cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22652597
title: A missense SNP in the proopiomelanocortin (POMC) gene is associated with growth traits in Awassi and Karakul sheep

description: This study was conducted to assess the association between proopiomelanocortin <i>(POMC)</i> gene and growth traits in Awassi and Karakul sheep. PCR-single strand conformation polymorphism (SSCP) method was utilized to assess the polymorphism of <i>POMC</i> PCR amplicons with body weight and length, wither and rump height, chest and abdominal circumference measured at birth, 3, 6, 9, and 12 months intervals. Only one missense SNP (rs424417456:C &gt; A) was detected in exon-2, in which glycine was converted to cysteine in the 65th position in POMC (p.65Gly &gt; Cys). rs424417456 SNP showed significant associations with all growth traits in the third, sixth, ninth, and twelfth months. At the age of 3 months onward, lambs with CC genotype showed higher body weight, body length, wither and rump heights, and chest and abdominal circumferences than lambs with CA and AA genotypes, respectively. Prediction analyses indicated a deleterious effect of p.65Gly &gt; Cys on POMC structure, function, and stability. Owing to the strong correlation between rs424417456:CC and better growth characteristics, this genotype is proposed as a promising marker to enhance growth traits in Awassi and Karakul sheep. The predicted damaging effects caused by rs424417456:CA and rs424417456:AA genotypes may entail a putative mechanism through which lambs with these genotypes exhibit lower growth traits.
DOI: 10.6084/m9.figshare.22652597.v1
title: A missense SNP in the proopiomelanocortin (POMC) gene is associated with growth traits in Awassi and Karakul sheep

description: This study was conducted to assess the association between proopiomelanocortin <i>(POMC)</i> gene and growth traits in Awassi and Karakul sheep. PCR-single strand conformation polymorphism (SSCP) method was utilized to assess the polymorphism of <i>POMC</i> PCR amplicons with body weight and length, wither and rump height, chest and abdominal circumference measured at birth, 3, 6, 9, and 12 months intervals. Only one missense SNP (rs424417456:C &gt; A) was detected in exon-2, in which glycine was converted to cysteine in the 65th position in POMC (p.65Gly &gt; Cys). rs424417456 SNP showed significant associations with all growth traits in the third, sixth, ninth, and twelfth months. At the age of 3 months onward, lambs with CC genotype showed higher body weight, body length, wither and rump heights, and chest and abdominal circumferences than lambs with CA and AA genotypes, respectively. Prediction analyses indicated a deleterious effect of p.65Gly &gt; Cys on POMC structure, function, and stability. Owing to the strong correlation between rs424417456:CC and better growth characteristics, this genotype is proposed as a promising marker to enhance growth traits in Awassi and Karakul sheep. The predicted damaging effects caused by rs424417456:CA and rs424417456:AA genotypes may entail a putative mechanism through which lambs with these genotypes exhibit lower growth traits.
DOI: 10.6084/m9.figshare.21595145.v1
title: Expression profiling of cytokine genes in peripheral blood mononuclear cells from <i>Anaplasma marginale</i> infected and healthy cattle

description: In this study, changes in expression profiles of genes encoding 14 cytokines (<i>IL1A, IL1B, IL2, IL4, IL6, IL8, IL10, IL12A, IL12B, IL16, IFNA, IFNB, TGFB</i>1, and <i>TNFA</i>) were investigated amongst six <i>Anaplasma marginale</i> infected and six healthy crossbred cattle. Health status of the animals was determined based on clinical signs, blood smear examination and molecular detection using <i>A. marginale</i>-specific primers. Total RNA was isolated from the peripheral blood mononuclear cells of the infected animals as well as the healthy controls, which was further reverse transcribed to cDNA. Primers for real time PCR were designed using Primer3 software and the results were analyzed by the 2<sup>–ΔΔCt</sup> method with <i>RPS15</i> and <i>GAPDH</i> as the reference genes. The expression levels of <i>IL1A, IL1B, IL6, IL10, IL12A, IL12B,</i> and <i>TNFA</i> varied significantly between the two groups, with higher expression in the infected cattle. The transcript abundance of <i>IL4, IL16,</i> and <i>TGFB1</i> did not vary between the diseased and healthy animals. The expression of <i>IL2</i> and <i>IL8</i> was higher in the healthy animals, but the results were non-significant. Taken together, this study provides evidence for difference in expression of cytokine genes in response to anaplasmosis in crossbred cattle.
DOI: 10.6084/m9.figshare.21595145
title: Expression profiling of cytokine genes in peripheral blood mononuclear cells from <i>Anaplasma marginale</i> infected and healthy cattle

description: In this study, changes in expression profiles of genes encoding 14 cytokines (<i>IL1A, IL1B, IL2, IL4, IL6, IL8, IL10, IL12A, IL12B, IL16, IFNA, IFNB, TGFB</i>1, and <i>TNFA</i>) were investigated amongst six <i>Anaplasma marginale</i> infected and six healthy crossbred cattle. Health status of the animals was determined based on clinical signs, blood smear examination and molecular detection using <i>A. marginale</i>-specific primers. Total RNA was isolated from the peripheral blood mononuclear cells of the infected animals as well as the healthy controls, which was further reverse transcribed to cDNA. Primers for real time PCR were designed using Primer3 software and the results were analyzed by the 2<sup>–ΔΔCt</sup> method with <i>RPS15</i> and <i>GAPDH</i> as the reference genes. The expression levels of <i>IL1A, IL1B, IL6, IL10, IL12A, IL12B,</i> and <i>TNFA</i> varied significantly between the two groups, with higher expression in the infected cattle. The transcript abundance of <i>IL4, IL16,</i> and <i>TGFB1</i> did not vary between the diseased and healthy animals. The expression of <i>IL2</i> and <i>IL8</i> was higher in the healthy animals, but the results were non-significant. Taken together, this study provides evidence for difference in expression of cytokine genes in response to anaplasmosis in crossbred cattle.
DOI: 10.6084/m9.figshare.22047322
title: Dynamic transcriptome analysis of Maiwa yak corpus luteum during the estrous cycle

description: Maiwa yak is a special breed of animal living on the Qinghai-Tibet Plateau, which has great economic value, but its fertility rate is low. The corpus luteum (CL) is a temporary tissue that plays a crucial role in maintaining the physiological cycle. However, little is known about the transcriptome profile in Maiwa yak CL. In the present study, the transcriptome of Maiwa yak CL at early (EYCL), middle (MYCL) and late-stages (LYCL) was studied employing high-throughput sequencing. A total of 25,922 transcripts were identified, including 22,277 known as well as 3,645 novel ones. Furthermore, 690 and 212 differentially expressed (DE) mRNAs were detected in the EYCL vs. MYCL and MYCL vs. LYCL groups, respectively. KEGG pathway enrichment analysis of DEGs illustrated that the most enriched pathway was PI3K-Akt pathway. Furthermore, twenty-six DEGs were totally found to be associated with different biological processes of CL development. One of these genes, <i>PGRMC1</i>, displayed a dynamical expression trend during the lifespan of yak CL. The knockdown of <i>PGRMC1</i> in luteinized yak granulosa cells resulted in defective steroidogenesis. In conclusion, this study analyzed the transcriptome profiles in yak CL of different stages, and provided a novel database for analyzing the gene network in yak CL.HIGHLIGHTSThe manuscript analyzed the transcriptome profiles in yak CL during the estrous cycle.Twenty-six DEGs were found to be associated with the development or function of CL.One of the DEGs, <i>PGRMC1</i>, was found to be responsible for steroidogenesis in luteinized yak granulosa cells. The manuscript analyzed the transcriptome profiles in yak CL during the estrous cycle. Twenty-six DEGs were found to be associated with the development or function of CL. One of the DEGs, <i>PGRMC1</i>, was found to be responsible for steroidogenesis in luteinized yak granulosa cells.
DOI: 10.6084/m9.figshare.22047322.v1
title: Dynamic transcriptome analysis of Maiwa yak corpus luteum during the estrous cycle

description: Maiwa yak is a special breed of animal living on the Qinghai-Tibet Plateau, which has great economic value, but its fertility rate is low. The corpus luteum (CL) is a temporary tissue that plays a crucial role in maintaining the physiological cycle. However, little is known about the transcriptome profile in Maiwa yak CL. In the present study, the transcriptome of Maiwa yak CL at early (EYCL), middle (MYCL) and late-stages (LYCL) was studied employing high-throughput sequencing. A total of 25,922 transcripts were identified, including 22,277 known as well as 3,645 novel ones. Furthermore, 690 and 212 differentially expressed (DE) mRNAs were detected in the EYCL vs. MYCL and MYCL vs. LYCL groups, respectively. KEGG pathway enrichment analysis of DEGs illustrated that the most enriched pathway was PI3K-Akt pathway. Furthermore, twenty-six DEGs were totally found to be associated with different biological processes of CL development. One of these genes, <i>PGRMC1</i>, displayed a dynamical expression trend during the lifespan of yak CL. The knockdown of <i>PGRMC1</i> in luteinized yak granulosa cells resulted in defective steroidogenesis. In conclusion, this study analyzed the transcriptome profiles in yak CL of different stages, and provided a novel database for analyzing the gene network in yak CL.HIGHLIGHTSThe manuscript analyzed the transcriptome profiles in yak CL during the estrous cycle.Twenty-six DEGs were found to be associated with the development or function of CL.One of the DEGs, <i>PGRMC1</i>, was found to be responsible for steroidogenesis in luteinized yak granulosa cells. The manuscript analyzed the transcriptome profiles in yak CL during the estrous cycle. Twenty-six DEGs were found to be associated with the development or function of CL. One of the DEGs, <i>PGRMC1</i>, was found to be responsible for steroidogenesis in luteinized yak granulosa cells.
DOI: 10.6084/m9.figshare.22183617
title: Population-wide genetic analysis of <i>Ovar-DQA1 and DQA2</i> loci across sheep breeds in India revealed their evolutionary importance and fitness of sheep in a tropical climate

description: Genetic variability at the major histocompatibility complex (MHC) is important in any species due to significant role played by MHC for antigen presentation. DQA locus has not been studied for its genetic variability across sheep population in India. In the present study, MHC of sheep at DQA1 and DQA2 loci were evaluated across 17 Indian sheep breeds. Results revealed high degree of heterozygosity (10.34% to 100% for DQA1 and 37.39 to 100% for DQA2). 18 DQA1 alleles and 22 DQA2 alleles were isolated in different breeds. Nucleotide content for DQA region revealed richness of AT content (54.85% for DQA1 and 53.89% for DQA2). DQA1 and DQA2 sequences clustered independently. We could see evidence of divergence of DQA as DQA1 and DQA2 across sheep breeds. Wu-Kabat variability index revealed vast genetic variation across DQA1 and DQA2, specifically at peptide binding sites (PBS) that consisted 21 residues for DQA1 and 17 residues for DQA2. Evolutionary analysis revealed the presence of positive and balancing selection for DQA1 locus, however DQA2 was under purifying selection across sheep breeds. Higher heterozygosity and large diversity at both loci especially at PBS indicated the fitness of the sheep population for evading pathogens and adapt to the harsh tropical climate.
DOI: 10.6084/m9.figshare.22183617.v1
title: Population-wide genetic analysis of <i>Ovar-DQA1 and DQA2</i> loci across sheep breeds in India revealed their evolutionary importance and fitness of sheep in a tropical climate

description: Genetic variability at the major histocompatibility complex (MHC) is important in any species due to significant role played by MHC for antigen presentation. DQA locus has not been studied for its genetic variability across sheep population in India. In the present study, MHC of sheep at DQA1 and DQA2 loci were evaluated across 17 Indian sheep breeds. Results revealed high degree of heterozygosity (10.34% to 100% for DQA1 and 37.39 to 100% for DQA2). 18 DQA1 alleles and 22 DQA2 alleles were isolated in different breeds. Nucleotide content for DQA region revealed richness of AT content (54.85% for DQA1 and 53.89% for DQA2). DQA1 and DQA2 sequences clustered independently. We could see evidence of divergence of DQA as DQA1 and DQA2 across sheep breeds. Wu-Kabat variability index revealed vast genetic variation across DQA1 and DQA2, specifically at peptide binding sites (PBS) that consisted 21 residues for DQA1 and 17 residues for DQA2. Evolutionary analysis revealed the presence of positive and balancing selection for DQA1 locus, however DQA2 was under purifying selection across sheep breeds. Higher heterozygosity and large diversity at both loci especially at PBS indicated the fitness of the sheep population for evading pathogens and adapt to the harsh tropical climate.
DOI: 10.6084/m9.figshare.22666177.v1
title: A missense mutation of the <i>WNK1</i> gene affects cold tolerance in Chinese domestic cattle

description: Inclement weather conditions, especially cold stress, have threatened the cattle industry. Cattle exposed to cold environments for a longer time suffer developmental delay, immunity decline, and eventually death. <i>WNK1</i> is a member of With-no-lysine kinases (<i>WNK</i>s), widely expressed in animal organs and tissues. <i>WNK1</i> and <i>WNK4</i> are expressed in adipose tissue, and <i>WNK4</i> promotes adipogenesis. <i>WNK1</i> does not directly affect adipogenesis but has been shown to promote <i>WNK4</i> expression in several tissues or organs. One missense mutation NC_037346.1:g.107692244, A &gt; G, rs208265410 in the <i>WNK1</i> gene was detected from the database of bovine genomic variation (BGVD). Here, we collected 328 individuals of 17 breeds representing four groups of Chinese cattle, northern group cattle, southern group cattle, central group cattle, and special group cattle (Tibetan cattle). We also collected the temperature and humidity data records from their relative locations. The frequencies of the G allele in Chinese breeds increased from northern China to southern China, and the frequencies of the A allele showed an opposite trend. Our results indicate that the <i>WNK1</i> gene might be a candidate gene marker associated with cold tolerance.
DOI: 10.6084/m9.figshare.19611342.v1
title: Transcriptomic analysis to elucidate the response of <i>Apis mellifera</i> ligustica brain tissue to fluvalinate exposure

description: As a commonly used acaricide in apiculture, fluvalinate is used to kill Varroa mites, while it also damages the nervous system of honeybees. To date, the transcriptomic characteristics associated with fluvalinate-induced neuronal injury in the bee brain have not been reported. Here, we performed transcriptome sequencing on <i>Apis mellifera</i> ligustica (<i>A. mellifera</i> ligustica) brain tissues collected before and after fluvalinate treatment. A total of 546 differentially expressed genes (DEGs) were detected, and these DEGs mainly showed 4 different expression patterns. Further analysis revealed that DEGs with different expression patterns were mainly involved in lipid metabolism, amino acid metabolism, visual transduction, and neural response-related GO terms and KEGG pathways. Moreover, protein–protein interaction network analysis revealed five protein-coding DEGs as key genes, which may play important roles in the resistance to fluvalinate-induced honeybee brain nerve tissue damage. In summary, this study is the first to perform a detailed characterization and functional analysis of genes related to fluvalinate stimulation in honeybee brains.
DOI: 10.6084/m9.figshare.22059481
title: Transcriptome profiling of bovine endometrial epithelial cells induced by lipopolysaccharides <i>in vitro</i>

description: Endometritis is an inflammation of the surface of the endometrium that does not penetrate the submucosa and can cause infertility and increase the elimination rate in cows. Endometrial epithelial cells are the first barrier of the endometrium against foreign stimuli and bacterial infection. Understanding the genetic changes in stimulated endometrial epithelial cells will help in the efforts to prevent and treat endometritis. This study investigated changes in bovine endometrial epithelial (BEEC) gene expression induced by lipopolysaccharide (LPS)-induced inflammation and compared transcriptome-wide gene changes between LPS- and phosphate-buffered saline (PBS)- treated BEECs by RNA sequencing. Compared with the PBS group, the LPS group showed 60 differentially expressed genes (DEGs) (36 upregulated, 24 downregulated). Gene Ontology enrichment analysis revealed that most enrichment occurred during CXCR chemokine receptor binding, inflammatory response, and neutrophil migration. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed DEGs mainly concentrated in cytokine–cytokine receptor interactions; IL-17, tumor necrosis factor, NOD-like receptor, chemokine, Toll-like receptor, and nuclear factor-κB signaling pathways; and the cytoplasmic DNA sensing pathway. Moreover, results revealed that cytokines <i>SAA3</i> and <i>HP</i> increased significantly after LPS treatment. These effects of LPS on BEECs transcriptome and the molecular mechanism of endometritis provide a basis for improved clinical treatment and novel drug development.
DOI: 10.6084/m9.figshare.22568094
title: CircRRAS2 promotes myogenic differentiation of bovine MuSCs and is a novel regulatory molecule of muscle development

description: The proliferation and myogenic differentiation of muscle stem cells (MuSCs) are important factors affecting muscle development and beef quality. There is increasing evidence that circRNAs can regulate myogenesis. We found a novel circRNA, named circRRAS2 that is significantly upregulated in the differentiation phase of bovine MuSCs. Here, we aimed to determine its roles in the proliferation and myogenic differentiation of these cells. The results showed that circRRAS2 was expressed in several bovine tissues. CircRRAS2 inhibited MuSCs proliferation and promoted myoblast differentiation. In addition, chromatin isolation by using RNA purification and mass spectrometry in differentiated muscle cells identified 52 RNA-binding proteins that could potentially bind to circRRAS2, in order to regulate their differentiation. The results suggest that circRRAS2 could be a specific regulator of myogenesis in bovine muscle.HighlightsCircRRAS2 expression is higher in DM cells than in GM cells.CircRRAS2 could significantly inhibit the proliferation and apoptosis of bovine MuSCs.CircRRAS2 promotes the differentiation of bovine MuSCs into myotubes.CircRRAS2 may exert regulatory effects through multiple RNA binding proteins. CircRRAS2 expression is higher in DM cells than in GM cells. CircRRAS2 could significantly inhibit the proliferation and apoptosis of bovine MuSCs. CircRRAS2 promotes the differentiation of bovine MuSCs into myotubes. CircRRAS2 may exert regulatory effects through multiple RNA binding proteins.
DOI: 10.6084/m9.figshare.23144100
title: Development and evaluation of gold nanoprobe based lateral flow device for rapid and sensitive serodetection of Bluetongue in sheep

description: Bluetongue (BT) disease is a viral, insect borne, noncontagious illness of small ruminants caused by <i>Orbivirus</i>, impacting huge economic loss worldwide. The existing BT diagnostic techniques are costly, time-consuming and require both specialized equipment and also skilled personnel. So there is need to develop a rapid, sensitive, on site detection assay for diagnosis of BT. This study utilized secondary antibody derivatized Gold nanoprobes for rapid and sensitive detection of BT over lateral flow device (LFD). The detection limit for this assay was found 1.875 µg of BT IgG/ml and a comparison between LFD and indirect ELISA was performed and the sensitivity and specificity was found at 96% and 99.23%, respectively, with observed kappa value of 0.952. This developed LFD may therefore offer a quick, affordable and accurate diagnosis of BT disease at the field level.
DOI: 10.6084/m9.figshare.22568094.v1
title: CircRRAS2 promotes myogenic differentiation of bovine MuSCs and is a novel regulatory molecule of muscle development

description: The proliferation and myogenic differentiation of muscle stem cells (MuSCs) are important factors affecting muscle development and beef quality. There is increasing evidence that circRNAs can regulate myogenesis. We found a novel circRNA, named circRRAS2 that is significantly upregulated in the differentiation phase of bovine MuSCs. Here, we aimed to determine its roles in the proliferation and myogenic differentiation of these cells. The results showed that circRRAS2 was expressed in several bovine tissues. CircRRAS2 inhibited MuSCs proliferation and promoted myoblast differentiation. In addition, chromatin isolation by using RNA purification and mass spectrometry in differentiated muscle cells identified 52 RNA-binding proteins that could potentially bind to circRRAS2, in order to regulate their differentiation. The results suggest that circRRAS2 could be a specific regulator of myogenesis in bovine muscle.HighlightsCircRRAS2 expression is higher in DM cells than in GM cells.CircRRAS2 could significantly inhibit the proliferation and apoptosis of bovine MuSCs.CircRRAS2 promotes the differentiation of bovine MuSCs into myotubes.CircRRAS2 may exert regulatory effects through multiple RNA binding proteins. CircRRAS2 expression is higher in DM cells than in GM cells. CircRRAS2 could significantly inhibit the proliferation and apoptosis of bovine MuSCs. CircRRAS2 promotes the differentiation of bovine MuSCs into myotubes. CircRRAS2 may exert regulatory effects through multiple RNA binding proteins.
DOI: 10.6084/m9.figshare.22666177
title: A missense mutation of the <i>WNK1</i> gene affects cold tolerance in Chinese domestic cattle

description: Inclement weather conditions, especially cold stress, have threatened the cattle industry. Cattle exposed to cold environments for a longer time suffer developmental delay, immunity decline, and eventually death. <i>WNK1</i> is a member of With-no-lysine kinases (<i>WNK</i>s), widely expressed in animal organs and tissues. <i>WNK1</i> and <i>WNK4</i> are expressed in adipose tissue, and <i>WNK4</i> promotes adipogenesis. <i>WNK1</i> does not directly affect adipogenesis but has been shown to promote <i>WNK4</i> expression in several tissues or organs. One missense mutation NC_037346.1:g.107692244, A &gt; G, rs208265410 in the <i>WNK1</i> gene was detected from the database of bovine genomic variation (BGVD). Here, we collected 328 individuals of 17 breeds representing four groups of Chinese cattle, northern group cattle, southern group cattle, central group cattle, and special group cattle (Tibetan cattle). We also collected the temperature and humidity data records from their relative locations. The frequencies of the G allele in Chinese breeds increased from northern China to southern China, and the frequencies of the A allele showed an opposite trend. Our results indicate that the <i>WNK1</i> gene might be a candidate gene marker associated with cold tolerance.