cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19308199.v1
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.24354058
title: Data from: Genomic diversity of the endosymbiotic bacteria of human head lice.

description: This repository contains data associated with a study of endosymbiotic bacteria. Files beginning with "Phylo" indicate data used in or generated from phylogenetic analysis, beginning with "Cophy" indicated data used in phylogenetic comparisons of the host and endosymbiont, beginning with "Biogeography" indicating distributional data, beginning with "Skyline" indicating data used in generation of a Skyline plot. beginning with "VCFfiles" indicating vcf files resulting from alignment of reads to the genome of Ca. Riesia pediculicola, beginning with "Scaffolds" indicating partial genome assemblies of Ca. Riesia phthiripubis. Example software usage is included for certain phylogenetic software packages. Exact software used and the version of the software is document in the associated publication. VCF files are broken down into files containing structural variants, polymorphic sites, and fixed sites for each sample. File formats include fasta (.fa), newick (.tre), nexus (.nex), phylip (.phy), VCF (.vcf), and comma separated variable (.csv).
DOI: 10.6084/m9.figshare.21191228
title: Identification of core genes affecting IMF deposition in bovine

description: Intramuscular fat (IMF) content is an important economic factor in beef production. However, knowledge on the key factors controlling bovine IMF is limited. In this study, using weighted gene co-expression network analysis (WGCNA), nine modules were identified and the number of transcripts in these modules ranged from 36 to 3191. Two modules were found to be significantly associated with fat deposition and three genes (<i>TCAP</i>, <i>MYH</i>7, and <i>TNNC</i>1) were further identified by Protein–protein interaction (PPI), which may be the hub genes regulating bovine IMF deposition. In addition, considering the genetic variation, the <i>PCK1</i> gene was found by functional enrichment analysis of overlapping genes, which was previously reported to be involved in IMF deposition. We noted that the core promoter region of buffalo <i>PCK</i>1 binds to transcription factors involved in lipid metabolism while cattle <i>PCK</i>1 binds transcription factors involved in muscle development. The results suggest that <i>PCK1</i> participated in IMF deposition of buffalo and cattle in different ways. In summary, gene expression networks and new candidate genes associated with IMF deposition identified in this study. This would lay the foundation for further research into the molecular regulatory mechanisms underlying bovine IMF deposition.
DOI: 10.6084/m9.figshare.21076831
title: Effects of lncRNA MTC on protein expression in skin fibroblasts of Liaoning Cashmere goat based on iTRAQ technique

description: Existing experiments have found a new intergenic lncRNA activated by melatonin, which is called lncRNA MTC. However, the regulatory mechanism of lncRNA MTC in Liaoning Cashmere goat skin fibroblasts has not been clarified. Specific knockdown of lncRNA MTC inhibits cell proliferation and increases apoptosis. iTRAQ reagent was used for relative and absolute quantification of proteins in lncRNA MTC-KD and NC groups to evaluate changes in protein expression during dermal fibroblast development following lncRNA MTC deletion. A total of 5931 proteins were found in Liaoning Cashmere goat skin fibroblasts, of which 123 were differentially expressed, including 32 up-regulated proteins and 91 down-regulated proteins. Of the 91 down-regulated proteins, 32 act mainly through related pathways (e.g., cell cycle, mitochondrial function, ribosomal structure, vesicular transport, cytoskeletal components and skin morphogenesis). LncRNA MTC facilitates the proliferation of Liaoning Cashmere goat skin fibroblasts by regulating ITGB5, TlN2, CTSS, POLG, RAP1B, CHAF1A, CDCA8 and other proteins involved in cell proliferation. The results of this study provide some candidate proteins for the in-depth investigation of the molecular mechanism of lncRNA MTC, which facilitates hair growth in cashmere goats and provides more insights into their regulatory networks and biochemical pathways.
DOI: 10.6084/m9.figshare.20097184
title: Expression patterns and functional analysis of porcine lnc-34015

description: Long noncoding RNAs (lncRNAs) play important roles in immune regulation in humans and animals. The lnc-34015 was discovered to be critical for the development of muscles, based on the muscle transcriptome of pigs; however, the underlying molecular mechanism requires better understanding. Here, the sequence characteristics of lnc-34015 were analyzed and a competitive endogenous RNA regulatory network of lncRNA was predicted. The developmental expression trend and tissue expression profiles of lnc-34015 were investigated using quantitative polymerase chain reaction. The lnc-34015 sequence is overlapped with introns 11 and 12 of <i>CWF19L1</i>, while <i>CWF19L1</i>, <i>PKD2L1</i>, and <i>CHUK</i> were identified as cis-regulatory genes of lnc-34015. Bioinformatics analyses revealed that lnc-34015 binds to 15 microRNAs (miRNAs), including miR-3646, miR-377-3p, and miR-190b-3p, to regulate downstream gene expression. GO and KEGG enrichment results show that lnc-34015 was mainly involved in cell proliferation, stress response, transcriptional regulation, and alternative splicing. The expression trend of lnc-34015 in muscle was similar to that of target genes and opposite to that of miRNAs. The expression of lnc-34015 was significantly higher in the porcine small intestine and IPEC-J2 cells. Our findings suggest that lnc-34015 regulates <i>CHUK</i>, <i>ZBTB20</i>, and <i>XIAP</i> gene expression by competing with endogenous RNAs to regulate porcine inflammatory responses.
DOI: 10.6084/m9.figshare.20097184.v1
title: Expression patterns and functional analysis of porcine lnc-34015

description: Long noncoding RNAs (lncRNAs) play important roles in immune regulation in humans and animals. The lnc-34015 was discovered to be critical for the development of muscles, based on the muscle transcriptome of pigs; however, the underlying molecular mechanism requires better understanding. Here, the sequence characteristics of lnc-34015 were analyzed and a competitive endogenous RNA regulatory network of lncRNA was predicted. The developmental expression trend and tissue expression profiles of lnc-34015 were investigated using quantitative polymerase chain reaction. The lnc-34015 sequence is overlapped with introns 11 and 12 of <i>CWF19L1</i>, while <i>CWF19L1</i>, <i>PKD2L1</i>, and <i>CHUK</i> were identified as cis-regulatory genes of lnc-34015. Bioinformatics analyses revealed that lnc-34015 binds to 15 microRNAs (miRNAs), including miR-3646, miR-377-3p, and miR-190b-3p, to regulate downstream gene expression. GO and KEGG enrichment results show that lnc-34015 was mainly involved in cell proliferation, stress response, transcriptional regulation, and alternative splicing. The expression trend of lnc-34015 in muscle was similar to that of target genes and opposite to that of miRNAs. The expression of lnc-34015 was significantly higher in the porcine small intestine and IPEC-J2 cells. Our findings suggest that lnc-34015 regulates <i>CHUK</i>, <i>ZBTB20</i>, and <i>XIAP</i> gene expression by competing with endogenous RNAs to regulate porcine inflammatory responses.
DOI: 10.6084/m9.figshare.21076831.v1
title: Effects of lncRNA MTC on protein expression in skin fibroblasts of Liaoning Cashmere goat based on iTRAQ technique

description: Existing experiments have found a new intergenic lncRNA activated by melatonin, which is called lncRNA MTC. However, the regulatory mechanism of lncRNA MTC in Liaoning Cashmere goat skin fibroblasts has not been clarified. Specific knockdown of lncRNA MTC inhibits cell proliferation and increases apoptosis. iTRAQ reagent was used for relative and absolute quantification of proteins in lncRNA MTC-KD and NC groups to evaluate changes in protein expression during dermal fibroblast development following lncRNA MTC deletion. A total of 5931 proteins were found in Liaoning Cashmere goat skin fibroblasts, of which 123 were differentially expressed, including 32 up-regulated proteins and 91 down-regulated proteins. Of the 91 down-regulated proteins, 32 act mainly through related pathways (e.g., cell cycle, mitochondrial function, ribosomal structure, vesicular transport, cytoskeletal components and skin morphogenesis). LncRNA MTC facilitates the proliferation of Liaoning Cashmere goat skin fibroblasts by regulating ITGB5, TlN2, CTSS, POLG, RAP1B, CHAF1A, CDCA8 and other proteins involved in cell proliferation. The results of this study provide some candidate proteins for the in-depth investigation of the molecular mechanism of lncRNA MTC, which facilitates hair growth in cashmere goats and provides more insights into their regulatory networks and biochemical pathways.
DOI: 10.6084/m9.figshare.20037016
title: Androgen receptor gene deficiency results in the reduction of steroidogenic potential in porcine luteal cells

description: Luteal steroidogenesis is critical to implantation and pregnancy maintenance in mammals. The role of androgen receptors (AR) in the progesterone (P<sub>4</sub>) producing luteal cells of porcine corpus luteum (CL) remains unexplored. The aim of the present study was to establish <i>AR</i> gene knock out (KO) porcine luteal cell culture system model by CRISPR/Cas9 genome editing technology and to study the downstream effects of <i>AR</i> gene deficiency on steroidogenic potential and viability of luteal cells. For this purpose, genomic cleavage detection assay, microscopy, RT-qPCR, ELISA, annexin, MTT, and viability assay complemented by bioinformatics analysis were employed. There was significant downregulation (<i>p</i> &lt; 0.05) in the relative mRNA expression of steroidogenic marker genes <i>STAR, CYP11A1</i>, <i>HSD3B1</i> in <i>AR</i> KO luteal cells as compared to the control group, which was further validated by the significant (<i>p</i> &lt; 0.05) decrease in the P<sub>4</sub> production. Significant decrease (<i>p</i> &lt; 0.05) in relative viability on third passage were also observed. The relative mRNA expression of hypoxia related gene <i>HIF1A</i> was significantly (<i>p</i> &lt; 0.05) downregulated in <i>AR</i> KO luteal cells. Protein-protein interaction analysis mapped AR to signaling pathways associated with luteal cell functionality. These findings suggests that <i>AR</i> gene functionality is critical to luteal cell steroidogenesis in porcine.
DOI: 10.6084/m9.figshare.20037016.v1
title: Androgen receptor gene deficiency results in the reduction of steroidogenic potential in porcine luteal cells

description: Luteal steroidogenesis is critical to implantation and pregnancy maintenance in mammals. The role of androgen receptors (AR) in the progesterone (P<sub>4</sub>) producing luteal cells of porcine corpus luteum (CL) remains unexplored. The aim of the present study was to establish <i>AR</i> gene knock out (KO) porcine luteal cell culture system model by CRISPR/Cas9 genome editing technology and to study the downstream effects of <i>AR</i> gene deficiency on steroidogenic potential and viability of luteal cells. For this purpose, genomic cleavage detection assay, microscopy, RT-qPCR, ELISA, annexin, MTT, and viability assay complemented by bioinformatics analysis were employed. There was significant downregulation (<i>p</i> &lt; 0.05) in the relative mRNA expression of steroidogenic marker genes <i>STAR, CYP11A1</i>, <i>HSD3B1</i> in <i>AR</i> KO luteal cells as compared to the control group, which was further validated by the significant (<i>p</i> &lt; 0.05) decrease in the P<sub>4</sub> production. Significant decrease (<i>p</i> &lt; 0.05) in relative viability on third passage were also observed. The relative mRNA expression of hypoxia related gene <i>HIF1A</i> was significantly (<i>p</i> &lt; 0.05) downregulated in <i>AR</i> KO luteal cells. Protein-protein interaction analysis mapped AR to signaling pathways associated with luteal cell functionality. These findings suggests that <i>AR</i> gene functionality is critical to luteal cell steroidogenesis in porcine.
DOI: 10.6084/m9.figshare.21342153
title: Candidate genes for litter size in Xinjiang sheep identified by Specific Locus Amplified Fragment (SLAF) sequencing

description: The aim of this study was to investigate the selection signatures at a genome-wide level in ‘Pishan’ sheep using Specific Locus Amplified Fragment (SLAF)-seq. Blood samples from 126 ewes were sequenced using SLAF tags, and the ovarian tissues from 8 ewes (Bashbay sheep, a single litter size group (SG group); ‘Pishan’ sheep, double litter size group (DG group)) were collected to detect expression levels by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Selection signature analysis was performed using global fixation index (Fst) and nucleotide diversity (π) ratio. A total of 1,192,168 high-quality SLAFs were identified. Notably, 2380 candidate regions under selection using two approaches were identified. A total of 2069 genes were identified, which were involved in dopaminergic synapses, thyroid hormone synthesis, ovarian steroidogenesis and thyroid hormone signalling pathways. Furthermore, Growth Differentiation Factor 9 (<i>GDF9</i>), Period Circadian Regulator 2 (<i>PER2</i>), Thyroid Stimulating Hormone Receptor (<i>TSHR</i>), and Nuclear Receptor Coactivator 1 (<i>NCOA1</i>) reside within these regions and pathways. The expression levels of <i>GDF9</i> and <i>PER2</i> genes in sheep tissue of the DG group were significantly higher than those in the SG group. These genes are interesting candidates for litter size and provide a starting point for further identification of conservation strategies for ‘Pishan’ sheep.
DOI: 10.6084/m9.figshare.21287492
title: Whole-genome resequencing of Dorper and Hu sheep to reveal selection signatures associated with important traits

description: Dorper and Hu sheep exhibit different characteristics in terms of reproduction, growth, and meat quality. Comparison of the genomes of two breeds help to reveal important genomic information. In this study, whole genome resequencing of 30 individuals (Dorper, DB and Hu sheep, HY) identified 15,108,125 single nucleotide polymorphisms (SNPs). Population differentiation (<i>Fst</i>) and cross population extended haplotype homozygosity (XP-EHH) were performed for selective signal analysis. In total, 106 and 515 overlapped genes were present in both the <i>Fst</i> results and XP-EHH results in HY vs DB and in DB vs HY, respectively. In HY vs DB, 106 genes were enriched in 12 GO terms and 83 KEGG pathways, such as ATP binding (GO:0005524) and PI3K-Akt signaling pathway (oas04151). In DB vs HY, 515 genes were enriched in 109 GO terms and 215 KEGG pathways, such as skeletal muscle cell differentiation (GO:0035914) and MAPK signaling pathway (oas04010). According to the annotation results, we identified a series of candidate genes associated with reproduction (<i>UNC5C</i>, <i>BMPR1B</i>, and <i>GLIS1</i>), meat quality (<i>MECOM</i>, <i>MEF2C</i>, and <i>MYF6</i>), and immunity (<i>GMDS</i>, <i>GALK1</i>, and <i>ITGB4</i>). Our investigation has uncovered genomic information for important traits in sheep and provided a basis for subsequent studies of related traits.
DOI: 10.6084/m9.figshare.21287492.v1
title: Whole-genome resequencing of Dorper and Hu sheep to reveal selection signatures associated with important traits

description: Dorper and Hu sheep exhibit different characteristics in terms of reproduction, growth, and meat quality. Comparison of the genomes of two breeds help to reveal important genomic information. In this study, whole genome resequencing of 30 individuals (Dorper, DB and Hu sheep, HY) identified 15,108,125 single nucleotide polymorphisms (SNPs). Population differentiation (<i>Fst</i>) and cross population extended haplotype homozygosity (XP-EHH) were performed for selective signal analysis. In total, 106 and 515 overlapped genes were present in both the <i>Fst</i> results and XP-EHH results in HY vs DB and in DB vs HY, respectively. In HY vs DB, 106 genes were enriched in 12 GO terms and 83 KEGG pathways, such as ATP binding (GO:0005524) and PI3K-Akt signaling pathway (oas04151). In DB vs HY, 515 genes were enriched in 109 GO terms and 215 KEGG pathways, such as skeletal muscle cell differentiation (GO:0035914) and MAPK signaling pathway (oas04010). According to the annotation results, we identified a series of candidate genes associated with reproduction (<i>UNC5C</i>, <i>BMPR1B</i>, and <i>GLIS1</i>), meat quality (<i>MECOM</i>, <i>MEF2C</i>, and <i>MYF6</i>), and immunity (<i>GMDS</i>, <i>GALK1</i>, and <i>ITGB4</i>). Our investigation has uncovered genomic information for important traits in sheep and provided a basis for subsequent studies of related traits.
DOI: 10.6084/m9.figshare.20538317
title: Immunolocalization of antibacterial peptide S100A7 in mastitis goat mammary gland and lipopolysaccharide induces the expression and secretion of S100A7 in goat mammary gland epithelial cells via TLR4/NFκB signal pathway

description: The antimicrobial peptide S100A7, with antimicrobial activities for a broad spectrum of bacteria, has attracted more and more attention for the prevention and treatment of mastitis. However, there is little information about the expression and regulation mechanism of S100A7 in mastitis goats. This study revealed that S100A7 was mainly expressed in the stratified squamous epithelium of teat skin and streak canal, and S100A7 was present weakly in the healthy goat alveolus yet densely in the mastitis goat collapsed alveolus. Goat mammary epithelial cells (MECs) were isolated and treated with 2.5, 5, 10 and 20 µg/mL lipopolysaccharide (LPS) respectively for a different time, S100A7 mRNA expression and protein secretion were upregulated significantly with LPS treatment for 3 h, and the secretion level of S100A7 descended after 48 h treatment for all of these four groups. Moreover, after treatment with LPS, the mRNA levels of Toll-like receptor 4 (TLR4) and MyD88 were up-regulated, and the phosphorylation of p65 was up-regulated markedly. However, adding TLR4 inhibitor TAK-242 or/and NF-κB inhibitor QNZ significantly suppressed the phosphorylation of p65, and then inhibited the expression and secretion of S100A7 induced by LPS treatment. In conclusion, LPS induced the expression and secretion of S100A7 in goat MECs via TLR4/NF-κB signaling pathway.
DOI: 10.6084/m9.figshare.20538317.v1
title: Immunolocalization of antibacterial peptide S100A7 in mastitis goat mammary gland and lipopolysaccharide induces the expression and secretion of S100A7 in goat mammary gland epithelial cells via TLR4/NFκB signal pathway

description: The antimicrobial peptide S100A7, with antimicrobial activities for a broad spectrum of bacteria, has attracted more and more attention for the prevention and treatment of mastitis. However, there is little information about the expression and regulation mechanism of S100A7 in mastitis goats. This study revealed that S100A7 was mainly expressed in the stratified squamous epithelium of teat skin and streak canal, and S100A7 was present weakly in the healthy goat alveolus yet densely in the mastitis goat collapsed alveolus. Goat mammary epithelial cells (MECs) were isolated and treated with 2.5, 5, 10 and 20 µg/mL lipopolysaccharide (LPS) respectively for a different time, S100A7 mRNA expression and protein secretion were upregulated significantly with LPS treatment for 3 h, and the secretion level of S100A7 descended after 48 h treatment for all of these four groups. Moreover, after treatment with LPS, the mRNA levels of Toll-like receptor 4 (TLR4) and MyD88 were up-regulated, and the phosphorylation of p65 was up-regulated markedly. However, adding TLR4 inhibitor TAK-242 or/and NF-κB inhibitor QNZ significantly suppressed the phosphorylation of p65, and then inhibited the expression and secretion of S100A7 induced by LPS treatment. In conclusion, LPS induced the expression and secretion of S100A7 in goat MECs via TLR4/NF-κB signaling pathway.
DOI: 10.6084/m9.figshare.21215314
title: <i>Neospora caninum</i> seroprevalence in water buffaloes in Guangxi, China

description: <i>Neospora caninum</i> is an important obligate intracellular apicomplexan parasite that causes spontaneous abortions in cattle and leads to huge economic losses to the farming industry. Although a high prevalence of <i>N. caninum</i> infection has been reported in Asia, data on the prevalence of water buffaloes in China remain unclear. To understand the seroprevalence of <i>N. caninum</i> infection in water buffaloes and its definitive host dogs in China, a total of 987 water buffalo sera from Guangxi Province were tested using an indirect enzyme-linked immunosorbent assay. We obtained an overall seroprevalence of 50.9% (502/987) for water buffalo samples. And the positive rate was higher in border cities (56.8%, 425/748) than in central cities (32.3%, 77/239). We further tested 240 serum samples from dogs in Guangxi and found an overall prevalence of 57.9% (139/240). The high prevalence of <i>N. caninum</i> infection in both dogs and water buffaloes was first reported in southern China, and these data will surely contribute to the prevention and control of the disease.