cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1569337.v1
title: Effects of cold stress and <i>Salmonella Heidelberg</i> infection on bacterial load and immunity of chickens.

description: We analyzed the effects of cold stress (19 ± 1°C, 6 h /day, from the 1<sup>st</sup> to the 7<sup>th</sup> days of life) applied to SPF chickens. On experimental Day 1 (ED1), chicks were divided into four groups: C (not infected and kept under thermoneutral condition); CS (not infected and cold stressed); PC (<i>Salmonella</i> Heidelberg (SH) infected and kept under thermoneutral condition) and PCS (SH infected and cold stressed). High concentrations of corticosterone were found in the cold stressed birds on ED7 and ED21, with a greater increase in birds of the PCS group. Stress or non-stressed SH-infected birds had high levels of norepinephrine on ED21. On ED21, an increased percentage and number of SH were found in birds of the PCS group. On ED7, a decrease in macrophages presenting MHCII, CD8<sup>+</sup> and CD8<sup>+</sup>γδ cells was observed in the chickens of the CS group. Decrease was observed in CD3<sup>+</sup>cells in the birds of the PCS group and increase in macrophages presenting MHCII cells and of the CD4<sup>+</sup>/CD8<sup>+</sup> ratio in chickens of the CS group on ED21. A decrease in CD8<sup>+</sup>γδ cells to birds of the CS group on ED21 and in the CD3<sup>+</sup> and CD8<sup>+</sup>cell numbers in chickens of the PCS group on ED21. Our results suggest that cold stress applied to chickens in the first 7 days of life increases both the hypothalamus pituitary adrenal axis and the sympathetic nervous system activities, leading to long-term immune cell dysfunction, thus allowing increased SH invasion and persistence within the animals’ body.Supplementary Data
DOI: 10.6084/m9.figshare.1569313
title: Whole genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case.

description: Supplementary Table 4 as published in <em>Microbial Genomics</em> in the article: 'Whole genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case.' [DOI: 10.1099/mgen.0.000042]
DOI: 10.6084/m9.figshare.1569313.v1
title: Whole genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case.

description: Supplementary Table 4 as published in <em>Microbial Genomics</em> in the article: 'Whole genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case.' [DOI: 10.1099/mgen.0.000042]
DOI: 10.6084/m9.figshare.1569306
title: Low Variation in a Y-Chromosomal Growth Hormone Pseudogene Relative to its Functional Autosomal Progenitor Gene in Chinook Salmon

description: Most fish species do not have single-chromosome-based sex determination or display cytologically distinguishable sex chromosomes. The selective forces acting on homologous sequences in diploid autosomal versus haploid sex-chromosomal regions are expected to be distinct and thus to differentially influence genetic variation. In Chinook Salmon <i>Oncorhynchus tshawytscha</i>, the Y chromosome possesses a growth hormone pseudogene (<i>ghp</i>) that is linked to the sex-determination locus and is derived from the functional autosomal growth hormone 2 gene (<i>gh2</i>). Thus, examining these two paralogues provides a model with which to study the forces affecting the persistence of genetic variation between sex-linked and autosomal loci among individuals in Chinook Salmon populations. We characterized single-nucleotide polymorphisms in a 1.6-kb contiguous homologous region in <i>gh2</i> and <i>ghp</i> in 315 individuals from 19 Chinook Salmon populations ranging from Russia to Alaska, British Columbia, and California. The <i>ghp</i> sequence was highly similar among individuals and populations, with variant haplotypes being detected in only 5.4% of individuals and restricted to just two populations. In contrast, <i>gh2</i> variants from the most common haplotype were found in 46.7% of individuals. We detected more sites of variation in <i>ghp</i> (nine positions, five haplotypes) than in <i>gh2</i> (three positions, five haplotypes), but these were restricted to just four genotypes for <i>ghp</i>, compared with nine for <i>gh2</i>. Selection may have caused a single Y chromosome to become fixed among most populations in this species, while the variation at the <i>gh2</i> locus is maintained under diploid autosomal conditions. Since the <i>ghp</i> locus variants are not likely to be directly associated with strong functions, other linked Y<i>-</i>chromosomal loci may have important functions that, when selected, cause Y chromosomes to either be damaged and rapidly eliminated or to have enhanced fitness and sweep through the species. Whether such loci include the sex-determination locus itself or other functional loci is not yet known.Received January 15, 2015; accepted June 3, 2015
DOI: 10.6084/m9.figshare.1569306.v1
title: Low Variation in a Y-Chromosomal Growth Hormone Pseudogene Relative to its Functional Autosomal Progenitor Gene in Chinook Salmon

description: Most fish species do not have single-chromosome-based sex determination or display cytologically distinguishable sex chromosomes. The selective forces acting on homologous sequences in diploid autosomal versus haploid sex-chromosomal regions are expected to be distinct and thus to differentially influence genetic variation. In Chinook Salmon <i>Oncorhynchus tshawytscha</i>, the Y chromosome possesses a growth hormone pseudogene (<i>ghp</i>) that is linked to the sex-determination locus and is derived from the functional autosomal growth hormone 2 gene (<i>gh2</i>). Thus, examining these two paralogues provides a model with which to study the forces affecting the persistence of genetic variation between sex-linked and autosomal loci among individuals in Chinook Salmon populations. We characterized single-nucleotide polymorphisms in a 1.6-kb contiguous homologous region in <i>gh2</i> and <i>ghp</i> in 315 individuals from 19 Chinook Salmon populations ranging from Russia to Alaska, British Columbia, and California. The <i>ghp</i> sequence was highly similar among individuals and populations, with variant haplotypes being detected in only 5.4% of individuals and restricted to just two populations. In contrast, <i>gh2</i> variants from the most common haplotype were found in 46.7% of individuals. We detected more sites of variation in <i>ghp</i> (nine positions, five haplotypes) than in <i>gh2</i> (three positions, five haplotypes), but these were restricted to just four genotypes for <i>ghp</i>, compared with nine for <i>gh2</i>. Selection may have caused a single Y chromosome to become fixed among most populations in this species, while the variation at the <i>gh2</i> locus is maintained under diploid autosomal conditions. Since the <i>ghp</i> locus variants are not likely to be directly associated with strong functions, other linked Y<i>-</i>chromosomal loci may have important functions that, when selected, cause Y chromosomes to either be damaged and rapidly eliminated or to have enhanced fitness and sweep through the species. Whether such loci include the sex-determination locus itself or other functional loci is not yet known.Received January 15, 2015; accepted June 3, 2015
DOI: 10.6084/m9.figshare.1569306.v2
title: Low Variation in a Y-Chromosomal Growth Hormone Pseudogene Relative to its Functional Autosomal Progenitor Gene in Chinook Salmon

description: Most fish species do not have single-chromosome-based sex determination or display cytologically distinguishable sex chromosomes. The selective forces acting on homologous sequences in diploid autosomal versus haploid sex-chromosomal regions are expected to be distinct and thus to differentially influence genetic variation. In Chinook Salmon <i>Oncorhynchus tshawytscha</i>, the Y chromosome possesses a growth hormone pseudogene (<i>ghp</i>) that is linked to the sex-determination locus and is derived from the functional autosomal growth hormone 2 gene (<i>gh2</i>). Thus, examining these two paralogues provides a model with which to study the forces affecting the persistence of genetic variation between sex-linked and autosomal loci among individuals in Chinook Salmon populations. We characterized single-nucleotide polymorphisms in a 1.6-kb contiguous homologous region in <i>gh2</i> and <i>ghp</i> in 315 individuals from 19 Chinook Salmon populations ranging from Russia to Alaska, British Columbia, and California. The <i>ghp</i> sequence was highly similar among individuals and populations, with variant haplotypes being detected in only 5.4% of individuals and restricted to just two populations. In contrast, <i>gh2</i> variants from the most common haplotype were found in 46.7% of individuals. We detected more sites of variation in <i>ghp</i> (nine positions, five haplotypes) than in <i>gh2</i> (three positions, five haplotypes), but these were restricted to just four genotypes for <i>ghp</i>, compared with nine for <i>gh2</i>. Selection may have caused a single Y chromosome to become fixed among most populations in this species, while the variation at the <i>gh2</i> locus is maintained under diploid autosomal conditions. Since the <i>ghp</i> locus variants are not likely to be directly associated with strong functions, other linked Y<i>-</i>chromosomal loci may have important functions that, when selected, cause Y chromosomes to either be damaged and rapidly eliminated or to have enhanced fitness and sweep through the species. Whether such loci include the sex-determination locus itself or other functional loci is not yet known.Received January 15, 2015; accepted June 3, 2015
DOI: 10.6084/m9.figshare.1569306.v4
title: Low Variation in a Y-Chromosomal Growth Hormone Pseudogene Relative to its Functional Autosomal Progenitor Gene in Chinook Salmon

description: Most fish species do not have single-chromosome-based sex determination or display cytologically distinguishable sex chromosomes. The selective forces acting on homologous sequences in diploid autosomal versus haploid sex-chromosomal regions are expected to be distinct and thus to differentially influence genetic variation. In Chinook Salmon <i>Oncorhynchus tshawytscha</i>, the Y chromosome possesses a growth hormone pseudogene (<i>ghp</i>) that is linked to the sex-determination locus and is derived from the functional autosomal growth hormone 2 gene (<i>gh2</i>). Thus, examining these two paralogues provides a model with which to study the forces affecting the persistence of genetic variation between sex-linked and autosomal loci among individuals in Chinook Salmon populations. We characterized single-nucleotide polymorphisms in a 1.6-kb contiguous homologous region in <i>gh2</i> and <i>ghp</i> in 315 individuals from 19 Chinook Salmon populations ranging from Russia to Alaska, British Columbia, and California. The <i>ghp</i> sequence was highly similar among individuals and populations, with variant haplotypes being detected in only 5.4% of individuals and restricted to just two populations. In contrast, <i>gh2</i> variants from the most common haplotype were found in 46.7% of individuals. We detected more sites of variation in <i>ghp</i> (nine positions, five haplotypes) than in <i>gh2</i> (three positions, five haplotypes), but these were restricted to just four genotypes for <i>ghp</i>, compared with nine for <i>gh2</i>. Selection may have caused a single Y chromosome to become fixed among most populations in this species, while the variation at the <i>gh2</i> locus is maintained under diploid autosomal conditions. Since the <i>ghp</i> locus variants are not likely to be directly associated with strong functions, other linked Y<i>-</i>chromosomal loci may have important functions that, when selected, cause Y chromosomes to either be damaged and rapidly eliminated or to have enhanced fitness and sweep through the species. Whether such loci include the sex-determination locus itself or other functional loci is not yet known.Received January 15, 2015; accepted June 3, 2015
DOI: 10.6084/m9.figshare.1569306.v3
title: Low Variation in a Y-Chromosomal Growth Hormone Pseudogene Relative to its Functional Autosomal Progenitor Gene in Chinook Salmon

description: Most fish species do not have single-chromosome-based sex determination or display cytologically distinguishable sex chromosomes. The selective forces acting on homologous sequences in diploid autosomal versus haploid sex-chromosomal regions are expected to be distinct and thus to differentially influence genetic variation. In Chinook Salmon <i>Oncorhynchus tshawytscha</i>, the Y chromosome possesses a growth hormone pseudogene (<i>ghp</i>) that is linked to the sex-determination locus and is derived from the functional autosomal growth hormone 2 gene (<i>gh2</i>). Thus, examining these two paralogues provides a model with which to study the forces affecting the persistence of genetic variation between sex-linked and autosomal loci among individuals in Chinook Salmon populations. We characterized single-nucleotide polymorphisms in a 1.6-kb contiguous homologous region in <i>gh2</i> and <i>ghp</i> in 315 individuals from 19 Chinook Salmon populations ranging from Russia to Alaska, British Columbia, and California. The <i>ghp</i> sequence was highly similar among individuals and populations, with variant haplotypes being detected in only 5.4% of individuals and restricted to just two populations. In contrast, <i>gh2</i> variants from the most common haplotype were found in 46.7% of individuals. We detected more sites of variation in <i>ghp</i> (nine positions, five haplotypes) than in <i>gh2</i> (three positions, five haplotypes), but these were restricted to just four genotypes for <i>ghp</i>, compared with nine for <i>gh2</i>. Selection may have caused a single Y chromosome to become fixed among most populations in this species, while the variation at the <i>gh2</i> locus is maintained under diploid autosomal conditions. Since the <i>ghp</i> locus variants are not likely to be directly associated with strong functions, other linked Y<i>-</i>chromosomal loci may have important functions that, when selected, cause Y chromosomes to either be damaged and rapidly eliminated or to have enhanced fitness and sweep through the species. Whether such loci include the sex-determination locus itself or other functional loci is not yet known.Received January 15, 2015; accepted June 3, 2015
DOI: 10.6084/m9.figshare.1569280
title: A simple and versatile protocol for the preparation of functionalized heterocycles utilizing 4-benzoyl-5-phenylamino-2,3-dihydrothiophene-2,3-dione

description: The reaction of ethyl benzoylpyruvate with phenyl isothiocyanate in alkaline medium yields 4-benzoyl-5-phenylamino-2,3-dihydrothiophene-2,3-dione (<b>1</b>). Reaction of the intermediate <b>1</b> with primary aromatic amines such as aniline derivatives, benzidine and secondary aliphatic amines, namely diethylamine, piperidine, morpholine and piperazine afforded the corresponding thiophene <b>2a–2g</b> and amide <b>3a–3d</b> derivatives. Compound <b>1</b> reacts with <i>N,N</i>′- and <i>N,O</i>-dinucleophiles such as 1,2-diaminoalkanes, 2-aminoethanol, 1-aminoguanidine, guanidine, urea, 1,2-phenylenediamine and 2-amino-4-methylphenol to form the heterocylic compounds <b>4–10</b>.
DOI: 10.6084/m9.figshare.1569280.v1
title: A simple and versatile protocol for the preparation of functionalized heterocycles utilizing 4-benzoyl-5-phenylamino-2,3-dihydrothiophene-2,3-dione

description: The reaction of ethyl benzoylpyruvate with phenyl isothiocyanate in alkaline medium yields 4-benzoyl-5-phenylamino-2,3-dihydrothiophene-2,3-dione (<b>1</b>). Reaction of the intermediate <b>1</b> with primary aromatic amines such as aniline derivatives, benzidine and secondary aliphatic amines, namely diethylamine, piperidine, morpholine and piperazine afforded the corresponding thiophene <b>2a–2g</b> and amide <b>3a–3d</b> derivatives. Compound <b>1</b> reacts with <i>N,N</i>′- and <i>N,O</i>-dinucleophiles such as 1,2-diaminoalkanes, 2-aminoethanol, 1-aminoguanidine, guanidine, urea, 1,2-phenylenediamine and 2-amino-4-methylphenol to form the heterocylic compounds <b>4–10</b>.
DOI: 10.6084/m9.figshare.12918698.v2
title: nehirdata.sav

description: This research data belong to my research paper regarding "The relationship between parenting attitudes and perceived narcissism in young adults in Turkey".
DOI: 10.6084/m9.figshare.1569267
title: A defect of the vacuolar putative lipase Atg15 accelerates degradation of lipid droplets through lipolysis

description: Lipid droplets (LDs) are the conserved organelles for the deposit of neutral lipids, and function as reservoirs of membrane and energy sources. To date, functional links between autophagy and LD dynamics have not been fully elucidated. Here, we report that a vacuolar putative lipase, Atg15, required for degradation of autophagic bodies, is crucial for the maintenance of LD amount in the yeast <i>Saccharomyces cerevisiae</i> in the stationary phase. Mutant analyses revealed that the putative lipase motif and vacuolar localization of Atg15 are important for the maintenance of LD amount. Loss of autophagosome formation by simultaneous deletion of core <i>ATG</i> genes cancelled the reduction in the LD amount in <i>ATG15</i>-deleted cells, indicating that degradation of autophagic bodies accounts for the functional involvement of Atg15 in LD dynamics. The reduced level of LDs in the mutant strain was dependent on Tgl3 and Tgl4, major lipases for lipolysis in <i>S. cerevisiae</i>. An altered phosphorylation status of Tgl3, higher accumulation of Tgl4, and closer associations of Tgl3 and Tgl4 with LDs were detected in the <i>ATG15</i>-deleted cells. Furthermore, increased levels of downstream metabolites of lipolysis in the mutant strain strongly suggested enhanced lipolytic activity caused by loss of <i>ATG15</i>. Our data provide evidence for a novel link between autophagic flux and LD dynamics integrated with Atg15 activity.
DOI: 10.6084/m9.figshare.1569267.v2
title: A defect of the vacuolar putative lipase Atg15 accelerates degradation of lipid droplets through lipolysis

description: Lipid droplets (LDs) are the conserved organelles for the deposit of neutral lipids, and function as reservoirs of membrane and energy sources. To date, functional links between autophagy and LD dynamics have not been fully elucidated. Here, we report that a vacuolar putative lipase, Atg15, required for degradation of autophagic bodies, is crucial for the maintenance of LD amount in the yeast <i>Saccharomyces cerevisiae</i> in the stationary phase. Mutant analyses revealed that the putative lipase motif and vacuolar localization of Atg15 are important for the maintenance of LD amount. Loss of autophagosome formation by simultaneous deletion of core <i>ATG</i> genes cancelled the reduction in the LD amount in <i>ATG15</i>-deleted cells, indicating that degradation of autophagic bodies accounts for the functional involvement of Atg15 in LD dynamics. The reduced level of LDs in the mutant strain was dependent on Tgl3 and Tgl4, major lipases for lipolysis in <i>S. cerevisiae</i>. An altered phosphorylation status of Tgl3, higher accumulation of Tgl4, and closer associations of Tgl3 and Tgl4 with LDs were detected in the <i>ATG15</i>-deleted cells. Furthermore, increased levels of downstream metabolites of lipolysis in the mutant strain strongly suggested enhanced lipolytic activity caused by loss of <i>ATG15</i>. Our data provide evidence for a novel link between autophagic flux and LD dynamics integrated with Atg15 activity.
DOI: 10.6084/m9.figshare.1569266.v2
title: Mitochondrial outer-membrane E3 ligase MUL1 ubiquitinates ULK1 and regulates selenite-induced mitophagy

description: Mitochondria serve as membrane sources and signaling platforms for regulating autophagy. Accumulating evidence has also shown that damaged mitochondria are removed through both selective mitophagy and general autophagy in response to mitochondrial and oxidative stresses. Protein ubiquitination through mitochondrial E3 ligases plays an integrative role in mitochondrial outer membrane protein degradation, mitochondrial dynamics, and mitophagy. Here we showed that MUL1, a mitochondria-localized E3 ligase, regulates selenite-induced mitophagy in an ATG5 and ULK1-dependent manner. ULK1 partially translocated to mitochondria after selenite treatment and interacted with MUL1. We also demonstrated that ULK1 is a novel substrate of MUL1. These results suggest the association of mitochondria with autophagy regulation and provide a new mechanism for the beneficial effects of selenium as a chemopreventive agent.
DOI: 10.6084/m9.figshare.1569267.v1
title: A defect of the vacuolar putative lipase Atg15 accelerates degradation of lipid droplets through lipolysis

description: Lipid droplets (LDs) are the conserved organelles for the deposit of neutral lipids, and function as reservoirs of membrane and energy sources. To date, functional links between autophagy and LD dynamics have not been fully elucidated. Here, we report that a vacuolar putative lipase, Atg15, required for degradation of autophagic bodies, is crucial for the maintenance of LD amount in the yeast <i>Saccharomyces cerevisiae</i> in the stationary phase. Mutant analyses revealed that the putative lipase motif and vacuolar localization of Atg15 are important for the maintenance of LD amount. Loss of autophagosome formation by simultaneous deletion of core <i>ATG</i> genes cancelled the reduction in the LD amount in <i>ATG15</i>-deleted cells, indicating that degradation of autophagic bodies accounts for the functional involvement of Atg15 in LD dynamics. The reduced level of LDs in the mutant strain was dependent on Tgl3 and Tgl4, major lipases for lipolysis in <i>S. cerevisiae</i>. An altered phosphorylation status of Tgl3, higher accumulation of Tgl4, and closer associations of Tgl3 and Tgl4 with LDs were detected in the <i>ATG15</i>-deleted cells. Furthermore, increased levels of downstream metabolites of lipolysis in the mutant strain strongly suggested enhanced lipolytic activity caused by loss of <i>ATG15</i>. Our data provide evidence for a novel link between autophagic flux and LD dynamics integrated with Atg15 activity.
DOI: 10.6084/m9.figshare.1569266.v1
title: Mitochondrial outer-membrane E3 ligase MUL1 ubiquitinates ULK1 and regulates selenite-induced mitophagy

description: Mitochondria serve as membrane sources and signaling platforms for regulating autophagy. Accumulating evidence has also shown that damaged mitochondria are removed through both selective mitophagy and general autophagy in response to mitochondrial and oxidative stresses. Protein ubiquitination through mitochondrial E3 ligases plays an integrative role in mitochondrial outer membrane protein degradation, mitochondrial dynamics, and mitophagy. Here we showed that MUL1, a mitochondria-localized E3 ligase, regulates selenite-induced mitophagy in an ATG5 and ULK1-dependent manner. ULK1 partially translocated to mitochondria after selenite treatment and interacted with MUL1. We also demonstrated that ULK1 is a novel substrate of MUL1. These results suggest the association of mitochondria with autophagy regulation and provide a new mechanism for the beneficial effects of selenium as a chemopreventive agent.