input": "Detection of serum - soluble - HER2 extracellular domain ( ECD ) and establishment of its potential clinical usefulness has created much debate.", "output": "There is no related enetity." }, { "input": "We assessed whether identification of circulating concentrations of HER2 ECD have clinical usefulness for management of patients with HER2 - positive breast cancer.", "output": "There is no related enetity." }, { "input": "We examined data from 63 studies of patients with breast cancer.", "output": "There is no related enetity." }, { "input": "Prevalence of increased concentrations varied greatly between studies.", "output": "There is no related enetity." }, { "input": "Some studies showed significant associations between raised concentrations and poor prognosis, poor response to treatments including trastuzumab, or tumour characteristics associated with aggressive disease, whereas others did not.", "output": "There is no related enetity." }, { "input": "Examination of existing data showed that concentrations of HER2 ECD are not consistently related to patient outcomes; therefore, there is insufficient evidence to support the clinical use of serum HER2 ECD testing.", "output": "There is no related enetity." }, { "input": "Design and execution of future large - scale trials to investigate the clinical use of HER2 ECD testing, in view of the progressive non - supportive evidence, is not recommended.", "output": "There is no related enetity." }, { "input": "Oncologists should continue to adhere to national guidelines for determining HER2 status.", "output": "There is no related enetity." }, { "input": "Furthermore, oncologists should continue to use clinical parameters when making decisions about initiation, continuation, and discontinuation of HER2 - targeted treatments.", "output": "There is no related enetity." }, { "input": "Breast - cancer early detection in low - income and middle - income countries: do what you can versus one size fits all.", "output": "There is no related enetity." }, { "input": "In general, rates of breast cancer are lower in low - income and middle - income countries ( LMCs ) than they are in more industrialised countries of North America and Europe.", "output": "There is no related enetity." }, { "input": "This lower incidence means that screening programmes aimed at early detection in asymptomatic women would have a lower yield - - ie, substantially more women would need to be examined to find a true case of breast cancer.", "output": "There is no related enetity." }, { "input": "Because the average age of breast cancer is generally younger in LMCs, it has been suggested that breast - cancer screening programmes begin at an earlier age in these settings.", "output": "There is no related enetity." }, { "input": "However, the younger average age of breast cancer is mainly driven by the age distribution of the population, and fewer older women with breast cancer, rather than by higher age - specific incidence rates in younger women.", "output": "There is no related enetity." }, { "input": "Resources in LMCs might be better used to raise awareness and encourage more women with palpable breast lumps to seek and receive treatment in a timely manner.", "output": "There is no related enetity." }, { "input": "Towards a conceptual framework to support one - health research for policy on emerging zoonoses.", "output": "There is no related enetity." }, { "input": "In the past two decades there has been a growing realisation that the livestock sector was in a process of change, resulting from an expansion of intensive animal production systems and trade to meet a globalised world ' s increasing demand for livestock products.", "output": "There is no related enetity." }, { "input": "One unintended consequence has been the emergence and spread of transboundary animal diseases and, more specifically, the resurgence and emergence of zoonotic diseases.", "output": "There is no related enetity." }, { "input": "Concurrent with changes in the livestock sector, contact with wildlife has increased.", "output": "There is no related enetity." }, { "input": "This development has increased the risk of transmission of infections from wildlife to human beings and livestock.", "output": "human." }, { "input": "Two overarching questions arise with respect to the real and perceived threat from emerging infectious diseases: why are these problems arising with increasing frequency, and how should we manage and control them?", "output": "There is no related enetity." }, { "input": "A clear conceptual research framework can provide a guide to ensure a research strategy that coherently links to the overarching goals of policy makers.", "output": "There is no related enetity." }, { "input": "We propose such a new framework in support of a research and policy - generation strategy to help to address the challenges posed by emerging zoonoses.", "output": "There is no related enetity." }, { "input": "Compartmentalization of a glycolytic enzyme in Diplonema, a non - kinetoplastid euglenozoan.", "output": "There is no related enetity." }, { "input": "Glycosomes are peroxisome - related organelles containing glycolytic enzymes that have been found only in kinetoplastids.", "output": "There is no related enetity." }, { "input": "We show here that a glycolytic enzyme is compartmentalized in diplonemids, the sister group of kinetoplastids.", "output": "There is no related enetity." }, { "input": "We found that, similar to kinetoplastid aldolases, the fructose 1, 6 - bisphosphate aldolase of Diplonema papillatum possesses a type 2 - peroxisomal targeting signal.", "output": "Diplonema papillatum." }, { "input": "Western blotting showed that this aldolase was present predominantly in the membrane / organellar fraction.", "output": "There is no related enetity." }, { "input": "Immunofluorescence analysis showed that this aldolase had a scattered distribution in the cytosol, suggesting its compartmentalization.", "output": "There is no related enetity." }, { "input": "In contrast, orotidine - 5 ' - monophosphate decarboxylase, a non - glycolytic glycosomal enzyme in kinetoplastids, was shown to be a cytosolic enzyme in D. papillatum.", "output": "D . papillatum." }, { "input": "Since euglenoids, the earliest diverging branch of Euglenozoa, do not possess glycolytic compartments, these findings suggest that the routing of glycolytic enzymes into peroxisomes may have occurred in a common ancestor of diplonemids and kinetoplastids, followed by diversification of these newly established organelles in each of these euglenozoan lineages.", "output": "There is no related enetity." }, { "input": "Responses of the pea aphid transcriptome to infection by facultative symbionts.", "output": "pea aphid." }, { "input": "Serratia symbiotica is a facultative symbiont of pea aphids ( Acyrthosiphon pisum ) that provides tolerance to heat stress.", "output": "Serratia symbiotica, pea aphids, Acyrthosiphon pisum." }, { "input": "Although the phenotypic effects of facultative symbionts upon hosts have been studied in some detail, little is known about the molecular and genomic basis of these interactions.", "output": "There is no related enetity." }, { "input": "Previous studies show a large impact of S. symbiotica upon the aphid metabolome.", "output": "S . symbiotica." }, { "input": "Whole - genome transcriptional profiling and next - generation sequencing demonstrated expression of 94 % of RefSeq genes from the pea aphid genome, providing the largest dataset to date on aphid gene expression.", "output": "pea aphid." }, { "input": "However, only 28 genes showed changes in expression with S. symbiotica infection, and these changes were of small magnitude.", "output": "S . symbiotica." }, { "input": "No expression differences in genes involved in innate immunity in other insects were observed.", "output": "There is no related enetity." }, { "input": "Therefore, the large metabolic impact of S. symbiotica is most likely a result of metabolism of the symbiont itself, or of post - transcriptional modification of host gene expression.", "output": "S . symbiotica." }, { "input": "Although S. symbiotica has a major influence on its host ' s metabolome and resistance to heat, it induces little change in gene expression in its host.", "output": "S . symbiotica." }, { "input": "Molecular cloning and characterization of a thioredoxin peroxidase gene from Apis cerana cerana.", "output": "Apis cerana cerana." }, { "input": "Thioredoxin peroxidases ( Tpxs ) play important roles in protecting organisms against the toxicity of reactive oxygen species ( ROS ) and regulating intracellular signal transduction.", "output": "There is no related enetity." }, { "input": "In the present study, we cloned the full cDNA of Tpx1 encoding a 195 - amino acid protein from Apis cerana cerana ( Acc ).", "output": "Apis cerana cerana ( Acc )." }, { "input": "Based on the genomic DNA sequence, a 1442 - bp 5 ' - flanking region was obtained, and the putative transcription factor binding sites were predicted.", "output": "There is no related enetity." }, { "input": "Quantitative PCR analysis showed that AccTpx1 was highly expressed in thorax and that the AccTpx1 transcript reached its highest level in two - week - old adult worker honeybees.", "output": "worker honeybees." }, { "input": "Moreover, expression of the AccTpx1 transcript was increased by various abiotic stresses, such as ultraviolet light, HgCl ( 2 ), and insecticide treatments.", "output": "There is no related enetity." }, { "input": "In addition, the recombinant AccTpx1 protein exhibited antioxidant activity; it removed hydrogen peroxide and protected DNA.", "output": "There is no related enetity." }, { "input": "These results suggest that AccTpx1 plays an important role in protecting honeybees from oxidative injury and may act in extending the lifespan of them.", "output": "honeybees." }, { "input": "Predation and patchiness in the tropical litter: do swarm - raiding army ants skim the cream or drain the bottle?", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Swarm - raiding army ants have long been considered as episodic, catastrophic agents of disturbance in the tropical litter, but few quantitative data exist on their diets, preferences, and, critically, their ability to deplete prey.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Here, we provide such data for two common species of swarm raiders broadly sympatric throughout the Neotropics: the iconic Eciton burchellii and the more secretive, less studied Labidus praedator.", "output": "Eciton burchellii." }, { "input": "In Ecuador, Costa Rica, Venezuela and Panama, patches of forest floor were sampled for litter invertebrates immediately before and after army ant raids.", "output": "There is no related enetity." }, { "input": "These invertebrates have been shown to regulate decomposition and vary 100 - fold in local densities across the forest floor.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Contrary to Eciton ' s popular image, only Labidus consistently reduced the biomass of litter invertebrates and only then by an average of 25 %.", "output": "There is no related enetity." }, { "input": "Eciton ' s impacts were concentrated on rich patches of invertebrates, while Labidus prey depletion showed no such density dependence.", "output": "There is no related enetity." }, { "input": "Labidus reduced the biomass of some invertebrates - isopods, larviforms and coleoptera - by up to 75 %; Eciton showed no such prey preferences.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Our results suggest that Eciton specializes on high biomass patches, while Labidus feeds profitably from any litter patch.", "output": "There is no related enetity." }, { "input": "Combined, these swarm raiders sum to be chronic, but not catastrophic, predators of common litter invertebrates of the brown food web.", "output": "There is no related enetity." }, { "input": "Community - wide character displacement in the presence of clines: a test of Holarctic weasel guilds.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Competition is thought to be a major influence on community assembly, ecology and evolution; presence of competitors may cause divergence in traits related to resource use ( character displacement ).", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Such traits, however, often vary clinally, and this phenomenon may be independent of the presence or absence of competing species.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "The presence of such clines can either obscure the effects of competition, or create an impression that competition is operating when, in fact, it is not.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "We corrected for clinal variation while testing for character displacement in two well - studied weasel ( Mustela ) guilds, in the Nearctic and the west Palaearctic.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Without accounting for clines, our results agreed with previous studies suggesting character displacement in these guilds.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "However, when we corrected for clines, predictions of competition theory were not met - and often we obtained evidence for character convergence in sympatry.", "output": "There is no related enetity." }, { "input": "7.", "output": "There is no related enetity." }, { "input": "This may suggest that the nature of the resource base may be more important than interspecific competition in shaping morphology and size in these carnivores.", "output": "There is no related enetity." }, { "input": "8.", "output": "There is no related enetity." }, { "input": "Our results highlight the need to account for geographic variation when studying character displacement and cast some doubt on prevailing ideas regarding the effect of competition on morphological evolution.", "output": "There is no related enetity." }, { "input": "Agrobacterium tumefasciens - mediated transformation of the aquatic fungus Blastocladiella emersonii.", "output": "Agrobacterium tumefasciens, Blastocladiella emersonii." }, { "input": "Agrobacterium tumefaciens is widely used for plant DNA transformation and more recently, has also been used to transform yeast, filamentous fungi and even human cells.", "output": "Agrobacterium tumefaciens, yeast, human." }, { "input": "Using this technique, we developed the first transformation protocol for the saprobic aquatic fungus Blastocladiella emersonii, a Blastocladiomycete localized at the base of fungal phylogenetic tree, which has been shown as a promising and interesting model of study of cellular function and differentiation.", "output": "Blastocladiella emersonii." }, { "input": "We constructed binary T - DNA vectors containing hygromycin phosphotransferase ( hph ) or enhanced green fluorescent protein ( egfp ) genes, under the control of Aspergillus nidulans trpC promoter and terminator sequences.", "output": "Aspergillus nidulans." }, { "input": "24 h of co - cultivation in induction medium ( IM ) agar plates, followed by transfer to PYG - agar plates containing cefotaxim to kill Agrobacterium tumefsciens and hygromycin to select transformants, resulted in growth and sporulation of resistant transformants.", "output": "Agrobacterium tumefsciens." }, { "input": "Genomic DNA from the pool o resistant zoospores were shown to contain T - DNA insertion as evidenced by PCR amplification of hph gene.", "output": "There is no related enetity." }, { "input": "Using a similar protocol we could also evidence the expression of enhanced green fluorescent protein ( EGFP ) in zoospores derived from transformed cells.", "output": "There is no related enetity." }, { "input": "This protocol can also open new perspectives for other non - transformable closely related fungi, like the Chytridiomycete class.", "output": "There is no related enetity." }, { "input": "Chronic pancreatitis.", "output": "There is no related enetity." }, { "input": "Chronic pancreatitis is a progressive fibroinflammatory disease that exists in large - duct ( often with intraductal calculi ) or small - duct form.", "output": "There is no related enetity." }, { "input": "In many patients this disease results from a complex mix of environmental ( eg, alcohol, cigarettes, and occupational chemicals ) and genetic factors ( eg, mutation in a trypsin - controlling gene or the cystic fibrosis transmembrane conductance regulator ); a few patients have hereditary or autoimmune disease.", "output": "There is no related enetity." }, { "input": "Pain in the form of recurrent attacks of pancreatitis ( representing paralysis of apical exocytosis in acinar cells ) or constant and disabling pain is usually the main symptom.", "output": "There is no related enetity." }, { "input": "Management of the pain is mainly empirical, involving potent analgesics, duct drainage by endoscopic or surgical means, and partial or total pancreatectomy.", "output": "There is no related enetity." }, { "input": "However, steroids rapidly reduce symptoms in patients with autoimmune pancreatitis, and micronutrient therapy to correct electrophilic stress is emerging as a promising treatment in the other patients.", "output": "There is no related enetity." }, { "input": "Steatorrhoea, diabetes, local complications, and psychosocial issues associated with the disease are additional therapeutic challenges.", "output": "There is no related enetity." }, { "input": "Occurrence of the lobose testate amoeba Pseudonebela africana ( Amoebozoa, Arcellinida ) in the Brazilian & quot; cerrado & quot;.", "output": "There is no related enetity." }, { "input": "Flagship species are defined as microbial eukaryote species with characteristic morphologies and restricted geographic distributions.", "output": "There is no related enetity." }, { "input": "These are proposed as ideal systems to elucidate patterns of geographical distribution in microbial eukaryotes.", "output": "There is no related enetity." }, { "input": "Here we present new records of the putative flagship species Pseudonebela africana, a lobose testate amoeba ( Arcellinida ) characterized by a cross or clover - shaped aperture and geographic distribution previously believed to be restricted to Africa.", "output": "There is no related enetity." }, { "input": "We have sampled P. africana from 5 separate ponds in the Central and Southwest Brazillian & quot; cerrado & quot;, and characterized individuals both by light and electron microscopy.", "output": "There is no related enetity." }, { "input": "We provide a brief description to facilitate further studies on this poorly understood taxon, and show that light microscopy is sufficient for identification, an important feature for ecological and biogeographical studies.", "output": "There is no related enetity." }, { "input": "Comparing isotopic niche widths among and within communities: SIBER - Stable Isotope Bayesian Ellipses in R.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "The use of stable isotope data to infer characteristics of community structure and niche width of community members has become increasingly common.", "output": "There is no related enetity." }, { "input": "Although these developments have provided ecologists with new perspectives, their full impact has been hampered by an inability to statistically compare individual communities using descriptive metrics.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We solve these issues by reformulating the metrics in a Bayesian framework.", "output": "There is no related enetity." }, { "input": "This reformulation takes account of uncertainty in the sampled data and naturally incorporates error arising from the sampling process, propagating it through to the derived metrics.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Furthermore, we develop novel multivariate ellipse - based metrics as an alternative to the currently employed Convex Hull methods when applied to single community members.", "output": "There is no related enetity." }, { "input": "We show that unlike Convex Hulls, the ellipses are unbiased with respect to sample size, and their estimation via Bayesian inference allows robust comparison to be made among data sets comprising different sample sizes.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "These new metrics, which we call SIBER ( Stable Isotope Bayesian Ellipses in R ), open up more avenues for direct comparison of isotopic niches across communities.", "output": "There is no related enetity." }, { "input": "The computational code to calculate the new metrics is implemented in the free - to - download package Stable Isotope Analysis for the R statistical environment.", "output": "There is no related enetity." }, { "input": "The role of body mass in diet contiguity and food - web structure.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "The idea that species occupy distinct niches is a fundamental concept in ecology.", "output": "There is no related enetity." }, { "input": "Classically, the niche was described as an n - dimensional hypervolume where each dimension represents a biotic or abiotic characteristic.", "output": "There is no related enetity." }, { "input": "More recently, it has been hypothesised that a single dimension may be sufficient to explain the system - level organization of trophic interactions observed between species in a community.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Here, we test the hypothesis that species body mass is that single dimension.", "output": "There is no related enetity." }, { "input": "Specifically, we determine how the intervality of food webs ordered by body size compares to that of randomly ordered food webs.", "output": "There is no related enetity." }, { "input": "We also extend this analysis beyond the community level to the effect of body mass in explaining the diets of individual species.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We conclude that body mass significantly explains the ordering of species and the contiguity of diets in empirical communities.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "At the species - specific level, we find that the degree to which body mass is a significant explanatory variable depends strongly on the phylogenetic history, suggesting that other evolutionarily conserved traits partly account for species ' roles in the food web.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Our investigation of the role of body mass in food webs thus helps us to better understand the important features of community food - web structure and the evolutionary forces that have led us to the communities we observe.", "output": "There is no related enetity." }, { "input": "Beyond phytohaemagglutinin: assessing vertebrate immune function across ecological contexts.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Over the past decade, there has been a substantial increase in interest in the immune system and the role it plays in the regulation of disease susceptibility, giving rise to the field of eco - immunology.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Eco - immunology aims to understand changes in host immune responses in the broader framework of an organism ' s evolutionary, ecological and life - history contexts.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "The immune system, however, is complex and multifaceted and can be intimidating for the nonimmunologist interested in incorporating immunological questions into their research.", "output": "There is no related enetity." }, { "input": "Which immune responses should one measure and what is the biological significance of these measures?", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "The focus of this review is to describe a wide range of eco - immunology techniques, from the simple to the sophisticated, with the goal of providing researchers with a range of options to consider incorporating in their own research programs.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "These techniques were chosen because they provide relatively straightforward, biologically meaningful assessments of immune function, many of which can be performed across a range of ecological contexts ( i. e. field vs. laboratory ) and in a wide range of vertebrate animals without relying on species - specific reagents.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "By incorporating assessments of immune function into their specific research questions, animal ecologists will gain a more comprehensive understanding of organism - environment interactions.", "output": "There is no related enetity." }, { "input": "Genome - wide analysis of brain transcriptional changes in honey bee ( Apis mellifera L. ) queens exposed to carbon dioxide and physical manipulation.", "output": "honey bee, Apis mellifera." }, { "input": "Mating is a complex process causing many behavioural and physiological changes, but the factors triggering them and the underlying molecular processes are not well characterized.", "output": "There is no related enetity." }, { "input": "In the present study we examine the effects of CO ( 2 ) ( a commonly used anaesthetic in instrumental insemination that causes changes similar to those occurring after mating ) and physical manipulation ( which may mimic certain aspects of copulation ) on the behavioural, physiological and brain transcriptional changes in honey bee queens.", "output": "honey bee." }, { "input": "We show that while CO ( 2 ) causes cessation of mating flights and ovary activation, physical manipulation has additional effects on ovary activation and brain transcriptional changes.", "output": "There is no related enetity." }, { "input": "Comparisons with previous studies of honey bees and female Drosophila indicate that common molecular mechanisms may be responsible for regulating reproductive changes across different mating regimes and insect orders.", "output": "honey bees, Drosophila." }, { "input": "Does variation in movement tactics and trophic interactions among American alligators create habitat linkages?", "output": "American alligators." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Highly mobile top predators are hypothesized to spatially and / or temporally link disparate habitats through the combination of their movement and feeding patterns, but recent studies suggest that individual specialization in habitat use and feeding could keep habitats compartmentalized.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We used passive acoustic telemetry and stable isotope analysis to investigate whether specialization in movement and feeding patterns of American alligators ( Alligator mississippiensis ) in an oligotrophic subtropical estuary created habitat linkages between marine and estuarine / freshwater food webs.", "output": "American alligators, Alligator mississippiensis." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Individual alligators adopted one of the three relatively distinct movement tactics that were linked to variation in diets.", "output": "There is no related enetity." }, { "input": "Fifty - six per cent of alligators regularly travelled from the upstream ( freshwater / mid - estuary ) areas into the downstream ( marine - influenced ) areas where salinities exceed those typically tolerated by alligators.", "output": "There is no related enetity." }, { "input": "Thirty - one per cent of the alligators made regular trips from the mid - estuarine habitat into the upstream habitat; 13 % remained in the mid - estuary zone year - round.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Stable isotopic analysis indicated that, unlike individuals remaining in the mid - estuary and upstream zones, alligators that used the downstream zone fed at least partially from marine food webs and likely moved to access higher prey abundance at the expense of salt stress.", "output": "There is no related enetity." }, { "input": "Therefore, ' commuting ' alligators may link marine food webs with those of the estuary and marshes in the coastal Everglades and create an upstream vector for allochthonous nutrient inputs into the estuary.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "This study lends further support to the hypothesis that large - bodied highly mobile predators faced with trade - offs are likely to exhibit individual specialization leading to habitat linkages, rather than compartmentalization.", "output": "There is no related enetity." }, { "input": "However, the conditions under which this scenario occurs require further investigation.", "output": "There is no related enetity." }, { "input": "Relative fitness of alternative male reproductive tactics in a mammal varies between years.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "In many species, males can use different behavioural tactics to achieve fertilization, so - called alternative reproductive tactics ( ARTs ).", "output": "There is no related enetity." }, { "input": "Few field studies have measured fitness consequences of ARTs under varying environmental conditions.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Here, we describe fitness consequences of three phenotypically plastic ARTs in the African striped mouse ( Rhabdomys pumilio ) and show that relative fitness of ARTs differs between years.", "output": "African striped mouse, Rhabdomys pumilio." }, { "input": "Each year represents a different generation.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "For the generation living under high population density, tactics differed in relative fitness in accordance with the theory of conditional strategies, with highly successful territorial breeding males having 10 times higher success than solitary roaming males and 102 times higher success than adult natally philopatric males.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "For the generation living under intermediate population density, the territorial breeding and roaming tactics yielded similar fitness, which would be in agreement with the theory of mixed strategies.", "output": "There is no related enetity." }, { "input": "No philopatric males occurred.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "For the generation living under low population density, roaming was the only tactic used and some roamers had very high fitness.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "The main prediction of status - dependent selection for conditional strategies is a correlation between fitness and status, often measured as body mass, but we did not find this correlation within tactics when more than one tactic was expressed in the population.", "output": "There is no related enetity." }, { "input": "7.", "output": "There is no related enetity." }, { "input": "Female distribution seems to have an effect on which reproductive tactics male chose: female defence polygyny when females are clumped ( interference competition ), but a searching tactic when females are dispersed ( scramble competition ).", "output": "There is no related enetity." }, { "input": "In contrast to predictions arising from theory on scramble competition, male body mass was important in determining fitness only in the year when females were dispersed, but not in other years.", "output": "There is no related enetity." }, { "input": "8.", "output": "There is no related enetity." }, { "input": "Our results indicate that the differentiation between conditional and mixed strategies is not an absolute one.", "output": "There is no related enetity." }, { "input": "In many other species, environmental conditions might fluctuate temporally and spatially so that the normally suboptimal tactic yields similar fitness to the ( usually ) dominant tactic or that only a single tactic prevails.", "output": "There is no related enetity." }, { "input": "9.", "output": "There is no related enetity." }, { "input": "We suggest the term single strategy, independent of current fitness consequences, for systems where tactics are not genetically determined, in contrast to genetically determined alternative strategies.", "output": "There is no related enetity." }, { "input": "Predicting diet and consumption rate differences between and within species using gut ecomorphology.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Rapid environmental changes and pressing human needs to forecast the consequences of environmental change are increasingly driving ecology to become a predictive science.", "output": "human." }, { "input": "The need for effective prediction requires both the development of new tools and the refocusing of existing tools that may have previously been used primarily for purposes other than prediction.", "output": "There is no related enetity." }, { "input": "One such tool that historically has been more descriptive in nature is ecomorphology ( the study of relationships between ecological roles and morphological adaptations of species and individuals ).", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Here, we examine relationships between diet and gut morphology for 15 species of brachyuran crabs, a group of pervasive and highly successful consumers for which trophic predictions would be highly valuable.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We show that patterns in crab stomach volume closely match some predictions of metabolic theory and demonstrate that individual diet differences and associated morphological variation reflect, at least in some instances, individual choice or diet specialization.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "We then present examples of how stomach volume can be used to predict both the per cent herbivory of brachyuran crabs and the relative consumption rates of individual crabs.", "output": "There is no related enetity." }, { "input": "Completing the purine utilisation pathway of Aspergillus nidulans.", "output": "Aspergillus nidulans." }, { "input": "We have previously identified by classical genetics and biochemistry, all the genes of Aspergillus nidulans predicted to be involved in purine utilisation, together with cognate regulatory genes and one gene encoding a novel xanthine hydroxylation activity.", "output": "Aspergillus nidulans." }, { "input": "In this article we complete the description of the purine utilisation pathway with the identification of the two genes ( uaX and uaW ) encoding the enzymes catalysing the conversion of the product of urate oxidation by urate oxidase, 5 - hydroxyisourate, to optically active allantoin.", "output": "There is no related enetity." }, { "input": "The identification of these additional genes confirms the complete absence of clustering of the genes involved in purine utilisation in A. nidulans.", "output": "A . nidulans." }, { "input": "The ultrastructure of Ancyromonas, a eukaryote without supergroup affinities.", "output": "There is no related enetity." }, { "input": "The small heterotrophic flagellate Ancyromonas ( = Planomonas ) lacks close relatives in most molecular phylogenies, and it is suspected that it does not belong to any of the recognized eukaryote ' supergroups ', making it an organism of great evolutionary interest.", "output": "There is no related enetity." }, { "input": "Proposed relatives include apusomonads and excavates, but limited understanding of the ancyromonad cytoskeleton has precluded identification of candidate structural homologies.", "output": "There is no related enetity." }, { "input": "We present a detailed analysis of the ultrastructure of Ancyromonas through computer - based reconstruction of serial sections.", "output": "There is no related enetity." }, { "input": "We confirm or extend previous observations of its major organelles ( mitochondria, Golgi body, extrusomes, etc. ) and pellicle, and distinguish a system of stacked endomembranes that may be developmentally connected to the glycocalyx.", "output": "There is no related enetity." }, { "input": "Ancyromonas has two basal bodies, each with its own flagellar pocket.", "output": "There is no related enetity." }, { "input": "The anterior basal body associates with two microtubular elements: a doublet root that runs from between the basal bodies to support the cell ' s rostrum, and a short singlet root.", "output": "There is no related enetity." }, { "input": "The posterior basal body is associated with two multi - microtubular structures and a singlet root.", "output": "There is no related enetity." }, { "input": "One multi - microtubular structure, L1, is a conventional microtubular root.", "output": "There is no related enetity." }, { "input": "The other structure appears as a curved ribbon of - 8 microtubules near the basal body, but then flares out into two multi - microtubular elements, L2 and L3, plus two single microtubules.", "output": "There is no related enetity." }, { "input": "The posterior singlet root originates independently near this second complex.", "output": "There is no related enetity." }, { "input": "L1, the singlet, L2, and L3 all support the posterior flagellar pocket and channel.", "output": "There is no related enetity." }, { "input": "We also identified several groups of peripheral microtubules.", "output": "There is no related enetity." }, { "input": "Possible homologies with the flagellar apparatus of both apusomonads and excavates include a splitting root on the right side of the posterior basal body and a singlet root, both supporting a longitudinal channel or groove associated with the posterior flagellum.", "output": "There is no related enetity." }, { "input": "The anterior flagellar apparatus in each includes a root supporting structures to the left of the anterior flagellum.", "output": "There is no related enetity." }, { "input": "Given the probable deep divergences of Ancyromonas, apusomonads and excavates within eukaryotes, it is possible that the eukaryotic cenancestor also possessed these features.", "output": "There is no related enetity." }, { "input": "Phylogenetic validation of the genera Angomonas and Strigomonas of trypanosomatids harboring bacterial endosymbionts with the description of new species of trypanosomatids and of proteobacterial symbionts.", "output": "There is no related enetity." }, { "input": "We comparatively examined the nutritional, molecular and optical and electron microscopical characteristics of reference species and new isolates of trypanosomatids harboring bacterial endosymbionts.", "output": "There is no related enetity." }, { "input": "Sequencing of the V7V8 region of the small subunit of the ribosomal RNA ( SSU rRNA ) gene distinguished six major genotypes among the 13 isolates examined.", "output": "There is no related enetity." }, { "input": "The entire sequences of the SSU rRNA and glycosomal glyceraldehyde phosphate dehydrogenase ( gGAPDH ) genes were obtained for phylogenetic analyses.", "output": "There is no related enetity." }, { "input": "In the resulting phylogenetic trees, the symbiont - harboring species clustered as a major clade comprising two subclades that corresponded to the proposed genera Angomonas and Strigomonas.", "output": "There is no related enetity." }, { "input": "The genus Angomonas comprised 10 flagellates including former Crithidia deanei and C. desouzai plus a new species.", "output": "Crithidia deanei, C . desouzai." }, { "input": "The genus Strigomonas included former Crithidia oncopelti and Blastocrithidia culicis plus a new species.", "output": "Crithidia oncopelti, Blastocrithidia culicis." }, { "input": "Sequences from the internal transcribed spacer of ribosomal DNA ( ITS rDNA ) and size polymorphism of kinetoplast DNA ( kDNA ) minicircles revealed considerable genetic heterogeneity within the genera Angomonas and Strigomonas.", "output": "There is no related enetity." }, { "input": "Phylogenetic analyses based on 16S rDNA and ITS rDNA sequences demonstrated that all of the endosymbionts belonged to the Betaproteobacteria and revealed three new species.", "output": "There is no related enetity." }, { "input": "The congruence of the phylogenetic trees of trypanosomatids and their symbionts support a co - divergent host - symbiont evolutionary history.", "output": "There is no related enetity." }, { "input": "Introduced brown trout alter native acanthocephalan infections in native fish.", "output": "brown trout." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Native parasite acquisition provides introduced species with the potential to modify native host - parasite dynamics by acting as parasite reservoirs ( with the ' spillback ' of infection increasing the parasite burdens of native hosts ) or sinks ( with the ' dilution ' of infection decreasing the parasite burdens of native hosts ) of infection.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "In New Zealand, negative correlations between the presence of introduced brown trout ( Salmo trutta ) and native parasite burdens of the native roundhead galaxias ( Galaxias anomalus ) have been observed, suggesting that parasite dilution is occurring.", "output": "brown trout, Salmo trutta, roundhead galaxias, Galaxias anomalus." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We used a multiple - scale approach combining field observations, experimental infections and dynamic population modelling to investigate whether native Acanthocephalus galaxii acquisition by brown trout alters host - parasite dynamics in native roundhead galaxias.", "output": "brown trout, roundhead galaxias." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Field observations demonstrated higher infection intensity in introduced trout than in native galaxias, but only small, immature A. galaxii were present in trout.", "output": "native galaxias, trout." }, { "input": "Experimental infections also demonstrated that A. galaxii does not mature in trout, although parasite establishment and initial growth were similar in the two hosts.", "output": "trout." }, { "input": "Taken together, these results support the hypothesis that trout may serve as an infection sink for the native parasite.", "output": "trout." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "However, dynamic population modelling predicts that A. galaxii infections in native galaxias should at most only be slightly reduced by dilution in the presence of trout.", "output": "galaxias, trout." }, { "input": "Rather, model exploration indicates parasite densities in galaxias are highly sensitive to galaxias predation on infected amphipods, and to relative abundances of galaxias and trout.", "output": "galaxias, galaxias, galaxias, trout." }, { "input": "Hence, trout presence may instead reduce parasite burdens in galaxias by either reducing galaxias density or by altering galaxias foraging behaviour.", "output": "trout, galaxias, galaxias, galaxias." }, { "input": "Fitness effects of endemic malaria infections in a wild bird population: the importance of ecological structure.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Parasites can have important effects on host populations influencing either fecundity or mortality, but understanding the magnitude of these effects in endemic host - parasite systems is challenging and requires an understanding of ecological processes affecting both host and parasite.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Avian blood parasites ( Haemoproteus and Plasmodium ) have been much studied, but the effects of these parasites on hosts in areas where they are endemic remains poorly known.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We used a multistate modelling framework to explore the effects of chronic infection with Plasmodium on survival and recapture probability in a large data set of breeding blue tits, involving 3424 individuals and 3118 infection diagnoses over nine years.", "output": "blue tits." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "We reveal strong associations between chronic malaria infection and both recapture and survival, effects that are dependent on the clade of parasite, on host traits and on the local risk of infection.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Infection with Plasmodium relictum was associated with reduced recapture probability and increased survival, compared to P. circumflexum, suggesting that these parasites have differing virulence and cause different types of selection on this host.", "output": "Plasmodium relictum, P . circumflexum." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "Our results suggest a large potential survival cost of acute infections revealed by modelling host survival as a function of the local risk of infection.", "output": "There is no related enetity." }, { "input": "7.", "output": "There is no related enetity." }, { "input": "Our analyses suggest not only that endemic avian malaria may have multiple fitness effects on their hosts and that these effects are species dependent, but also that adding ecological structure ( in this case parasite species and spatial variation in disease occurrence ) to analyses of host - parasite interactions is an important step in understanding the ecology and evolution of these systems.", "output": "There is no related enetity." }, { "input": "Host phylogeography and beta diversity in avian haemosporidian ( Plasmodiidae ) assemblages of the Lesser Antilles.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "We estimated the correlation between host phylogeographical structure and beta diversity of avian haemosporidian assemblages of passerine birds to determine the degree to which parasite communities change with host evolution, expressed as genetic divergence between island populations, and we investigated whether differences among islands in the haemosporidia of a particular host species reflect beta diversity in the entire parasite assemblage, beta diversity in vectors, turnover of bird species and / or geographical distance.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We used Mantel tests to assess the significance of partial correlations between host nucleotide difference ( based on cytochrome b ) and haemosporidian ( Haemoproteus spp. and Plasmodium spp. ) mitochondrial lineage beta diversity within a given host species and between Plasmodium mitochondrial lineage beta diversity and mosquito and bird species beta diversity ( or turnover ).", "output": "There is no related enetity." }, { "input": "Three abundant and widespread host species ( Tiaris bicolor, Coereba flaveola and Loxigilla noctis / barbadensis ) were included in the study.", "output": "Tiaris bicolor, Coereba flaveola, Loxigilla noctis, barbadensis." }, { "input": "Haemosporidian lineage beta diversity among nine islands was assessed using the Chao - Jaccard, Chao - Sorensen and Morisita - Horn indices of community similarity.", "output": "There is no related enetity." }, { "input": "Beta diversity indices of mosquito species and turnover of bird species were calculated from data in published records and field guides.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "In Loxigilla spp., we found a positive correlation with geographical distance and an unexpected negative correlation between haemosporidian beta diversity and host genetic distance.", "output": "There is no related enetity." }, { "input": "Tiaris bicolor exhibited a significant positive correlation between haemosporidian beta diversity and beta diversity within the entire parasite assemblage.", "output": "Tiaris bicolor." }, { "input": "We did not find significant correlations between parasite beta diversity and mosquito beta diversity or bird species turnover.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Host phylogeographical structure does not appear to drive within - host beta diversity of haemosporidian lineages.", "output": "There is no related enetity." }, { "input": "Instead, the array of parasites on one host can reflect the haemosporidian assemblage on other hosts.", "output": "There is no related enetity." }, { "input": "Dermamoeba algensis n. sp.", "output": "Dermamoeba algensis n . sp .." }, { "input": "( Amoebozoa, Dermamoebidae ): an algivorous lobose amoeba with complex cell coat and unusual feeding mode.", "output": "There is no related enetity." }, { "input": "The genus Dermamoeba unifies oblong, flattened amoebae of lingulate morphotype, possessing a thick multilayered cell coat.", "output": "There is no related enetity." }, { "input": "It includes two species, D. granifera and D. minor.", "output": "There is no related enetity." }, { "input": "In this paper we describe a third species of this genus, D. algensis n. sp.", "output": "D . algensis n . sp .." }, { "input": "This species is algivorous; engulfing a large algal cell, it destroys part of the cell coat liberating the plasma membrane, which forms the food vacuole.", "output": "There is no related enetity." }, { "input": "Thus the glycocalyx never appears inside the phagosome.", "output": "There is no related enetity." }, { "input": "This observation confirms that some of the thick - coated amoebae may use this way to avoid energetically costly digestion of their own glycocalyx.", "output": "There is no related enetity." }, { "input": "Studies of the physiology of this organism show that it feeds most actively at a temperature of 22 - 25 ^ 0C.", "output": "There is no related enetity." }, { "input": "Below and above this temperature the feeding intensity drastically decreases.", "output": "There is no related enetity." }, { "input": "The new species can survive NaCl concentrations up to 5 %, which roughly corresponds to 50 ppt salinity.", "output": "There is no related enetity." }, { "input": "Accordingly, D. algensis has a wide range of salinity tolerance.", "output": "D . algensis." }, { "input": "European guidelines on the clinical management of HIV - 1 tropism testing.", "output": "HIV - 1." }, { "input": "Viral tropism is the ability of viruses to enter and infect specific host cells and is based on the ability of viruses to bind to receptors on those cells.", "output": "There is no related enetity." }, { "input": "Testing for HIV tropism is recommended before prescribing a chemokine receptor blocker.", "output": "HIV." }, { "input": "In most European countries, HIV tropism is identified with tropism phenotype testing.", "output": "HIV." }, { "input": "New data support genotype analysis of the HIV third hypervariable loop ( V3 ) for the identification of tropism.", "output": "HIV." }, { "input": "The European Consensus Group on clinical management of tropism testing was established to make recommendations to clinicians and clinical virologists.", "output": "There is no related enetity." }, { "input": "The panel recommends HIV - tropism testing for the following groups: drug - naive patients in whom toxic effects are anticipated or for whom few treatment options are available; patients who have poor tolerability to or toxic effects from current treatment or who have CNS pathology; and patients for whom therapy has failed and a change in treatment is considered.", "output": "HIV." }, { "input": "In general, an enhanced sensitivity Trofile assay and V3 population genotyping are the recommended methods.", "output": "There is no related enetity." }, { "input": "Genotypic methods are anticipated to be used more frequently in the clinical setting because of their greater accessibility, lower cost, and faster turnaround time than other methods.", "output": "There is no related enetity." }, { "input": "For the interpretation of V3 loop genotyping, clinically validated systems should be used when possible.", "output": "There is no related enetity." }, { "input": "Laboratories doing HIV tropism tests should have adequate quality assurance measures.", "output": "HIV." }, { "input": "Similarly, close collaboration between HIV clinicians and virologists is needed to ensure adequate diagnostic and treatment decisions.", "output": "HIV." }, { "input": "Causal involvement of mammalian - type cryptochrome in the circadian cuticle deposition rhythm in the bean bug Riptortus pedestris.", "output": "bean bug, Riptortus pedestris." }, { "input": "Mammalian - type CRYPTOCHROME ( CRY - m ) is considered to be a core repressive component of the circadian clock in various insect species.", "output": "There is no related enetity." }, { "input": "However, this role is based only on the molecular function of CRY - m in cultured cells and it therefore remains unknown whether CRY - m is indispensable for governing physiological rhythms at the organismal level.", "output": "There is no related enetity." }, { "input": "In the present study, we show that RNA interference ( RNAi ) targeting of cry - m in the bean bug Riptortus pedestris disrupts the circadian clock governing the cuticle deposition rhythm and results in the generation of a single cuticle layer.", "output": "bean bug, Riptortus pedestris." }, { "input": "Furthermore, period expression was induced in cry - m RNAi insects.", "output": "There is no related enetity." }, { "input": "These results verified that CRY - m functions as a negative regulator in the circadian clock that generates physiological rhythm at the organismal level.", "output": "There is no related enetity." }, { "input": "Induced pluripotent stem cells: a new revolution for clinical neurology?", "output": "There is no related enetity." }, { "input": "Why specific neuronal populations are uniquely susceptible in neurodegenerative diseases remains a mystery.", "output": "There is no related enetity." }, { "input": "Brain tissue samples from patients are rarely available for testing, and animal models frequently do not recapitulate all features of a specific disorder; therefore, pathophysiological investigations are difficult.", "output": "There is no related enetity." }, { "input": "An exciting new avenue for neurological research and drug development is the discovery that patients ' somatic cells can be reprogrammed to a pluripotent state; these cells are known as induced pluripotent stem cells.", "output": "There is no related enetity." }, { "input": "Once pluripotency is reinstated, cell colonies can be expanded and differentiated into specific neural populations.", "output": "There is no related enetity." }, { "input": "The availability of these cells enables the monitoring in vitro of temporal features of disease initiation and progression, and testing of new drug treatments on the patient ' s own cells.", "output": "There is no related enetity." }, { "input": "Hence, this swiftly growing area of research has the potential to contribute greatly to our understanding of the pathophysiology of neurodegenerative and neurodevelopmental diseases.", "output": "There is no related enetity." }, { "input": "Viral pneumonia.", "output": "There is no related enetity." }, { "input": "About 200 million cases of viral community - acquired pneumonia occur every year - 100 million in children and 100 million in adults.", "output": "There is no related enetity." }, { "input": "Molecular diagnostic tests have greatly increased our understanding of the role of viruses in pneumonia, and findings indicate that the incidence of viral pneumonia has been underestimated.", "output": "There is no related enetity." }, { "input": "In children, respiratory syncytial virus, rhinovirus, human metapneumovirus, human bocavirus, and parainfluenza viruses are the agents identified most frequently in both developed and developing countries.", "output": "respiratory syncytial virus, human metapneumovirus, human bocavirus." }, { "input": "Dual viral infections are common, and a third of children have evidence of viral - bacterial co - infection.", "output": "There is no related enetity." }, { "input": "In adults, viruses are the putative causative agents in a third of cases of community - acquired pneumonia, in particular influenza viruses, rhinoviruses, and coronaviruses.", "output": "There is no related enetity." }, { "input": "Bacteria continue to have a predominant role in adults with pneumonia.", "output": "There is no related enetity." }, { "input": "Presence of viral epidemics in the community, patient ' s age, speed of onset of illness, symptoms, biomarkers, radiographic changes, and response to treatment can help differentiate viral from bacterial pneumonia.", "output": "There is no related enetity." }, { "input": "However, no clinical algorithm exists that will distinguish clearly the cause of pneumonia.", "output": "There is no related enetity." }, { "input": "No clear consensus has been reached about whether patients with obvious viral community - acquired pneumonia need to be treated with antibiotics.", "output": "There is no related enetity." }, { "input": "Apart from neuraminidase inhibitors for pneumonia caused by influenza viruses, there is no clear role for use of specific antivirals to treat viral community - acquired pneumonia.", "output": "There is no related enetity." }, { "input": "Influenza vaccines are the only available specific preventive measures.", "output": "There is no related enetity." }, { "input": "Further studies are needed to better understand the cause and pathogenesis of community - acquired pneumonia.", "output": "There is no related enetity." }, { "input": "Furthermore, regional differences in cause of pneumonia should be investigated, in particular to obtain more data from developing countries.", "output": "There is no related enetity." }, { "input": "Preventive therapy for breast cancer: a consensus statement.", "output": "There is no related enetity." }, { "input": "In March, 2010, a group of breast cancer experts met to develop a consensus statement on breast cancer prevention, with a focus on medical and therapeutic interventions.", "output": "There is no related enetity." }, { "input": "We present the conclusions in this Review.", "output": "There is no related enetity." }, { "input": "First we agreed that the term chemoprevention is inappropriate and suggested that the term preventive therapy better represents this feature of management.", "output": "There is no related enetity." }, { "input": "Two selective oestrogen - receptor modulators - - tamoxifen and raloxifene - - are so far the only medical options approved by the US Food and Drug Administration for preventive therapy.", "output": "There is no related enetity." }, { "input": "Of these tamoxifen has greater efficacy and can be used in premenopausal women, but raloxifene has fewer side - effects.", "output": "There is no related enetity." }, { "input": "Two newer drugs in this class, lasofoxifene and arzoxifene, also show efficacy and possibly a better overall risk - benefit profile, but need further assessment.", "output": "There is no related enetity." }, { "input": "Aromatase inhibitors might be more efficacious, and results of prevention trials are eagerly awaited.", "output": "There is no related enetity." }, { "input": "Newer agents, notably bisphosphonates and metformin, have shown promise in observational studies and need to be assessed in randomised prevention trials.", "output": "There is no related enetity." }, { "input": "Other agents, such as aspirin, other non - steroidal anti - inflammatory drugs, COX - 2 inhibitors, retinoids, rexinoids, and dietary components have limited effects or are in the early phases of investigation.", "output": "There is no related enetity." }, { "input": "New contralateral tumours in women with breast cancer might be generally useful as a model for prevention, as has been seen for tamoxifen.", "output": "There is no related enetity." }, { "input": "If valid such a model would facilitate the design of simpler, cheaper, and better - focused trials for assessing new agents.", "output": "There is no related enetity." }, { "input": "Structure and evolution of the Fusarium mating type locus: new insights from the Gibberellafujikuroi complex.", "output": "There is no related enetity." }, { "input": "Mating type genes are central to sexual reproduction and compatibility in Ascomycete fungi.", "output": "There is no related enetity." }, { "input": "However the & quot; MAT & quot; loci experience unique evolutionary pressures that can result in rapid divergence and enhanced inter - specific gene - flow ( lateral gene transfer ).", "output": "There is no related enetity." }, { "input": "In this study, molecular evolution of MAT loci was considered using the genus Fusarium ( Teleomorph: Gibberella ) as a model.", "output": "There is no related enetity." }, { "input": "Both MAT1 - 1 and MAT1 - 2 & quot; idiomorphs & quot; from eleven species of the Gibberellafujikuroi species complex were sequenced.", "output": "There is no related enetity." }, { "input": "Molecular evolution of the MAT loci from these heterothallic ( self - sterile ) species was compared with that of the MAT loci from nine homothallic ( self - fertile ) species in the Fusariumgraminearum species complex.", "output": "Fusariumgraminearum species complex." }, { "input": "Although Fusarium has previously been thought to have the same complement of four MAT genes that are found in Neurospora, we found evidence of a novel gene, MAT1 - 2 - 3, that may be specific to the Hypocreales.", "output": "There is no related enetity." }, { "input": "All MAT genes share a similar set of cis - regulatory motifs, although homothallic species might have recruited novel regulatory elements, which could potentially facilitate alternate expression of MAT1 - 1 - 1 and MAT1 - 2 - 1.", "output": "There is no related enetity." }, { "input": "FusariumMAT loci displayed evidence consistent with historical lateral gene - flow.", "output": "There is no related enetity." }, { "input": "Most notably, the MAT1 - 1 idiomorph of Fusariumsacchari appears to be unrelated to those of other species in the G. fujikuroi complex.", "output": "Fusariumsacchari." }, { "input": "In general, FusariumMAT genes are highly divergent.", "output": "There is no related enetity." }, { "input": "Both positive selection and relaxed selective constraint could account for this phenomenon.", "output": "There is no related enetity." }, { "input": "However, the extent of both recombination and inter - specific gene - flow in the MAT locus also appears to affect the rate of divergence.", "output": "There is no related enetity." }, { "input": "Mucormycosis: its contemporary face and management strategies.", "output": "There is no related enetity." }, { "input": "Several countries have seen rising frequencies of mucormycosis among patients with haematological disorders, malignancies, or diabetes mellitus, and among transplant recipients.", "output": "There is no related enetity." }, { "input": "Growing numbers of immunocompromised hosts, widespread use of antifungal agents inactive against mucormycosis, or other unidentified factors, could be contributing to this situation.", "output": "There is no related enetity." }, { "input": "The predominant clinical manifestations of mucormycosis vary from host to host.", "output": "There is no related enetity." }, { "input": "Additionally, risk factors specific to different subgroups have been identified, such as leukaemia, allogeneic haemopoietic stem - cell transplant, voriconazole prophylaxis, diabetes, and malnutrition.", "output": "There is no related enetity." }, { "input": "We summarise the current state of knowledge of characteristics and risk factors and discuss topical developments in therapeutic methods and strategies in the management of mucormycosis.", "output": "There is no related enetity." }, { "input": "Hygiene: new hopes, new horizons.", "output": "There is no related enetity." }, { "input": "Although promotion of safe hygiene is the single most cost - effective means of preventing infectious disease, investment in hygiene is low both in the health and in the water and sanitation sectors.", "output": "There is no related enetity." }, { "input": "Evidence shows the benefit of improved hygiene, especially for improved handwashing and safe stool disposal.", "output": "There is no related enetity." }, { "input": "A growing understanding of what drives hygiene behaviour and creative partnerships are providing fresh approaches to change behaviour.", "output": "There is no related enetity." }, { "input": "However, some important gaps in our knowledge exist.", "output": "There is no related enetity." }, { "input": "For example, almost no trials of the effectiveness of interventions to improve food hygiene in developing countries are available.", "output": "There is no related enetity." }, { "input": "We also need to figure out how best to make safe hygiene practices matters of daily routine that are sustained by social norms on a mass scale.", "output": "There is no related enetity." }, { "input": "Full and active involvement of the health sector in getting safe hygiene to all homes, schools, and institutions will bring major gains to public health.", "output": "There is no related enetity." }, { "input": "Visceral leishmaniasis: elimination with existing interventions.", "output": "There is no related enetity." }, { "input": "The world ' s burden of infectious diseases can be substantially reduced by more - effective use of existing interventions.", "output": "There is no related enetity." }, { "input": "Advances in case detection, diagnosis, and treatment strategies have made it possible to consider the elimination of visceral leishmaniasis in the Indian subcontinent.", "output": "There is no related enetity." }, { "input": "The priority must now be to effectively implement existing interventions at the community level by actively finding cases in endemic villages and treating them with single - dose liposomal amphotericin B at primary - health - care centres.", "output": "There is no related enetity." }, { "input": "Once the elimination target of one case per 10, 000 population has been reached, combination therapies involving miltefosine and paromomycin can be introduced to ensure long - term availability of several drugs for visceral leishmaniasis and to protect against resistance.", "output": "There is no related enetity." }, { "input": "Glaucoma.", "output": "There is no related enetity." }, { "input": "Most medical practitioners have regular contact with adults who have one of the two forms of glaucoma: open - angle glaucoma or angle - closure glaucoma.", "output": "There is no related enetity." }, { "input": "Data from population - based surveys indicate that one in 40 adults older than 40 years has glaucoma with loss of visual function, which equates to 60 million people worldwide being affected and 8 * 4 million being bilaterally blind.", "output": "There is no related enetity." }, { "input": "Even in developed countries, half of glaucoma cases are undiagnosed.", "output": "There is no related enetity." }, { "input": "Glaucoma is mostly asymptomatic until late in the disease when visual problems arise.", "output": "There is no related enetity." }, { "input": "Vision loss from glaucoma cannot be recovered, and improved case - detection methods for glaucoma are needed.", "output": "There is no related enetity." }, { "input": "Glaucoma is commonly treated with daily eye - drop drugs, but adherence to treatment is often unsatisfactory.", "output": "There is no related enetity." }, { "input": "As a usually asymptomatic and chronic disease, glaucoma has similar treatment challenges to chronic systemic diseases.", "output": "There is no related enetity." }, { "input": "Similarities to the pathogenesis of common CNS diseases mean that common neuroprotective strategies might exist.", "output": "There is no related enetity." }, { "input": "Successful gene therapy, which has been used for other eye diseases might be possible for the treatment of glaucoma in the future.", "output": "There is no related enetity." }, { "input": "Heating up relations between cold fish: competition modifies responses to climate change.", "output": "There is no related enetity." }, { "input": "Most predictions about species responses to climate change ignore species interactions.", "output": "There is no related enetity." }, { "input": "Helland and colleagues ( 2011 ) test whether this assumption is valid by evaluating whether ice cover affects competition between brown trout [ Salmo trutta ( L. ) ] and Arctic charr [ Salvelinus alpines ( L. ) ].", "output": "brown trout, Salmo trutta, Arctic charr, Salvelinus alpines." }, { "input": "They show that increasing ice cover correlates with lower trout biomass when Arctic charr co - occur, but not in charr ' s absence.", "output": "Arctic charr, charr ' s." }, { "input": "In experiments, charr grew better in the cold, dark environments that typify ice - covered lakes.", "output": "charr." }, { "input": "Decreasing ice cover with warmer winters could mean more trout and fewer charr.", "output": "charr." }, { "input": "More generally, their results provide an excellent example, suggesting that species interactions can strongly modify responses to climate change.", "output": "There is no related enetity." }, { "input": "An empirical link between the spectral colour of climate and the spectral colour of field populations in the context of climate change.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "The spectral colour of population dynamics and its causes have attracted much interest.", "output": "There is no related enetity." }, { "input": "The spectral colour of a time series can be determined from its power spectrum, which shows what proportion of the total variance in the time series occurs at each frequency.", "output": "There is no related enetity." }, { "input": "A time series with a red spectrum ( a negative spectral exponent ) is dominated by low - frequency oscillations, and a time series with a blue spectrum ( a positive spectral exponent ) is dominated by high - frequency oscillations.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Both climate variables and population time series are characterised by red spectra, suggesting that a population ' s environment might be partly responsible for its spectral colour.", "output": "There is no related enetity." }, { "input": "Laboratory experiments and models have been used to investigate this potential link.", "output": "There is no related enetity." }, { "input": "However, no study using field data has directly tested whether populations in redder environments are redder.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "This study uses the Global Population Dynamics Database together with climate data to test for this effect.", "output": "There is no related enetity." }, { "input": "We found that the spectral exponent of mean summer temperatures correlates positively and significantly with population spectral exponent.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "We also found that over the last century, temperature climate variables on most continents have become bluer.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Although population time series are not long or abundant enough to judge directly whether their spectral colours are changing, our two results taken together suggest that population spectral colour may be affected by the changing spectral colour of climate variables.", "output": "There is no related enetity." }, { "input": "Population spectral colour has been linked to extinction; we discuss the potential implications of our results for extinction probability.", "output": "There is no related enetity." }, { "input": "Response assessment in neuro - oncology ( a report of the RANO group ): assessment of outcome in trials of diffuse low - grade gliomas.", "output": "There is no related enetity." }, { "input": "Although low - grade gliomas ( LGG ) have a less aggressive course than do high - grade gliomas, the outcome of these tumours is ultimately fatal in most patients.", "output": "There is no related enetity." }, { "input": "Both the tumour and its treatment can cause disabling morbidity, particularly of cognitive functions.", "output": "There is no related enetity." }, { "input": "Because many patients present with seizures only, with no other signs and symptoms, maintenance of quality of life and function constitutes a particular challenge in LGG.", "output": "There is no related enetity." }, { "input": "The slow growth pattern of most LGG, and the rare radiological true responses despite a favourable clinical response to treatment, interferes with the use of progression - free survival as the primary endpoint in trials.", "output": "There is no related enetity." }, { "input": "Overall survival as an endpoint brings logistical challenges, and is sensitive to other non - investigational salvage therapies.", "output": "There is no related enetity." }, { "input": "Clinical trials for LGG need to consider other measures of patient benefit such as cognition, symptom burden, and seizure activity, to establish whether improved survival is reflected in prolonged wellbeing.", "output": "There is no related enetity." }, { "input": "This Review investigates clinical and imaging endpoints in trials of LGG, and provides response assessment in neuro - oncology ( RANO ) criteria for non - enhancing tumours.", "output": "There is no related enetity." }, { "input": "Additionally, other measures for patients with brain tumours that assess outcome are described.", "output": "There is no related enetity." }, { "input": "Similar considerations are relevant for trials of high - grade gliomas, although for these tumours survival is shorter and survival endpoints generally have more value than they do for LGG.", "output": "There is no related enetity." }, { "input": "Baculovirus cyclobutane pyrimidine dimer photolyases show a close relationship with lepidopteran host homologues.", "output": "Baculovirus." }, { "input": "Cyclobutane pyrimidine dimer ( CPD ) photolyases repair ultraviolet ( UV ) - induced DNA damage using blue light.", "output": "There is no related enetity." }, { "input": "To get insight in the origin of baculovirus CPD photolyase ( phr ) genes, homologues in the lepidopteran insects Chrysodeixis chalcites, Spodoptera exigua and Trichoplusia ni were identified and characterized.", "output": "baculovirus, Chrysodeixis chalcites, Spodoptera exigua, Trichoplusia ni." }, { "input": "Lepidopteran and baculovirus phr genes each form a monophyletic group, and together form a well - supported clade within the insect photolyases.", "output": "baculovirus." }, { "input": "This suggests that baculoviruses obtained their phr genes from an ancestral lepidopteran insect host.", "output": "baculoviruses." }, { "input": "A likely evolutionary scenario is that a granulovirus, Spodoptera litura GV or a direct ancestor, obtained a phr gene.", "output": "Spodoptera litura GV." }, { "input": "Subsequently, it was horizontally transferred from this granulovirus to several group II nucleopolyhedroviruses ( NPVs ), including those that infect noctuids of the Plusiinae subfamily.", "output": "There is no related enetity." }, { "input": "The importance of marine vs. human - induced subsidies in the maintenance of an expanding mesocarnivore in the arctic tundra.", "output": "human." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Most studies addressing the causes of the recent increases and expansions of mesopredators in many ecosystems have focused on the top - down, releasing effect of extinctions of large apex predators.", "output": "There is no related enetity." }, { "input": "However, in the case of the northward expansion of the red fox into the arctic tundra, a bottom - up effect of increased resource availability has been proposed, an effect that can counteract prey shortage in the low phase of the multi - annual rodent cycle.", "output": "red fox." }, { "input": "Resource subsidies both with marine and with terrestrial origins could potentially be involved.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "During different phases of a multi - annual rodent cycle, we investigated the seasonal dynamics and spatial pattern of resource use by red foxes across a coast to inland low arctic tundra gradient, Varanger Peninsula, Norway.", "output": "red foxes." }, { "input": "We employed two complementary methods of diet analyses: stomach contents and stable isotope analysis.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We found that inland red foxes primarily subsisted on reindeer carrions during the low phase of a small rodent population cycle.", "output": "red foxes, reindeer." }, { "input": "Lemmings became the most important food item towards the peak phase of the rodent cycle, despite being less abundant than sympatric voles.", "output": "voles." }, { "input": "Isotopic signatures of tissue from both predator and prey also revealed that red foxes near the coast used marine - derived subsidies in the winter, but these allochthonous resources did not spillover to adult foxes living beyond 20 - 25 km from the coast.", "output": "red foxes." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Although more needs to be learned about the link between increasing primary productivity due to climatic warming and trophic dynamics in tundra ecosystems, we suggest that changes in reindeer management through a bottom - up effect, at least regionally, may have paved the way towards the establishment of a new mesopredator in the tundra biome.", "output": "reindeer." }, { "input": "Mathematical models in the evaluation of health programmes.", "output": "There is no related enetity." }, { "input": "Modelling is valuable in the planning and evaluation of interventions, especially when a controlled trial is ethically or logistically impossible.", "output": "There is no related enetity." }, { "input": "Models are often used to calculate the expected course of events in the absence of more formal assessments.", "output": "There is no related enetity." }, { "input": "They are also used to derive estimates of rare or future events from recorded intermediate points.", "output": "There is no related enetity." }, { "input": "When developing models, decisions are needed about the appropriate level of complexity to be represented and about model structure and assumptions.", "output": "There is no related enetity." }, { "input": "The degree of rigor in model development and assessment can vary greatly, and there is a danger that existing beliefs inappropriately influence judgments about model assumptions and results.", "output": "There is no related enetity." }, { "input": "Scale and state dependence of the relationship between personality and dispersal in a great tit population.", "output": "great tit." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Dispersal is a key process in population biology and ecology.", "output": "There is no related enetity." }, { "input": "Although the general ecological conditions that lead to dispersal have been well studied, the causes of individual variation in dispersal are less well understood.", "output": "There is no related enetity." }, { "input": "A number of recent studies suggest that heritable temperament - or personality - traits are correlated with dispersal in the wild but the extent to which these ' personality - dispersal syndromes ' are general, how they depend on an individual ' s state and on spatial scale and whether they are temporally stable, both within and across individuals, remains unclear.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "Here, we examine the relationship between exploration behaviour - an axis of personality that appears to be important in animals generally - and a variety of dispersal processes over 6 years in a population of the great tit Parus major.", "output": "great tit, Parus major." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Exploration behaviour was higher in immigrant than in locally born juveniles, but the difference was much larger for individuals with a small body mass, though independent of sex, representing one of the first examples of a state - dependent effect in a personality - dispersal syndrome.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Despite a temporal trend in exploration behaviour at the population level, the difference between immigrants and locally born birds remained stable over time, both across and within individuals.", "output": "There is no related enetity." }, { "input": "This suggests that the personality difference between immigrants and locally born birds is established early in development, but that the process of immigration interacts with both personality and state.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "We found that the number of immigrant parents a locally born bird had did not influence exploration behaviour, suggesting either the difference between immigrants and residents was environmental or that the effect is overridden by local environmental sources of variation.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "In contrast to previous work, we found no evidence for links between personality and natal dispersal distance within the population, either in terms of an individual ' s own exploration behaviour or that of its parents.", "output": "There is no related enetity." }, { "input": "7.", "output": "There is no related enetity." }, { "input": "Our results suggest that there are links between individual differences in personality and dispersal, but that these can be dependent on differences in state among individuals and on the scale over which dispersal is measured.", "output": "There is no related enetity." }, { "input": "Future work should aim to understand the differences between dispersal within and between populations and the ways in which personality and state interact to determine the outcome of these processes.", "output": "There is no related enetity." }, { "input": "A role for endosomal proteins in alphavirus dissemination in mosquitoes.", "output": "There is no related enetity." }, { "input": "Little is known about endosomal pathway proteins involved in arthropod - borne virus ( arbovirus ) assembly and cell - to - cell spread in vector mosquitoes.", "output": "There is no related enetity." }, { "input": "UNC93A and synaptic vesicle - 2 ( SV2 ) proteins are involved in intracellular transport in mammals.", "output": "There is no related enetity." }, { "input": "They show amino acid sequence conservation from mosquitoes to humans, and their transcripts are highly enriched in Aedes aegypti during arbovirus infection.", "output": "humans, Aedes aegypti." }, { "input": "Transient gene silencing of SV2 or UNC93A in mosquitoes infected with the recombinant alphavirus Sindbis MRE16 - enhanced green fluorescent protein ( SINV; family Togaviridae ) resulted in the accumulation of viral positive - and negative - strand RNA, congregation of virus envelope antigen in intracellular networks, and reduced virus dissemination outside of the midgut.", "output": "Sindbis, SINV." }, { "input": "Further, UNC93A silencing, but not SV2 silencing, resulted in a 10 - fold reduction in viral titres at 4 days post - infection.", "output": "There is no related enetity." }, { "input": "Together, these data support a role for UNC93A and SV2 in virus assembly or budding.", "output": "There is no related enetity." }, { "input": "Cis - regulatory elements ( CREs ) were identified at the 5 ' - ends of genes from the original data set in which SV2 and UNC93A were identified.", "output": "There is no related enetity." }, { "input": "Common CREs at the 5 ' - end genomic regions of a subset of enriched transcripts support the hypothesis that UNC93A transcription may be co - regulated with that of other ion transport and endosomal trafficking proteins.", "output": "There is no related enetity." }, { "input": "Pyrethroid resistance in Sitophilus zeamais is associated with a mutation ( T929I ) in the voltage - gated sodium channel.", "output": "Sitophilus zeamais." }, { "input": "The maize weevil, Sitophilus zeamais, is the most important pest affecting stored grain in Brazil and its control relies heavily on the use of insecticides.", "output": "maize weevil, Sitophilus zeamais." }, { "input": "The intensive use of compounds such as the pyrethroids has led to the emergence of resistance, and previous studies have suggested that resistance to both pyrethroids and 1, 1, 1 - trichloro - 2, 2 - bis ( p - chlorophenyl ) ethane ( DDT ) may result from reduced sensitivity of the insecticide target, the voltage - gated sodium channel.", "output": "There is no related enetity." }, { "input": "To identify the molecular mechanisms underlying pyrethroid resistance in S. zeamais, the domain II region of the voltage - gated sodium channel ( para - orthologue ) gene was amplified by PCR and sequenced from susceptible and resistant laboratory S. zeamais strains that were selected with a discriminating dose of DDT.", "output": "S . zeamais, S . zeamais." }, { "input": "A single point mutation, T929I, was found in the para gene of the resistant S. zeamais populations and its presence in individual weevils was strongly associated with survival after DDT exposure.", "output": "S . zeamais." }, { "input": "This is the first identification of a target - site resistance mutation in S. zeamais and unusually it is a super - kdr type mutation occurring in the absence of the more common kdr ( L1014F ) substitution.", "output": "S . zeamais." }, { "input": "A high - throughput assay based on TaqMan single nucleotide polymorphism genotyping was developed for sensitive detection of the mutation and used to screen field - collected strains of S. zeamais.", "output": "S . zeamais." }, { "input": "This showed that the mutation is present at low frequency in field populations and is a useful tool for informing control strategies.", "output": "There is no related enetity." }, { "input": "Stillbirths: the way forward in high - income countries.", "output": "There is no related enetity." }, { "input": "Stillbirth rates in high - income countries declined dramatically from about 1940, but this decline has slowed or stalled over recent times.", "output": "There is no related enetity." }, { "input": "The present variation in stillbirth rates across and within high - income countries indicates that further reduction in stillbirth is possible.", "output": "There is no related enetity." }, { "input": "Large disparities ( linked to disadvantage such as poverty ) in stillbirth rates need to be addressed by providing more educational opportunities and improving living conditions for women.", "output": "There is no related enetity." }, { "input": "Placental pathologies and infection associated with preterm birth are linked to a substantial proportion of stillbirths.", "output": "There is no related enetity." }, { "input": "The proportion of unexplained stillbirths associated with under investigation continues to impede efforts in stillbirth prevention.", "output": "There is no related enetity." }, { "input": "Overweight, obesity, and smoking are important modifiable risk factors for stillbirth, and advanced maternal age is also an increasingly prevalent risk factor.", "output": "There is no related enetity." }, { "input": "Intensified efforts are needed to ameliorate the effects of these factors on stillbirth rates.", "output": "There is no related enetity." }, { "input": "Culturally appropriate preconception care and quality antenatal care that is accessible to all women has the potential to reduce stillbirth rates in high - income countries.", "output": "There is no related enetity." }, { "input": "Implementation of national perinatal mortality audit programmes aimed at improving the quality of care could substantially reduce stillbirths.", "output": "There is no related enetity." }, { "input": "Better data on numbers and causes of stillbirth are needed, and international consensus on definition and classification related to stillbirth is a priority.", "output": "There is no related enetity." }, { "input": "All parents should be offered a thorough investigation including a high - quality autopsy and placental histopathology.", "output": "There is no related enetity." }, { "input": "Parent organisations are powerful change agents and could have an important role in raising awareness to prevent stillbirth.", "output": "There is no related enetity." }, { "input": "Future research must focus on screening and interventions to reduce antepartum stillbirth as a result of placental dysfunction.", "output": "There is no related enetity." }, { "input": "Identification of ways to reduce maternal overweight and obesity is a high priority for high - income countries.", "output": "There is no related enetity." }, { "input": "Stillbirths: Where?", "output": "There is no related enetity." }, { "input": "When?", "output": "There is no related enetity." }, { "input": "Why?", "output": "There is no related enetity." }, { "input": "How to make the data count?", "output": "There is no related enetity." }, { "input": "Despite increasing attention and investment for maternal, neonatal, and child health, stillbirths remain invisible - not counted in the Millennium Development Goals, nor tracked by the UN, nor in the Global Burden of Disease metrics.", "output": "There is no related enetity." }, { "input": "At least 2 * 65 million stillbirths ( uncertainty range 2 * 08 million to 3 * 79 million ) were estimated worldwide in 2008 ( > = 1000 g birthweight or > = 28 weeks of gestation ).", "output": "There is no related enetity." }, { "input": "98 % of stillbirths occur in low - income and middle - income countries, and numbers vary from 2 * 0 per 1000 total births in Finland to more than 40 per 1000 total births in Nigeria and Pakistan.", "output": "There is no related enetity." }, { "input": "Worldwide, 67 % of stillbirths occur in rural families, 55 % in rural sub - Saharan Africa and south Asia, where skilled birth attendance and caesarean sections are much lower than that for urban births.", "output": "There is no related enetity." }, { "input": "In total, an estimated 1 * 19 million ( range 0 * 82 million to 1 * 97 million ) intrapartum stillbirths occur yearly.", "output": "There is no related enetity." }, { "input": "Most intrapartum stillbirths are associated with obstetric emergencies, whereas antepartum stillbirths are associated with maternal infections and fetal growth restriction.", "output": "There is no related enetity." }, { "input": "National estimates of causes of stillbirths are scarce, and multiple ( > 35 ) classification systems impede international comparison.", "output": "There is no related enetity." }, { "input": "Immediate data improvements are feasible through household surveys and facility audit, and improvements in vital registration, including specific perinatal certificates and revised International Classification of Disease codes, are needed.", "output": "There is no related enetity." }, { "input": "A simple, programme - relevant stillbirth classification that can be used with verbal autopsy would provide a basis for comparable national estimates.", "output": "There is no related enetity." }, { "input": "A new focus on all deaths around the time of birth is crucial to inform programmatic investment.", "output": "There is no related enetity." }, { "input": "Stillbirths: the vision for 2020.", "output": "There is no related enetity." }, { "input": "Stillbirth is a common adverse pregnancy outcome, with nearly 3 million third - trimester stillbirths occurring worldwide each year.", "output": "There is no related enetity." }, { "input": "98 % occur in low - income and middle - income countries, and more than 1 million stillbirths occur in the intrapartum period, despite many being preventable.", "output": "There is no related enetity." }, { "input": "Nevertheless, stillbirth is practically unrecognised as a public health issue and few data are reported.", "output": "There is no related enetity." }, { "input": "In this final paper in the Stillbirths Series, we call for inclusion of stillbirth as a recognised outcome in all relevant international health reports and initiatives.", "output": "There is no related enetity." }, { "input": "We ask every country to develop and implement a plan to improve maternal and neonatal health that includes a reduction in stillbirths, and to count stillbirths in their vital statistics and other health outcome surveillance systems.", "output": "There is no related enetity." }, { "input": "We also ask for increased investment in stillbirth - related research, and especially research aimed at identifying and addressing barriers to the aversion of stillbirths within the maternal and neonatal health systems of low - income and middle - income countries.", "output": "There is no related enetity." }, { "input": "Finally, we ask all those interested in reducing stillbirths to join with advocates for the improvement of other pregnancy - related outcomes, for mothers and their offspring, so that a united front for improved pregnancy and neonatal care for all will become a reality.", "output": "There is no related enetity." }, { "input": "Stillbirths: why they matter.", "output": "There is no related enetity." }, { "input": "In this first paper of The Lancet ' s Stillbirths Series we explore the present status of stillbirths in the world - from global health policy to a survey of community perceptions in 135 countries.", "output": "There is no related enetity." }, { "input": "Our findings highlight the need for a strong call for action.", "output": "There is no related enetity." }, { "input": "In times of global focus on motherhood, the mother ' s own aspiration of a liveborn baby is not recognised on the world ' s health agenda.", "output": "There is no related enetity." }, { "input": "Millions of deaths are not counted; stillbirths are not in the Global Burden of Disease, nor in disability - adjusted life - years lost, and they are not part of the UN Millennium Development Goals.", "output": "There is no related enetity." }, { "input": "The grief of mothers might be aggravated by social stigma, blame, and marginalisation in regions where most deaths occur.", "output": "There is no related enetity." }, { "input": "Most stillborn babies are disposed of without any recognition or ritual, such as naming, funeral rites, or the mother holding or dressing the baby.", "output": "There is no related enetity." }, { "input": "Beliefs in the mother ' s sins and evil spirits as causes of stillbirth are rife, and stillbirth is widely believed to be a natural selection of babies never meant to live.", "output": "There is no related enetity." }, { "input": "Stillbirth prevention is closely linked with prevention of maternal and neonatal deaths.", "output": "There is no related enetity." }, { "input": "Knowledge of causes and feasible solutions for prevention is key to health professionals ' priorities, to which this Stillbirths Series paper aims to contribute.", "output": "There is no related enetity." }, { "input": "Dynamic behaviour of stationary pronuclei during their positioning in Paramecium caudatum.", "output": "Paramecium caudatum." }, { "input": "During conjugation of Paramecium caudatum, there are two well - known stages when nuclear migration occurs.", "output": "Paramecium caudatum." }, { "input": "What happens to the nuclei is closely related to their localisations in cells.", "output": "There is no related enetity." }, { "input": "The first of these stages is the entrance of one meiotic product into the paroral region.", "output": "There is no related enetity." }, { "input": "This nucleus survives, while the remaining three outside this area degenerate.", "output": "There is no related enetity." }, { "input": "The second stage is the antero - posterior localisation of eight synkaryon division products.", "output": "There is no related enetity." }, { "input": "Four posterior nuclei are differentiated into macronuclear anlagen, whereas four anterior nuclei remain as the presumptive micronuclei.", "output": "There is no related enetity." }, { "input": "In this experiment, the process of the third prezygotic division of P. caudatum was studied with the help of protargol staining.", "output": "P . caudatum." }, { "input": "Here, a third nuclear migration was discovered.", "output": "There is no related enetity." }, { "input": "By two spindle turnings and two spindle elongations, stationary pronuclei were positioned near migratory pronuclei.", "output": "There is no related enetity." }, { "input": "This positioning of stationary pronuclei could shorten the distance for transferred migratory pronuclei to recognise and reach the stationary pronuclei.", "output": "There is no related enetity." }, { "input": "This fosters the synkaryon formation of P. caudatum.", "output": "P . caudatum." }, { "input": "Complete sructure of nuclear rDNA of the obligate plant parasite Plasmodiophora brassicae: intraspecific polymorphisms in the exon and group I intron of the large subunit rDNA.", "output": "Plasmodiophora brassicae." }, { "input": "Plasmodiophora brassicae is a soil - borne obligate intracellular parasite in the phylum Cercozoa of the Rhizaria that causes clubroot disease of crucifer crops.", "output": "Plasmodiophora brassicae." }, { "input": "To control the disease, understanding the distribution and infection routes of the pathogen is essential, and thus development of reliable molecular markers to discriminate geographic populations is required.", "output": "There is no related enetity." }, { "input": "In this study, the nuclear ribosomal RNA gene ( rDNA ) repeat unit of P. brassicae was determined, with particular emphasis on the structure of large subunit ( LSU ) rDNA, in which polymorphic regions were expected to be present.", "output": "P . brassicae." }, { "input": "The complete rDNA complex was 9513bp long, which included the small subunit, 5. 8S and LSU rDNAs as well as the internal transcribed spacer and intergenic spacer regions.", "output": "There is no related enetity." }, { "input": "Among eight field populations collected from throughout Honshu Island, Japan, a 1. 1 kbp region of the LSU rDNA, including the divergent 8 domain, exhibited intraspecific polymorphisms that reflected geographic isolation of the populations.", "output": "There is no related enetity." }, { "input": "Two new group I introns were found in this region in six out of the eight populations, and the sequences also reflected their geographic isolation.", "output": "There is no related enetity." }, { "input": "The polymorphic region found in this study may have potential for the development of molecular markers for discrimination of field populations / isolates of this organism.", "output": "There is no related enetity." }, { "input": "Taxonomy and phylogeny of a new kleptoplastidal dinoflagellate, Gymnodinium myriopyrenoides sp. nov.", "output": "Gymnodinium myriopyrenoides." }, { "input": "( Gymnodiniales, Dinophyceae ), and its cryptophyte symbiont.", "output": "There is no related enetity." }, { "input": "A new kleptoplastidal dinoflagellate, Gymnodinium myriopyrenoides sp. nov., was described using light microscopy, electron microscopy and phylogengetic analysis based on partial LSU rDNA sequences.", "output": "Gymnodinium myriopyrenoides." }, { "input": "Cells were dorsiventrally flattened, elongate - elliptical in ventral view.", "output": "There is no related enetity." }, { "input": "There was no displacement of the cingulum encircling the anterior part of the cell.", "output": "There is no related enetity." }, { "input": "The cingulum was curved posteriorly at the terminal junction with the sulcus.", "output": "There is no related enetity." }, { "input": "The sulcus was generally narrow but expanded in the posterior end.", "output": "There is no related enetity." }, { "input": "The epicone possessed an apical groove made of one and one - half counterclockwise revolutions.", "output": "There is no related enetity." }, { "input": "Phylogenetic analysis based on LSU rDNA showed that the sequence of G. myriopyrenoides was included in the Gymnodiniales sensu stricto clade and had special affinities with the species Amphidinium poecilochroum and Gymnodinium acidotum, which also harbor kleptochloroplasts.", "output": "G . myriopyrenoides, Amphidinium poecilochroum, Gymnodinium acidotum." }, { "input": "Phylogenetic analysis based on plastid - encoded SSU rDNA and ultrastructural observations suggested that the symbionts of G. myriopyrenoides were cryptophytes of the genus Chroomonas or Hemiselmis.", "output": "G . myriopyrenoides." }, { "input": "Organelles including the nucleus, the nucleomorph, mitochondria, Golgi bodies and large chloroplasts remained in the cytoplasm of the symbionts, but not the periplast, ejectosomes or flagellar apparatus.", "output": "There is no related enetity." }, { "input": "The symbiotic level of G. myriopyrenoides was estimated to be a relatively early stage in the unarmored kleptoplastidal dinoflagellates.", "output": "G . myriopyrenoides." }, { "input": "No paradox, no progress: inverse cancer comorbidity in people with other complex diseases.", "output": "There is no related enetity." }, { "input": "In the past 5 years, several leading groups have attempted to explain why individuals with Down ' s syndrome have a reduced risk of many solid tumours and an increased risk of leukaemia and testicular cancer.", "output": "There is no related enetity." }, { "input": "Niels Bohr, the Danish physicist, noted that a paradox could initiate progress.", "output": "There is no related enetity." }, { "input": "We think that the paradox of a medical disorder protecting against cancer could be formalised in a new model of inverse cancer morbidity in people with other serious diseases.", "output": "There is no related enetity." }, { "input": "In this Personal View, we review evidence from epidemiological and clinical studies that supports a consistently lower than expected occurrence of cancer in patients with Down ' s syndrome, Parkinson ' s disease, schizophrenia, diabetes, Alzheimer ' s disease, multiple sclerosis, and anorexia nervosa.", "output": "There is no related enetity." }, { "input": "Intriguingly, most comorbidities are neuropsychiatric or CNS disorders.", "output": "There is no related enetity." }, { "input": "We provide a brief overview of evidence indicating genetic and molecular connections between cancer and these complex diseases.", "output": "There is no related enetity." }, { "input": "Inverse comorbidity could be a valuable model to investigate common or related pathways or processes and test new therapies, but, most importantly, to understand why certain people are protected from the malignancy.", "output": "There is no related enetity." }, { "input": "Milestones in Candida albicans gene manipulation.", "output": "Candida albicans." }, { "input": "In the United States, candidemia is one of the most common hospital - acquired infections and is estimated to cause 10, 000 deaths per year.", "output": "There is no related enetity." }, { "input": "The species Candida albicans is responsible for the majority of these cases.", "output": "Candida albicans." }, { "input": "As C. albicans is capable of developing resistance against the currently available drugs, understanding the molecular basis of drug resistance, finding new cellular targets, and further understanding the overall mechanism of C. albicans pathogenesis are important goals.", "output": "C . albicans, C . albicans." }, { "input": "To study this pathogen it is advantageous to manipulate its genome.", "output": "There is no related enetity." }, { "input": "Numerous strategies of C. albicans gene manipulation have been introduced.", "output": "C . albicans." }, { "input": "This review evaluates a majority of these strategies and should be a helpful guide for researchers to identify gene targeting strategies to suit their requirements.", "output": "There is no related enetity." }, { "input": "The pharmacological treatment of epilepsy in adults.", "output": "There is no related enetity." }, { "input": "Treatment decisions in epilepsy need to be individualised on the basis of careful analysis of the risk - benefit ratio of each available option.", "output": "There is no related enetity." }, { "input": "Key decision steps include the time at which antiepileptic drug treatment should be started, which drug should be chosen for first - line therapy, and which strategy is most appropriate for people who did not respond to the initially prescribed drug.", "output": "There is no related enetity." }, { "input": "With more than 20 antiepileptic drugs currently available to treat epilepsy in adults, opportunities to tailor drug therapy have never been greater, but optimum use of such a complex armamentarium is a challenge even for the epilepsy specialist.", "output": "There is no related enetity." }, { "input": "Antiepileptic drug choice is primarily based on evidence of efficacy and effectiveness for the individual ' s seizure type, but other patient - specific factors need to be considered, including age, sex, childbearing potential, comorbidities, and concomitant medications.", "output": "There is no related enetity." }, { "input": "Stroke and the immune system: from pathophysiology to new therapeutic strategies.", "output": "There is no related enetity." }, { "input": "Stroke is the second most common cause of death worldwide and a major cause of acquired disability in adults.", "output": "There is no related enetity." }, { "input": "Despite tremendous progress in understanding the pathophysiology of stroke, translation of this knowledge into effective therapies has largely failed, with the exception of thrombolysis, which only benefits a small proportion of patients.", "output": "There is no related enetity." }, { "input": "Systemic and local immune responses have important roles in causing stroke and are implicated in the primary and secondary progression of ischaemic lesions, as well as in repair, recovery, and overall outcome after a stroke.", "output": "There is no related enetity." }, { "input": "However, potential therapeutic targets in the immune system and inflammatory responses have not been well characterised.", "output": "There is no related enetity." }, { "input": "Development of novel and effective therapeutic strategies for stroke will require further investigation of these pathways in terms of their temporal profile ( before, during, and after stroke ) and risk - to - benefit therapeutic ratio of modulating them.", "output": "There is no related enetity." }, { "input": "Emerging targets and treatments in amyotrophic lateral sclerosis.", "output": "There is no related enetity." }, { "input": "Amyotrophic lateral sclerosis ( ALS ) is a progressive motor neuron disease that is currently untreatable.", "output": "There is no related enetity." }, { "input": "Many compounds have been tested in laboratory - based models and in patients with ALS, but so far only one drug, riluzole, has shown efficacy, yet it only slightly slows disease progression.", "output": "There is no related enetity." }, { "input": "Several new insights into the causes of motor neuron death have led to the identification of some important novel targets for intervention.", "output": "There is no related enetity." }, { "input": "At no time have studies involved such a wide range of innovations and such advanced technologies.", "output": "There is no related enetity." }, { "input": "Many promising studies are underway to test potential targets that will hopefully translate into meaningful therapeutics for patients with ALS.", "output": "There is no related enetity." }, { "input": "Hepatitis delta virus.", "output": "Hepatitis delta virus." }, { "input": "Hepatitis delta virus ( HDV ) is a small, defective RNA virus that can infect only individuals who have hepatitis B virus ( HBV ); worldwide more than 15 million people are co - infected.", "output": "Hepatitis delta virus, HDV, hepatitis B virus, HBV." }, { "input": "There are eight reported genotypes of HDV with unexplained variations in their geographical distribution and pathogenicity.", "output": "HDV." }, { "input": "The hepatitis D virion is composed of a coat of HBV envelope proteins surrounding the nucleocapsid, which consists of a single - stranded, circular RNA genome complexed with delta antigen, the viral protein.", "output": "hepatitis D, HBV." }, { "input": "HDV is clinically important because although it suppresses HBV replication, it causes severe liver disease with rapid progression to cirrhosis and hepatic decompensation.", "output": "HDV, HBV." }, { "input": "The range of clinical presentation is wide, varying from mild disease to fulminant liver failure.", "output": "There is no related enetity." }, { "input": "The prevalence of HDV is declining in some endemic areas but increasing in northern and central Europe because of immigration.", "output": "HDV." }, { "input": "Treatment of HDV is with pegylated interferon alfa; however, response rates are poor.", "output": "HDV." }, { "input": "Increased understanding of the molecular virology of HDV will identify novel therapeutic targets for this most severe form of chronic viral hepatitis.", "output": "HDV." }, { "input": "Altering sexual reproductive mode by interspecific exchange of MAT loci.", "output": "There is no related enetity." }, { "input": "Sexual fungi can be self - sterile ( heterothallic, requiring genetically distinct partners ) or self - fertile ( homothallic, no partner required ).", "output": "There is no related enetity." }, { "input": "In most ascomycetes, a single mating type locus ( MAT ) controls the ability to reproduce sexually.", "output": "There is no related enetity." }, { "input": "In the genus Cochliobolus, all heterothallic species have either MAT1 - 1 or MAT1 - 2 ( but never both ) in different individuals whereas all homothallic species carry both MAT1 - 1 and MAT1 - 2 in the same nucleus of an individual.", "output": "There is no related enetity." }, { "input": "It has been demonstrated, previously, that a MAT gene from homothallic Cochliobolus luttrellii can confer self - mating ability on a mat - deleted strain of its heterothallic relative, Cochliobolus heterostrophus.", "output": "Cochliobolus luttrellii, Cochliobolus heterostrophus." }, { "input": "In this reciprocal study, we expressed, separately, the heterothallic C. heterostrophus MAT1 - 1 - 1 and MAT1 - 2 - 1 genes in a mat - deleted homothallic C. luttrellii strain and asked if this converts homothallic C. luttrellii to heterothallism.", "output": "C . heterostrophus, C . luttrellii, C . luttrellii." }, { "input": "We report that: ( 1 ) A C. luttrellii transgenic strain carrying C. heterostrophus MAT1 - 1 - 1 and a C. luttrellii transgenic strain carrying C. heterostrophus MAT1 - 2 - 1 can mate in a heterothallic manner and the fertility of the cross is similar to that of a wild type C. luttrellii self.", "output": "C . luttrellii, C . heterostrophus, C . luttrellii, C . heterostrophus, C . luttrellii." }, { "input": "Full tetrads are always found.", "output": "There is no related enetity." }, { "input": "( 2 ) A C. luttrellii transgenic strain carrying C. heterostrophus MAT1 - 1 - 1 can mate with the parental wild type C. luttrellii MAT1 - 1; MAT1 - 2 strain, indicating the latter is able to outcross, a result which was expected but has not been demonstrated previously.", "output": "C . luttrellii, C . heterostrophus, C . luttrellii." }, { "input": "( 3 ) A C. luttrellii transgenic strain carrying C. heterostrophus MAT1 - 2 - 1 cannot mate with the parental wild type C. luttrellii MAT1 - 1; MAT1 - 2 strain, indicating outcrossing specificity.", "output": "C . luttrellii, C . heterostrophus, C . luttrellii." }, { "input": "( 4 ) Each transgenic C. luttrellii strain, carrying only a single C. heterostrophus MAT gene, is able to self, although all pseudothecia produced are smaller than those of wild type and fertility is low ( about 4 - 15 % of the number of wild type asci ).", "output": "C . luttrellii, C . heterostrophus." }, { "input": "These data support the argument that in Cochliobolus spp., the primary determinant of reproductive mode is MAT itself, and that a heterothallic strain can be made homothallic or a homothallic strain can be made heterothallic by exchange of MAT genes.", "output": "There is no related enetity." }, { "input": "The selfing ability of transgenic C. luttrellii strains also suggests that both MAT1 - 1 - 1 and MAT1 - 2 - 1 genes of C. heterostrophus carry equivalent transcription regulatory activities, each capable of promoting sexual development when alone, in a suitable genetic background.", "output": "C . luttrellii, C . heterostrophus." }, { "input": "Rate of egg maturation in marine turtles exhibits ' universal temperature dependence '.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "The metabolic theory of ecology ( MTE ) predicts that, after correcting for body mass variation among organisms, the rates of most biological processes will vary as a universal function of temperature.", "output": "There is no related enetity." }, { "input": "However, empirical support for ' universal temperature dependence ' ( UTD ) is currently equivocal and based on studies of a limited number of traits.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "In many ectothermic animals, the rate at which females produce mature eggs is temperature dependent and may be an important factor in determining the costs of reproduction.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "We tested whether the rate of egg maturation in marine turtles varies with environmental temperature as predicted by MTE, using the time separating successive clutches of individual females to estimate the rate at which eggs are formed.", "output": "There is no related enetity." }, { "input": "We also assessed the phenotypic contribution to this rate, by using radio telemetry to make repeated measurements of interclutch intervals for individual green turtles ( Chelonia mydas ).", "output": "green turtles, Chelonia mydas." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Rates of egg maturation increased with seasonally increasing water temperatures in radio - tracked green turtles, but were not repeatable for individual females, and did not vary according to maternal body size or reproductive investment ( number and size of eggs produced ).", "output": "green turtles." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "Using a collated data set from several different populations and species of marine turtles, we then show that a single relationship with water temperature explains most of the variation in egg maturation rates, with a slope that is statistically indistinguishable from the UTD predicted by MTE.", "output": "There is no related enetity." }, { "input": "However, several alternative statistical models also described the relationship between temperature and egg maturation rates equally parsimoniously.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "Our results offer novel support for the MTE ' s predicted UTD of biological rates, although the underlying mechanisms require further study.", "output": "There is no related enetity." }, { "input": "The strong temperature dependence of egg maturation combined with the apparently weak phenotypic contribution to this rate has interesting behavioural implications in ectothermic animals.", "output": "There is no related enetity." }, { "input": "We suggest that maternal thermoregulatory behaviour in marine turtles, and many other reptiles, is consistent with a strategy of adaptively increasing body temperatures to accelerate egg maturation.", "output": "There is no related enetity." }, { "input": "Host plant effects on alkaline phosphatase activity in the whiteflies, Bemisia tabaci Biotype B and Trialeurodes vaporariorum.", "output": "Bemisia tabaci, Trialeurodes vaporariorum." }, { "input": "Bemisia tabaci ( Gennadius ) B - biotype and Trialeurodes vaporariorum ( Westwood ) ( Hemiptera: Aleyrodidae ) often coexist on greenhouse - grown vegetable crops in northern China.", "output": "Bemisia tabaci, Trialeurodes vaporariorum." }, { "input": "The recent spread of B. tabaci B - biotype has largely replaced T. vaporariorum, and B - biotype now overlaps with T. vaporariorum where common hosts occur in most invaded areas.", "output": "B . tabaci, T . vaporariorum, T . vaporariorum." }, { "input": "The impact of the B - biotype on the agro eco system appears to be widespread, and involves the ability to compete with and perhaps replace other phytophages like T. vaporariorum.", "output": "T . vaporariorum." }, { "input": "An emerging hypothesis is that the B - biotype is physiologically superior due at least in part to an improved ability to metabolically utilize the alkaline phosphatase pathway.", "output": "There is no related enetity." }, { "input": "To test this hypothesis, alkaline phosphatase activity was studied in the B - biotype and T. vaporariorum after feeding on a number of different hosts for a range of durations, with and without host switching.", "output": "T . vaporariorum." }, { "input": "Alkaline phosphatase activity in T. vaporariorum was 1. 45 to 2. 53 - fold higher than that of the B - biotype when fed on tomato for 4 and 24 h, or switched from tomato to cotton and cabbage for the same durations.", "output": "T . vaporariorum, tomato, tomato, cotton, cabbage." }, { "input": "However, alkaline phosphatase activity in the B - biotype was 1. 40 to 3. 35 - fold higher than that of T. vaporariorum when the host switching time was - 72 and - 120 h on the same plant.", "output": "T . vaporariorum." }, { "input": "Both short - term ( 4 h ) and long - term ( 72 h ) switching of plant hosts can significantly affect the alkaline phosphatase activity in the two species.", "output": "There is no related enetity." }, { "input": "After - 120 h, feeding on tomato and cotton alkaline phosphatase activity in the B - biotype was significantly higher than that of T. vaporariorum.", "output": "tomato, cotton, T . vaporariorum." }, { "input": "It was shown that alkaline phosphatase aids the species feeding on different plant species, and that the B - biotype is physiologically superior to T. vaporariorum in utilizing the enzyme compared to T. vaporariorum over longer periods of feeding.", "output": "T . vaporariorum, T . vaporariorum." }, { "input": "Evidence to support karyotypic variation of the mosquito, Anopheles peditaeniatus in Thailand.", "output": "Anopheles peditaeniatus." }, { "input": "Eight isoline colonies of Anopheles peditaeniatus Leicester ( Diptera: Culicidae ) were established from wild - caught females collected from buffalo - baited traps at 8 localities in Thailand.", "output": "Anopheles peditaeniatus, buffalo." }, { "input": "They showed 2 types of X ( X ( 2 ), X ( 3 ) ) and 4 types of Y ( Y ( 2 ), Y ( 3 ), Y ( 4 ), Y ( 5 ) ) chromosomes based on the number and amount of major block ( s ) of heterochromatin present in the heterochromatic arm, and were tentatively designated as Forms B ( X ( 2 ), X ( 3 ), Y ( 2 ) ), C ( X ( 3 ), Y ( 3 ) ), D ( X ( 3 ), Y ( 4 ) ) and E ( X ( 2 ), X ( 3 ), Y ( 5 ) ).", "output": "There is no related enetity." }, { "input": "Form B was found in Nan, Ratchaburi, and Chumphon provinces; Form C was obtained in Chon Buri province; Form D was recovered in Kamphaeng Phet province; and Form E was acquired in Chiang Mai, Udon Thani, and Ubon Ratchathani provinces.", "output": "There is no related enetity." }, { "input": "Crossing studies among the 8 isoline colonies, which were representative of 4 karyotypic forms of An. peditaeniatus, revealed genetic compatibility in providing viable progenies and synaptic salivary gland polytene chromosomes through F ( 2 ) - generations, thus suggesting the conspecific nature of these karyotypic forms.", "output": "An . peditaeniatus." }, { "input": "These results were supported by the very low intraspecific sequence variations ( 0. 0 - 1. 1 % ) of the nucleotide sequences in ribosomal DNA ( ITS2 ) and mitochondrial DNA ( COI and COII ) of the 4 forms.", "output": "There is no related enetity." }, { "input": "A review of the implications of heterozygosity and inbreeding on germplasm biodiversity and its conservation in the silkworm, Bombyx mori.", "output": "silkworm, Bombyx mori." }, { "input": "Abstract Silkworm genebanks assume paramount importance as the reservoirs of biodiversity and source of alleles that can be easily retrieved for genetic enhancement of popular breeds.", "output": "Silkworm." }, { "input": "More than 4000 Bombyx mori L ( Lepidoptera: Bombycidae ) strains are currently available and these strains are maintained through continuous sibling mating.", "output": "Bombyx mori L." }, { "input": "This repeated sibling mating makes the populations of each strain more homozygous, but leads to loss of unique and valuable genes through the process of inbreeding depression.", "output": "There is no related enetity." }, { "input": "Hence, it is essential to maintain a minimal degree of heterozygosity within the population of each silkworm strain, especially in the traditional geographic strains, to avoid such loss.", "output": "silkworm." }, { "input": "As a result, accurate estimation of genetic diversity is becoming more important in silkworm genetic resources conservation.", "output": "silkworm." }, { "input": "Application of molecular markers help estimate genetic diversity much more accurately than that of morphological traits.", "output": "There is no related enetity." }, { "input": "Since a minimal amount of heterozygosity in each silkworm strain is essential for better conservation by avoiding inbreeding depression, this article overviews both theoretical and practical importance of heterozygosity together with impacts of inbreeding depression and the merits and demerits of neutral molecular markers for measurements of both heterozygosity and inbreeding depression in the silkworm Bombyx mori.", "output": "silkworm, silkworm, Bombyx mori." }, { "input": "Characterization of nonjunctional hemichannels in caterpillar cells.", "output": "There is no related enetity." }, { "input": "Recent studies have demonstrated that hemichannels, which form gap junctions when paired from apposing cells, may serve additional roles when unpaired including cell adhesion and paracrine communication.", "output": "There is no related enetity." }, { "input": "Hemichannels in mammals are formed by connexins or pannexins, while in insects they are formed by pannexin homologues termed innexins.", "output": "There is no related enetity." }, { "input": "The formation of functional gap junctions by insect innexins has been established, although their ability to form functional nonjunctional hemichannels has not been reported.", "output": "There is no related enetity." }, { "input": "Here the characteristics of nonjunctional hemichannels were examined in three lepidopteran cell types, two cell lines ( High Five and Sf9 ) and explanted hemocytes from Heliothis virescens ( Fabricius ) ( Lepidoptera: Noctuidae ).", "output": "Heliothis virescens." }, { "input": "Selective fluorescent dye uptake by hemichannels was observed in a significant minority of cells, using fluorescence microscopy and flow cytometry.", "output": "There is no related enetity." }, { "input": "Carbenoxelone, an inhibitor of mammalian junctions, disrupted dye uptake, while flufenamic acid and mefloquine did not.", "output": "There is no related enetity." }, { "input": "The presence of Ca ( 2 + ) and Mg ( 2 + ) in the media increased hemichannel activity.", "output": "There is no related enetity." }, { "input": "Additionally, lipopolysaccharide, a stimulator of immune activity in lepidopterans, decreased dye uptake.", "output": "There is no related enetity." }, { "input": "These results demonstrate for the first time the activity of nonjunctional hemichannels in insect cells, as well as pharmacological tools to manipulate them.", "output": "There is no related enetity." }, { "input": "These results will facilitate the further examination of the role of innexins and nonjunctional hemichannels in insect cell biology, including paracrine signaling, and comparative studies of mammalian pannexins and insect innexins.", "output": "There is no related enetity." }, { "input": "Post - egression host tissue feeding is another strategy of host regulation by the Koinobiont wasp, Toxoneuron nigriceps.", "output": "Toxoneuron nigriceps." }, { "input": "Koinobiont wasps start their lives as hemolymph feeders inside the host body, but before they egress from the host many become tissue predators.", "output": "There is no related enetity." }, { "input": "One species, the endoparasitoid Toxoneuron nigriceps Viereck ( Hymenoptera: Braconidae ), exhibits the unusual behavior of egressing before initiating tissue predation.", "output": "Toxoneuron nigriceps." }, { "input": "After egression from the host, it reinserts its head into the host body to begin tissue feeding.", "output": "There is no related enetity." }, { "input": "These third instar T. nigriceps larvae show a significant increase in body size and mass after post - egression feeding.", "output": "T . nigriceps." }, { "input": "Through this project the importance of post - egression feeding in the development of T. nigriceps in its host the tobacco budworm, Heliothis virescens Fabricius ( Lepidoptera: Noctuidae ), has been evaluated.", "output": "T . nigriceps, tobacco budworm, Heliothis virescens." }, { "input": "The study was conducted by preventing the egressed third instar T. nigriceps larvae from feeding on host tissue and observing whether they could undergo further development.", "output": "T . nigriceps." }, { "input": "Though some of the larvae that were prevented from post - egression feeding did undergo cocoon formation, pupation, and adult emergence they were inferior in terms of size, body mass, and survival to those that developed from larvae allowed to feeding after egression.", "output": "There is no related enetity." }, { "input": "Hence, it is concluded that post - egression host tissue feeding is essential for the normal development of T. nigriceps, as the prevention of feeding resulted in significantly lighter and smaller larvae, cocoons, and adults as well as deformed adults and reduced adult survival.", "output": "T . nigriceps." }, { "input": "Post - egression feeding as a host regulatory strategy is discussed.", "output": "There is no related enetity." }, { "input": "Evaluating aggregation membership and copulatory success in the stink bug, Euschistus conspersus, using field and laboratory experiments.", "output": "stink bug." }, { "input": "The aggregation and mating behavior of the stink bug, Euschistus conspersus Uhler ( Hemiptera: Pentatomidae ) was investigated in a series of field and laboratory experiments.", "output": "stink bug." }, { "input": "Marking of E. conspersus mating in aggregations in the field demonstrated that both sexes mate multiple times within aggregations on successive nights and with different partners, although = 20 % of the individuals of both sexes returned to aggregations but did not mate.", "output": "There is no related enetity." }, { "input": "Further analysis of mating patterns in caged aggregations revealed that heavy males and light females mated more frequently than their respective counterparts.", "output": "There is no related enetity." }, { "input": "Data are interpreted in terms of elucidating the function of benefits of multiple mating within aggregations for males and females.", "output": "There is no related enetity." }, { "input": "Occurrence of entomopathogenic fungi from agricultural and natural ecosystems in Saltillo, Mexico, and their virulence towards thrips and whiteflies.", "output": "There is no related enetity." }, { "input": "Entomopathogenic fungi were collected from soil in four adjacent habitats ( oak forest, agricultural soil, pine reforestation and chaparral habitat ) in Saltillo, Mexico using the insect bait method with Tenebrio molitor ( L. ) ( Coleoptera: Tenebrionidae ) larvae as bait.", "output": "Tenebrio molitor." }, { "input": "Overall, of the larvae exposed to soil, 171 ( 20 % ) hosted Beauveria bassiana ( Balsamo ) Vuillemin ( Hypocreales: Cordycipitaceae ), 25 ( 3 % ) hosted Metarhizium anisopliae ( Metschnikoff ) Sorokin ( Hypocreales: Clavicipitaceae ) and 1 ( 0. 1 % ) hosted lsaria ( = Paecilomyces ) sp.", "output": "Beauveria bassiana, Metarhizium anisopliae, lsaria ( = Paecilomyces ) sp .." }, { "input": "( Hypocreales: Cordycipitaceae ).", "output": "There is no related enetity." }, { "input": "B. bassiana was significantly more frequent on larvae exposed to oak forest soil.", "output": "B . bassiana." }, { "input": "M. anisopliae was significantly more frequent on larvae exposed to agricultural soil.", "output": "M . anisopliae." }, { "input": "From the infected bait insects, 93 isolates of B. bassiana and 24 isolates of M. anisopliae were obtained.", "output": "There is no related enetity." }, { "input": "Strains were tested for their infectivity against Cuban laurel thrips, Gynaikothrips uzeli Zimmerman ( Thysanoptera: Phlaeothripidae ) and the greenhouse whitefly, Trialeurodes vaporariorum ( Westwood ) ( Hemiptera: Aleyrodidae ).", "output": "Cuban laurel thrips, greenhouse whitefly, Trialeurodes vaporariorum." }, { "input": "B. bassiana isolates caused the highest mortality on thrips ( some causing 88 % mortality after 6 days ); both fungal species caused similarly high mortality levels against whiteflies ( 75 % ) after 6 days.", "output": "B . bassiana." }, { "input": "Large amounts of germplasm of entomopathogenic fungi, fundamentally B. bassiana and M. anisopliae, exist in the habitats sampled; pathogenicity varied among strains, and some strains possessed significant virulence.", "output": "B . bassiana, M . anisopliae." }, { "input": "Soils in these habitats are reservoirs of diverse strains with potential for use in biocontrol.", "output": "There is no related enetity." }, { "input": "Lasting effects of maternal behaviour on the distribution of a dispersive stream insect.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Predicting population dynamics at large spatial scales requires integrating information about spatial distribution patterns, inter - patch movement rates and within - patch processes.", "output": "There is no related enetity." }, { "input": "Advective dispersal of aquatic species by water movement is considered paramount to understanding their population dynamics.", "output": "There is no related enetity." }, { "input": "Rivers are model advective systems, and the larvae of baetid mayflies are considered quintessential dispersers.", "output": "There is no related enetity." }, { "input": "Egg laying of baetids along channels is patchy and reflects the distribution of oviposition sites, but larvae are assumed to drift frequently and far, thereby erasing patterns created during oviposition.", "output": "There is no related enetity." }, { "input": "Dispersal kernels are often overestimated, however, and empirical tests of such assumptions are warranted because of the pivotal role distribution patterns can have on populations.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We tested empirically whether the egg distribution patterns arising from oviposition behaviours persisted and were reflected in the distribution patterns of larval Baetis rhodani.", "output": "Baetis rhodani." }, { "input": "In field surveys, we tested for associations between egg mass and larval densities over 1 km lengths of four streams.", "output": "There is no related enetity." }, { "input": "A control species, the mayfly Ephemerella ignita, was employed to test for covarying environmental factors.", "output": "There is no related enetity." }, { "input": "We estimated drift rates directly to test whether larvae dispersed between riffles ( patches of high egg mass density ) and whether drift rates were density - dependent or density - related - expected outcomes if drift erases patterns established by maternal behaviours.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "Positive associations between egg masses and larval benthic densities were found for neonate and mid - stage larvae of Baetis, but not the control species, suggesting persistence of the patchy distribution patterns established at oviposition.", "output": "There is no related enetity." }, { "input": "Drift rates were high, and riffles were net exporters of neonate and mid - stage larvae, but drift rates were unrelated to benthic densities and few drifters reached the next riffle.", "output": "There is no related enetity." }, { "input": "Riffles were sinks for large larvae, suggesting ontogenetic shifts in habitat use, but little long - distance dispersal.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Overall, the results suggest that most neonate and mid - stage larvae of B. rhodani remain close to the natal riffle, and late - stage larvae disperse shorter distances than routinely assumed.", "output": "B . rhodani." }, { "input": "The persistence of maternal effects on distribution patterns well into juvenile life of an allegedly iconic disperser suggests that traditional models of how dispersal influences the population dynamics of many lotic invertebrates may be incorrect.", "output": "There is no related enetity." }, { "input": "Effects of individual condition and habitat quality on natal dispersal behaviour in a small rodent.", "output": "There is no related enetity." }, { "input": "1.", "output": "There is no related enetity." }, { "input": "Individuals should benefit from settling in high - quality habitats, but dispersers born under favourable conditions have a better physical condition and should therefore be more successful at settling in high - quality habitats.", "output": "There is no related enetity." }, { "input": "2.", "output": "There is no related enetity." }, { "input": "We tested these predictions with root voles ( Microtus oeconomus ) by a manipulation of individual condition through litter - size enlargement and reduction during lactation combined with a manipulation of habitat quality through degradation of the vegetation cover.", "output": "root voles, Microtus oeconomus." }, { "input": "We accurately monitored movements of 149 juveniles during a settlement and breeding period of 3 months.", "output": "There is no related enetity." }, { "input": "3.", "output": "There is no related enetity." }, { "input": "The litter size treatment had long - lasting effects on body size, life - history traits and home range size, but did not influence dispersal behaviour.", "output": "There is no related enetity." }, { "input": "4.", "output": "There is no related enetity." }, { "input": "Different stages of dispersal were influenced by habitat quality.", "output": "There is no related enetity." }, { "input": "In low - quality patches, females dispersed earlier, spent more time prospecting their environment before settling, and settlers had a smaller adult body size than in high - quality patches.", "output": "There is no related enetity." }, { "input": "Preference and competition for high - quality patches is likely adaptive as it increased fitness both in terms of survival and reproduction.", "output": "There is no related enetity." }, { "input": "5.", "output": "There is no related enetity." }, { "input": "We found no interactive effect of individual condition and habitat quality on natal dispersal and habitat selection.", "output": "There is no related enetity." }, { "input": "6.", "output": "There is no related enetity." }, { "input": "These findings suggest that immediate conditions are more important determinants of dispersal decisions than conditions experienced early in life.", "output": "There is no related enetity." }, { "input": "Nesting biology and fungiculture of the fungus - growing ant, Mycetagroicus cerradensis: new light on the origin of higher attine agriculture.", "output": "There is no related enetity." }, { "input": "The genus Mycetagroicus is perhaps the least known of all fungus - growing ant genera, having been first described in 2001 from museum specimens.", "output": "There is no related enetity." }, { "input": "A recent molecular phylogenetic analysis of the fungus - growing ants demonstrated that Mycetagroicus is the sister to all higher attine ants ( Trachymyrmex, Sericomyrmex, Acromyrmex, Pseudoatta, and Atta ), making it of extreme importance for understanding the transition between lower and higher attine agriculture.", "output": "There is no related enetity." }, { "input": "Four nests of Mycetagroicus cerradensis near Uberlandia, Minas Gerais, Brazil were excavated, and fungus chambers for one were located at a depth of 3. 5 meters.", "output": "There is no related enetity." }, { "input": "Based on its lack of gongylidia ( hyphal - tip swellings typical of higher attine cultivars ), and a phylogenetic analysis of the ITS rDNA gene region, M. cerradensis cultivates a lower attine fungus in Clade 2 of lower attine ( G3 ) fungi.", "output": "There is no related enetity." }, { "input": "This finding refines a previous estimate for the origin of higher attine agriculture, an event that can now be dated at approximately 21 - 25 mya in the ancestor of extant species of Trachymyrmex and Sericomyrmex.", "output": "There is no related enetity." }, { "input": "The role of body size and shape in understanding competitive interactions within a community of Neotropical dung beetles.", "output": "There is no related enetity." }, { "input": "Geometric morphometrics is helpful for understanding how body size and body shape influence the strength of inter - specific competitive interactions in a community.", "output": "There is no related enetity." }, { "input": "Dung beetles, characterized by their use of decomposing organic material, provide a useful model for understanding the structuring of ecological communities and the role of competition based on their size and morphology.", "output": "There is no related enetity." }, { "input": "The relationship between body size and shape in a dung beetle community from the Atlantic Forest in Serra do Japi, Brazil was analyzed for 39 species.", "output": "There is no related enetity." } ] }