cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17704983.v1
title: Genome-wide identification and analysis of TMT-based proteomes in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle

description: With the gradual completion of the human genome project, proteomes have gained extremely important value in the fields of human disease and biological process research. In our previous research, we performed transcriptomic analyses of longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle and conducted in-depth studies on the muscles of both species through epigenetics. However, it is unclear whether differentially expressed proteins in Kazakh cattle and Xinjiang brown cattle regulate muscle production and development. In this study, a proteomic analysis was performed on Xinjiang brown cattle and Kazakh cattle by using TMT markers, HPLC classification, LC/MS and bioinformatics analysis. A total of 13,078 peptides were identified, including 11,258 unique peptides. We identified a total of 1874 proteins, among which 1565 were quantifiable. Compared to Kazakh cattle, Xinjiang brown cattle exhibited 75 upregulated proteins and 44 downregulated proteins. These differentially expressed proteins were enriched for the functions of adrenergic signaling in cardiomyocytes, fatty acid degradation and glutathione metabolism. In our research, we found differentially expressed proteins in longissimus dorsi tissue between Kazakh cattle and Xinjiang brown cattle. We predict that these proteins regulate muscle production and development through select enriched signaling pathways. This study provides novel insights into the roles of proteomes in cattle genetics and breeding.
DOI: 10.6084/m9.figshare.19308214.v1
title: Comparative gene expression profile in circulating PBMCs of <i>Bos indicus</i> and crossbred cattle to understand disease tolerance mechanism

description: The present investigation was performed to compare the global gene expression profile in peripheral blood mononuclear cells (PBMCs) of <i>Bos indicus</i> and crossbred (<i>Bos taurus</i> × <i>B. indicus</i>) cattle. Previously, several studies revealed the disease tolerance potential of <i>B. indicus</i> cattle but underlying genetic mechanism is still not fully explored. The PBMCs model was used for this investigation as it plays crucial role in the immune system regulation. Transcriptomic analysis revealed total 6767 significantly differentially expressed transcripts (fold change (absolute) &gt;2.0, <i>p</i> &lt; .05). In addition, 4149 transcripts were upregulated, 2618 transcripts were downregulated and fold change (absolute) of differentially expressed transcript varied from −223.32 to 213.63. Functional annotation analysis of differentially expressed genes confirmed their role in various molecular pathways <i>viz.</i> innate immune response, antigen processing and presentation, MHC protein complex, defense response to bacterium, regulation of immune response, positive regulation of JAK-STAT cascade, cytoskeletal protein binding, etc. Protein–protein interaction network analysis provided understanding of inter-relationship of immune genes with differentially expressed genes. In conclusion, this study could provide comprehensive information about the dysregulated genes and biological pathways in PBMCs which might be responsible for disease tolerance in <i>B. indicus</i> cattle.
DOI: 10.6084/m9.figshare.17711334
title: <i>TAS2R16</i> introgression from banteng into indigenous Chinese cattle

description: Historical hybridization between southern indigenous Chinese cattle and banteng has been well-documented and has resulted in gene introgression. Bitter taste receptors were reported in indigenous cattle as a result of introgression from banteng. To determine the level of introgression of the taste 2 receptor member 16 (<i>TAS2R16</i>) gene from banteng into Chinese cattle, two missense mutations in the bovine <i>TAS2R16</i> gene were examined. Here, we explored the prevalence of the two variants in 28 indigenous Chinese cattle and banteng breeds (comprising 750 individuals) to determine the influence of banteng introgressions on Chinese cattle based on PCR and DNA sequencing. In our study, the two mutant alleles had a higher frequency distribution in southern China with strong geographic distribution, especially in the south-central and southeast areas. In conclusion, this study examines the impact of introgression on the frequency distributions of mutations in variable regions and the subsequent adaptation of Chinese indigenous cattle to different environmental conditions.
DOI: 10.6084/m9.figshare.17711334.v1
title: <i>TAS2R16</i> introgression from banteng into indigenous Chinese cattle

description: Historical hybridization between southern indigenous Chinese cattle and banteng has been well-documented and has resulted in gene introgression. Bitter taste receptors were reported in indigenous cattle as a result of introgression from banteng. To determine the level of introgression of the taste 2 receptor member 16 (<i>TAS2R16</i>) gene from banteng into Chinese cattle, two missense mutations in the bovine <i>TAS2R16</i> gene were examined. Here, we explored the prevalence of the two variants in 28 indigenous Chinese cattle and banteng breeds (comprising 750 individuals) to determine the influence of banteng introgressions on Chinese cattle based on PCR and DNA sequencing. In our study, the two mutant alleles had a higher frequency distribution in southern China with strong geographic distribution, especially in the south-central and southeast areas. In conclusion, this study examines the impact of introgression on the frequency distributions of mutations in variable regions and the subsequent adaptation of Chinese indigenous cattle to different environmental conditions.
DOI: 10.6084/m9.figshare.19047455
title: Transcriptome analysis of miRNAs during myoblasts adipogenic differentiation

description: Intramuscular fat content is closely related to meat quality traits and has high heritability. miRNAs are a class of small non-coding RNA, which are highly conserved in animals and play important regulatory roles in adipogenesis. Therefore, they can be used as molecular markers for meat quality traits. Herein, we used <i>in vitro</i> model of myoblasts adipogenic differentiation to screen differential miRNAs by RNA-seq. A total of 71 differentially miRNAs were filtered, including 31 up-regulated miRNAs and 40 down-regulated miRNAs. Since, we selected 18 miRNAs for RT-qPCR validation, including some miRNAs likely miR-146a-5p, miR-210-3p, miR-199a, miR-224, and miR-214-3p that play important regulatory roles in adipogenesis. In addition, functional enrichment analysis results revealed that members of miRNA target genes were enriched into insulin signaling pathway and MAPK signaling pathway, which are closely related to adipogenesis. Taken together, these data will contribute to further investigate the function of miRNAs in intramuscular fat deposition. These differentially miRNAs can be developed as biomarkers for animal breeding.
DOI: 10.6084/m9.figshare.19047455.v1
title: Transcriptome analysis of miRNAs during myoblasts adipogenic differentiation

description: Intramuscular fat content is closely related to meat quality traits and has high heritability. miRNAs are a class of small non-coding RNA, which are highly conserved in animals and play important regulatory roles in adipogenesis. Therefore, they can be used as molecular markers for meat quality traits. Herein, we used <i>in vitro</i> model of myoblasts adipogenic differentiation to screen differential miRNAs by RNA-seq. A total of 71 differentially miRNAs were filtered, including 31 up-regulated miRNAs and 40 down-regulated miRNAs. Since, we selected 18 miRNAs for RT-qPCR validation, including some miRNAs likely miR-146a-5p, miR-210-3p, miR-199a, miR-224, and miR-214-3p that play important regulatory roles in adipogenesis. In addition, functional enrichment analysis results revealed that members of miRNA target genes were enriched into insulin signaling pathway and MAPK signaling pathway, which are closely related to adipogenesis. Taken together, these data will contribute to further investigate the function of miRNAs in intramuscular fat deposition. These differentially miRNAs can be developed as biomarkers for animal breeding.
DOI: 10.6084/m9.figshare.19308214
title: Comparative gene expression profile in circulating PBMCs of <i>Bos indicus</i> and crossbred cattle to understand disease tolerance mechanism

description: The present investigation was performed to compare the global gene expression profile in peripheral blood mononuclear cells (PBMCs) of <i>Bos indicus</i> and crossbred (<i>Bos taurus</i> × <i>B. indicus</i>) cattle. Previously, several studies revealed the disease tolerance potential of <i>B. indicus</i> cattle but underlying genetic mechanism is still not fully explored. The PBMCs model was used for this investigation as it plays crucial role in the immune system regulation. Transcriptomic analysis revealed total 6767 significantly differentially expressed transcripts (fold change (absolute) &gt;2.0, <i>p</i> &lt; .05). In addition, 4149 transcripts were upregulated, 2618 transcripts were downregulated and fold change (absolute) of differentially expressed transcript varied from −223.32 to 213.63. Functional annotation analysis of differentially expressed genes confirmed their role in various molecular pathways <i>viz.</i> innate immune response, antigen processing and presentation, MHC protein complex, defense response to bacterium, regulation of immune response, positive regulation of JAK-STAT cascade, cytoskeletal protein binding, etc. Protein–protein interaction network analysis provided understanding of inter-relationship of immune genes with differentially expressed genes. In conclusion, this study could provide comprehensive information about the dysregulated genes and biological pathways in PBMCs which might be responsible for disease tolerance in <i>B. indicus</i> cattle.
DOI: 10.6084/m9.figshare.17113911
title: Distribution of <i>DGAT1</i> copy number variation in Chinese goats and its associations with milk production traits

description: Goat is an important sector for meat and dairy products. Diacylglycerol O-acyltransferase 1 (<i>DGAT1</i>), which is a key gene in milk production, has been recently detected to overlap with a novel copy number variation (CNV) in goats. CNVs could be genetic markers providing new insights into the genetic basis of phenotypic variation. Up to now, there are no reports on the <i>DGAT1</i>-related CNV (<i>DGAT1</i> CNV) in Chinese goats. This study first detected the distribution of the <i>DGAT1</i> CNV in Chinese seven goat breeds, finding substantial differences among dairy, meat, and fiber goats (<i>P</i> &lt; 0.01). The association analysis between the <i>DGAT1</i> CNV and milk production traits revealed significant associations: Xinong Sannen (XS) dairy goat with copy number loss type had higher freezing point depression (FPD) (<i>P</i> &lt; 0.01) and milk solids-not-fat (SNF) content (<i>P</i> &lt; 0.05). Overall, our study unraveled the distribution of <i>DGAT1</i> CNV in Chinese goats for the first time and found the potential role of this CNV in the marker-assisted selection of dairy goat breeding.
DOI: 10.6084/m9.figshare.17113911.v1
title: Distribution of <i>DGAT1</i> copy number variation in Chinese goats and its associations with milk production traits

description: Goat is an important sector for meat and dairy products. Diacylglycerol O-acyltransferase 1 (<i>DGAT1</i>), which is a key gene in milk production, has been recently detected to overlap with a novel copy number variation (CNV) in goats. CNVs could be genetic markers providing new insights into the genetic basis of phenotypic variation. Up to now, there are no reports on the <i>DGAT1</i>-related CNV (<i>DGAT1</i> CNV) in Chinese goats. This study first detected the distribution of the <i>DGAT1</i> CNV in Chinese seven goat breeds, finding substantial differences among dairy, meat, and fiber goats (<i>P</i> &lt; 0.01). The association analysis between the <i>DGAT1</i> CNV and milk production traits revealed significant associations: Xinong Sannen (XS) dairy goat with copy number loss type had higher freezing point depression (FPD) (<i>P</i> &lt; 0.01) and milk solids-not-fat (SNF) content (<i>P</i> &lt; 0.05). Overall, our study unraveled the distribution of <i>DGAT1</i> CNV in Chinese goats for the first time and found the potential role of this CNV in the marker-assisted selection of dairy goat breeding.
DOI: 10.6084/m9.figshare.17826087
title: DUSP6 inhibits the proliferation of hair follicle stem cells (HFSCs) <i>in vitro</i>

description: RNA-seq has shown that the DUSP6 and MAPK signaling pathways are associated with the production of high-quality brush hair (type III hair) in Yangtze River Delta white goats. However, there are few reports on the regulatory effects of DUSP6 expression on hair follicle stem cells (HFSCs) and cellular processes, as well as the underlying mechanism. Here, we investigated the effect of DUSP6 level in HFSCs and the molecular mechanism underlying the functional regulation of HFSCs by DUSP6. Overexpression of DUSP6 significantly suppressed the proliferation of HFSCs by inducing cell cycle arrest in the G1 phase and by promoting apoptosis. Transcriptome analysis revealed a total of 217 differentially expressed genes between DUSP6-overexpressing and control HFSCs, of which 33 (15.2%) were upregulated in DUSP6-overexpressing cells. The two pathways with the most significant enrichment of differentially expressed genes were the TNF signaling pathway and cytokine-cytokine receptor interaction pathway, and the significantly enriched terms in the GO enrichment analysis involved cell attachment and cytokines. These results indicate that DUSP6 can function as an inhibitory factor in HFSCs through the induction of cell cycle arrest in the G1 phase and can promote apoptosis by mediating crosstalk among several pathways and cytokines.HighlightsWe constructed DUSP6 overexpression vectors to detect mRNA and protein expression levels related to high-quality brush hair in MAPK signaling pathway.We found that high expression level of DUSP6 can inhibit the proliferation of hair follicle stem cells (HFSCs) and promote cell apoptosis of HFSCs.DUSP6 may be involved in the growth regulation of HFSCs like Other studies in cancer, tumors by regulating the expression of cytokines, changing the transmission of signals between cells, activating or suppressing immune-related pathways. We constructed DUSP6 overexpression vectors to detect mRNA and protein expression levels related to high-quality brush hair in MAPK signaling pathway. We found that high expression level of DUSP6 can inhibit the proliferation of hair follicle stem cells (HFSCs) and promote cell apoptosis of HFSCs. DUSP6 may be involved in the growth regulation of HFSCs like Other studies in cancer, tumors by regulating the expression of cytokines, changing the transmission of signals between cells, activating or suppressing immune-related pathways.
DOI: 10.6084/m9.figshare.17826087.v1
title: DUSP6 inhibits the proliferation of hair follicle stem cells (HFSCs) <i>in vitro</i>

description: RNA-seq has shown that the DUSP6 and MAPK signaling pathways are associated with the production of high-quality brush hair (type III hair) in Yangtze River Delta white goats. However, there are few reports on the regulatory effects of DUSP6 expression on hair follicle stem cells (HFSCs) and cellular processes, as well as the underlying mechanism. Here, we investigated the effect of DUSP6 level in HFSCs and the molecular mechanism underlying the functional regulation of HFSCs by DUSP6. Overexpression of DUSP6 significantly suppressed the proliferation of HFSCs by inducing cell cycle arrest in the G1 phase and by promoting apoptosis. Transcriptome analysis revealed a total of 217 differentially expressed genes between DUSP6-overexpressing and control HFSCs, of which 33 (15.2%) were upregulated in DUSP6-overexpressing cells. The two pathways with the most significant enrichment of differentially expressed genes were the TNF signaling pathway and cytokine-cytokine receptor interaction pathway, and the significantly enriched terms in the GO enrichment analysis involved cell attachment and cytokines. These results indicate that DUSP6 can function as an inhibitory factor in HFSCs through the induction of cell cycle arrest in the G1 phase and can promote apoptosis by mediating crosstalk among several pathways and cytokines.HighlightsWe constructed DUSP6 overexpression vectors to detect mRNA and protein expression levels related to high-quality brush hair in MAPK signaling pathway.We found that high expression level of DUSP6 can inhibit the proliferation of hair follicle stem cells (HFSCs) and promote cell apoptosis of HFSCs.DUSP6 may be involved in the growth regulation of HFSCs like Other studies in cancer, tumors by regulating the expression of cytokines, changing the transmission of signals between cells, activating or suppressing immune-related pathways. We constructed DUSP6 overexpression vectors to detect mRNA and protein expression levels related to high-quality brush hair in MAPK signaling pathway. We found that high expression level of DUSP6 can inhibit the proliferation of hair follicle stem cells (HFSCs) and promote cell apoptosis of HFSCs. DUSP6 may be involved in the growth regulation of HFSCs like Other studies in cancer, tumors by regulating the expression of cytokines, changing the transmission of signals between cells, activating or suppressing immune-related pathways.
DOI: 10.6084/m9.figshare.19308199
title: Screening and characterization of Sahiwal cattle calves-origin lactic acid bacteria based on desired probiotic attributes for potential application

description: Probiotics are living microorganisms that confer health benefits to host when administered in adequate amounts. To develop novel host-specific probiotic for their application as feed additive, the present study was undertaken to isolate and characterize probiotic strains of indigenous cattle-calves origin. A total of 55 colonies were isolated from 12 healthy calves, with 34 of the isolates being Gram-positive, catalase-negative and vancomycin-resistant. Furthermore, eleven isolates showed tolerance to acid (pH 2.0) and thirteen isolates tolerated bile salts (0.3%). Seven common acid and bile tolerance strains were further investigated for other probiotic attributes and displayed higher (<i>p</i>&lt; 0.05) auto-aggregation and cell surface hydrophobicity values. Moreover, all seven isolates had potent antibacterial activity against pathobiont <i>E. coli</i> as well as significant co-aggregation capacity and enzyme activity. <i>In vitro</i> biosafety assessment revealed that all seven isolates were non-hemolytic, negative for mucin degradation and susceptible to most of the antibiotics. Based on the obtained findings, heatmap and principal component analysis identified four highly effective probiotic candidates confirmed by 16S rDNA sequencing as <i>Limosilactobacillus reuteri</i> SW23, <i>Limosilactobacillus reuteri</i> SW26, <i>Limosilactobacillus reuteri</i> SW27 and <i>Enterococcus faecium</i> SW28, respectively. Further studies on biosafety aspect are warranted for the application of these strains in animal as potential probiotics.HIGHLIGHTS<i>L. reuteri</i> SW23, <i>L. reuteri</i> SW26, <i>L. reuteri</i> SW28 and <i>Enterococcus faecium</i> SW28 were successfully isolated and identified from indigenous calves’ feces.These microbes were characterized for potential probiotics attributes.Heatmap analysis and principal component analysis (PCA) was used along with probiotic attributes to select highly effective probiotic candidates. <i>L. reuteri</i> SW23, <i>L. reuteri</i> SW26, <i>L. reuteri</i> SW28 and <i>Enterococcus faecium</i> SW28 were successfully isolated and identified from indigenous calves’ feces. These microbes were characterized for potential probiotics attributes. Heatmap analysis and principal component analysis (PCA) was used along with probiotic attributes to select highly effective probiotic candidates.
DOI: 10.6084/m9.figshare.17072865
title: Characterization of BoLA class II <i>DQA</i> and <i>DQB</i> by PCR-RFLP, cloning, and sequencing reveals sequence diversity in crossbred cattle

description: The BoLA class II <i>DQA</i> and <i>DQB</i> genes in crossbred cattle were studied using PCR-RFLP, cloning, and sequencing techniques. Seventy-two crossbred cattle (<i>Vrindavani</i>) were used in the current study. <i>Hae</i>III and <i>Xba</i>I restriction enzymes digested <i>DQA</i> exon 2-3, revealing seven (<i>Hae</i>III-A-G) and three (<i>Xba</i>I A-C) motifs, respectively. The BoLA-<i>DQB</i> gene was analyzed using PCR-RFLP with <i>Pst</i>I and <i>Taq</i>I restriction enzymes, yielding five restriction motifs for each restriction enzyme (<i>Pst</i>I-A-E and <i>Taq</i>I-A-E). In crossbred cattle, addition, deletion, and substitutions were observed in distinct sequences, resulting in variations in overall gene length. Changes in nucleotides at positions 64–80, 110–200, and 207–264 were largely responsible for polymorphism in <i>DQA</i> exon 2. The phylogenetic analysis predicted a high degree of nucleotide and amino acid changes in DQA exon 2-3 and DQB exon 2. <i>DQA</i> genes had a nucleotide dissimilarity of 0.3–25.4 percent, while <i>DQB</i> genes had a nucleotide dissimilarity of 1.5–14.3 percent. We cloned and sequenced 20 genotypes based on PCR-RFLP of the <i>DQA</i> and <i>DQB</i> genes. The current study observed variation in the <i>DQA</i> and <i>DQB</i> genes and will serve as a foundation for future research on the BoLA <i>DQA</i> and <i>DQB</i> genes.