cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17706111.v1
title: <i>Aeromonas hydrophila</i> inhibits autophagy triggering cytosolic translocation of mtDNA which activates the pro-apoptotic caspase-1/IL-1β-nitric oxide axis in headkidney macrophages

description: The molecular mechanisms underlying <i>Aeromonas hydrophila</i>-pathogenesis are not well understood. Using head kidney macrophages (HKM) of <i>Clarias gariepinus</i>, we previously reported the role of ER-stress in <i>A. hydrophila</i>-induced pathogenesis. Here, we report that PI3K/PLC-induced cytosolic-Ca<sup>2+</sup> imbalance induces the expression of pro-apoptotic ER-stress marker, CHOP in <i>A. hydrophila-</i>infected HKM. CHOP promotes HKM apoptosis by inhibiting AKT activation and enhancing JNK signaling. Elevated mitochondrial ROS (mtROS) was recorded which declined significantly by ameliorating ER-stress and in the presence of ER-Ca<sup>2+</sup> release modulators (2-APB and dantrolene) and mitochondrial-Ca<sup>2+</sup> uptake inhibitor, Ru360, together suggesting the role of ER-mitochondrial Ca<sup>2+</sup> dynamics in mtROS generation. Inhibiting mtROS production reduced HKM death implicating the pro-apoptotic role of mtROS in <i>A. hydrophila</i>-pathogenesis. The expression of autophagic proteins (LC3B, beclin-1, and atg 5) was suppressed in the infected HKM. Our results with autophagy-inducer rapamycin demonstrated that impaired autophagy favored the cytosolic accumulation of mitochondrial DNA (mtDNA) and the process depended on mtROS levels. Enhanced caspase-1 activity and IL-1β production was detected and transfection studies coupled with pharmacological inhibitors implicated mtROS/mtDNA axis to be crucial for activating the caspase-1/IL-1β cascade in infected HKM. RNAi studies further suggested the involvement of IL-1β in generating pro-apoptotic NO in <i>A. hydrophila</i>-infected HKM. Our study suggests a novel role of ER-mitochondria cross-talk in regulating <i>A. hydrophila</i> pathogenesis. Based on our observations, we conclude that <i>A. hydrophila</i> induces ER-stress and inhibits mitophagy resulting in mitochondrial dysfunction which leads to mtROS production and translocation of mtDNA into cytosol triggering the activation of caspase-1/IL-1β-mediated NO production, culminating in HKM apoptosis.
DOI: 10.6084/m9.figshare.20252660.v1
title: Using <i>in vivo</i> transcriptomics and RNA enrichment to identify genes involved in virulence of <i>Candida glabrata</i>

description: <i>Candida</i> species are the most commonly isolated opportunistic fungal pathogens in humans. These species exhibit very different infection strategies, since they acquired pathogenesis independently throughout evolution. <i>Candida albicans</i> causes most of the diagnosed infections, closely followed by <i>Candida glabrata</i>. <i>C. albicans</i> is well studied, and many genes have been shown to be important for infection and colonization of the host. It is, however, less clear how <i>C. glabrata</i> infects the host. With the help of a fungal RNA enrichment technology, we here investigated for the first time the transcriptomic profile of <i>C. glabrata</i> during urinary tract infection (UTI) in mice in order to determine which pathways and genes are regulated in the host compared to <i>in vitro</i> conditions. In the UTI model, bladders and kidneys are major target organs and therefore fungal transcriptomes were addressed in these organs. Our results showed that, next to adhesins and proteases, which seem to have a specific expression profile that may be linked to the niche in which the fungus grows, nitrogen metabolism and regulation play a vital role during <i>C. glabrata</i> UTI. Genes involved in nitrogen metabolism were upregulated and among them we show that <i>DUR1,2</i> (urea amidolyase) and <i>GAP1</i> (amino acid permease) are important for virulence. Furthermore, we confirmed the importance of the glyoxylate cycle in the host and identified <i>MLS1</i> (malate synthase) as an important gene necessary for <i>C. glabrata</i> virulence. In conclusion, our study shows with the support of <i>in vivo</i> transcriptomics how <i>C. glabrata</i> adapts to host conditions.
DOI: 10.6084/m9.figshare.20252660.v2
title: Using <i>in vivo</i> transcriptomics and RNA enrichment to identify genes involved in virulence of <i>Candida glabrata</i>

description: <i>Candida</i> species are the most commonly isolated opportunistic fungal pathogens in humans. <i>Candida albicans</i> causes most of the diagnosed infections, closely followed by <i>Candida glabrata</i>. <i>C. albicans</i> is well studied, and many genes have been shown to be important for infection and colonization of the host. It is however less clear how <i>C. glabrata</i> infects the host. With the help of fungal RNA enrichment, we here investigated for the first time the transcriptomic profile of <i>C. glabrata</i> during urinary tract infection (UTI) in mice. In the UTI model, bladders and kidneys are major target organs and therefore fungal transcriptomes were addressed in these organs. Our results showed that, next to adhesins and proteases, nitrogen metabolism and regulation play a vital role during <i>C. glabrata</i> UTI. Genes involved in nitrogen metabolism were upregulated and among them we show that <i>DUR1,2</i> (urea amidolyase) and <i>GAP1</i> (amino acid permease) were important for virulence. Furthermore, we confirmed the importance of the glyoxylate cycle in the host and identified <i>MLS1</i> (malate synthase) as an important gene necessary for <i>C. glabrata</i> virulence. In conclusion, our study shows with the support of <i>in vivo</i> transcriptomics how <i>C. glabrata</i> adapts to host conditions.
DOI: 10.6084/m9.figshare.20400463
title: Identification of the RNA-binding domain-containing protein RbpA that acts as a global regulator of the pathogenicity of <i>Streptococcus suis</i> serotype 2

description: <i>Streptococcus suis</i> serotype 2 (SS2), an emerging zoonotic pathogen, causes swine diseases and human cases of streptococcal toxic shock syndrome. RNA-binding proteins (RBPs) can modulate gene expression through post-transcriptional regulation. In this study, we identified an RBP harbouring an S1 domain, named RbpA, which facilitated SS2 adhesion to host epithelial cells and contributed to bacterial pathogenicity. Comparative proteomic analysis identified 145 proteins that were expressed differentially between Δ<i>rbpA</i> strain and wild-type strain, including several virulence-associated factors, such as the extracellular protein factor (EF), SrtF pilus, IgA1 protease, SBP2 pilus, and peptidoglycan-binding LysM’ proteins. The mechanisms underlying the regulatory effects of RbpA on their encoding genes were explored, and it was found that RbpA regulates gene expression through diverse mechanisms, including post-transcriptional regulation, and thus acts as a global regulator. These results partly reveal the pathogenic mechanism mediated by RbpA, improving our understanding of the regulatory systems of <i>S. suis</i> and providing new insights into bacterial pathogenicity.
DOI: 10.6084/m9.figshare.20400463.v1
title: Identification of the RNA-binding domain-containing protein RbpA that acts as a global regulator of the pathogenicity of <i>Streptococcus suis</i> serotype 2

description: <i>Streptococcus suis</i> serotype 2 (SS2), an emerging zoonotic pathogen, causes swine diseases and human cases of streptococcal toxic shock syndrome. RNA-binding proteins (RBPs) can modulate gene expression through post-transcriptional regulation. In this study, we identified an RBP harbouring an S1 domain, named RbpA, which facilitated SS2 adhesion to host epithelial cells and contributed to bacterial pathogenicity. Comparative proteomic analysis identified 145 proteins that were expressed differentially between Δ<i>rbpA</i> strain and wild-type strain, including several virulence-associated factors, such as the extracellular protein factor (EF), SrtF pilus, IgA1 protease, SBP2 pilus, and peptidoglycan-binding LysM’ proteins. The mechanisms underlying the regulatory effects of RbpA on their encoding genes were explored, and it was found that RbpA regulates gene expression through diverse mechanisms, including post-transcriptional regulation, and thus acts as a global regulator. These results partly reveal the pathogenic mechanism mediated by RbpA, improving our understanding of the regulatory systems of <i>S. suis</i> and providing new insights into bacterial pathogenicity.
DOI: 10.6084/m9.figshare.19612991
title: The African swine fever virus protease pS273R inhibits DNA sensing cGAS-STING pathway by targeting IKKε

description: African swine fever virus (ASFV), a large and complex cytoplasmic double-stranded DNA virus, has developed multiple strategies to evade the antiviral innate immune responses. Cytosolic DNA arising from invading ASFV is mainly detected by the cyclic GMP-AMP synthase (cGAS) and then triggers a series of innate immune responses to prevent virus invasion. However, the immune escape mechanism of ASFV remains to be fully clarified. The pS273R of ASFV is a member of the SUMO-1-specific protease family and is crucial for valid virus replication. In this study, we identified pS273R as a suppressor of cGAS-STING pathway mediated type I interferon (IFN) production by ASFV genomic open reading frame screening. The pS273R was further confirmed as an inhibitor of IFN production as well as its downstream antiviral genes in cGAS-STING pathway. Mechanistically, pS273R greatly decreased the cGAS-STING signaling by targeting IKKε but not TBK1, and pS273R was found to disturb the interaction between IKKε and STING through its interaction with IKKε. Further, mutational analyses revealed that pS273R antagonized the cGAS-STING pathway by enzyme catalytic activity, which might affect the IKKε sumoylation state required for the interaction with STING. In summary, our results revealed for the first time that pS273R acts as an obvious negative regulator of cGAS-STING pathway by targeting IKKε via its enzymatic activity, which shows a new immune evasion mechanism of ASFV.
DOI: 10.5281/zenodo.10850010
title: FRAP dataset associated with manuscript (https://doi.org/10.1101/2023.08.08.552291 )
DOI: 10.5281/zenodo.10850011
title: FRAP dataset associated with manuscript (https://doi.org/10.1101/2023.08.08.552291 )
DOI: 10.26207/2bwb-nw64
title: A climate-driven epidemiological model for fungal diseases in fruit orchards
DOI: 10.6084/m9.figshare.17302709
title: Transcriptome analysis and potential mechanisms of bovine oocytes under seasonal heat stress

description: Heat stress is the major factor affecting cattle fertility but molecular mechanisms of deleterious impacts of elevated temperature on oocyte are still not well known. Therefore, the aim of this study is to gain a better understanding of the underlying molecular mechanism of how heat stress affects GV-stage and MII-stage oocytes and discover hub genes to heat resistance for cow oocytes. In this study, we used the bioinformatics approach to discover the differentially expressed genes between GV-stage and MII-stage oocytes, which were collected during spring and summer. When GV-stage oocytes were compared to MII-stage oocytes collected in July (Jul DEGs group) a total of 1068 genes were found as differentially expressed as a result of heat stress. Also, <i>HSPA8, COPS5, POLR2L, PSMC6,</i> and <i>TPI1</i> were identified as the common top ranked genes for the Jul DEGs group. The highest connected hub gene for the Jul DEGs group was determined as <i>HSPA8.</i> Our results showed that different heat response mechanisms might be activated to protect oocytes from elevated temperatures in cattle. The identified genes and their associated pathways might play an important role in the response to heat stress that affects the oocytes in cattle.
DOI: 10.6084/m9.figshare.17302709.v1
title: Transcriptome analysis and potential mechanisms of bovine oocytes under seasonal heat stress

description: Heat stress is the major factor affecting cattle fertility but molecular mechanisms of deleterious impacts of elevated temperature on oocyte are still not well known. Therefore, the aim of this study is to gain a better understanding of the underlying molecular mechanism of how heat stress affects GV-stage and MII-stage oocytes and discover hub genes to heat resistance for cow oocytes. In this study, we used the bioinformatics approach to discover the differentially expressed genes between GV-stage and MII-stage oocytes, which were collected during spring and summer. When GV-stage oocytes were compared to MII-stage oocytes collected in July (Jul DEGs group) a total of 1068 genes were found as differentially expressed as a result of heat stress. Also, <i>HSPA8, COPS5, POLR2L, PSMC6,</i> and <i>TPI1</i> were identified as the common top ranked genes for the Jul DEGs group. The highest connected hub gene for the Jul DEGs group was determined as <i>HSPA8.</i> Our results showed that different heat response mechanisms might be activated to protect oocytes from elevated temperatures in cattle. The identified genes and their associated pathways might play an important role in the response to heat stress that affects the oocytes in cattle.
DOI: 10.6084/m9.figshare.16989733
title: Assessing genomic diversity and selective pressures in Bashan cattle by whole-genome sequencing data

description: Specific ecological environments and domestication have continuously influenced the physiological characteristics of Chinese indigenous cattle. Among them, Bashan cattle belongs to one of the indigenous breeds. However, the genomic diversity of Bashan cattle is still unknown. Published whole-genome sequencing (WGS) data of 13 Bashan cattle and 48 worldwide cattle were used to investigate the genetic composition and selection characteristics of Bashan cattle. The population structure analysis revealed that Bashan cattle harbored ancestries with East Asian taurine and Chinese indicine. Genetic diversity analysis implied the relatively high genomic diversity in Bashan cattle. Through the identification of containing &gt;5 nsSNPs or frameshift mutations genes in Bashan cattle, a large number of pathways related to sensory perception were discovered. CLR, θπ ratio, <i>F</i><sub>ST</sub>, and XP-EHH methods were used to detect the candidate signatures of positive selection in Bashan cattle. Among the identified genes, most of the enriched signal pathways were related to environmental information processing, biological systems, and metabolism. We mainly reported genes related to the nervous system (<i>HCN1</i>, <i>KATNA1</i>, <i>FSTL1</i>, <i>GRIK2</i>, and <i>CPLX2</i>), immune (<i>CD244</i>, <i>SLAMF1</i>, <i>LY9</i>, and <i>CD48</i>), and reproduction (<i>AKR1C1</i>, <i>AKR1C3</i>, <i>AKR1C4</i>, and <i>TUSC3</i>). Our findings will be significant in understanding the molecular basis underlying phenotypic variation of breed-related traits and improving productivity in Bashan cattle.
DOI: 10.6084/m9.figshare.17900820
title: Identification of differentially expressed long non-coding RNAs and messenger RNAs involved with muscle development in Dazu black goats through RNA sequencing

description: This study aimed to explore the genetic basis of muscle development in goats. The transcriptome dataset for differentially expressed lncRNAs (DELs) and differentially expressed genes (DEGs) of goat muscle at different developmental stages were obtained using RNA-Seq. A total of 447,806,481 and 587,559,465 clean reads in the longissimus dorsi muscle of Dazu black goats between 75d embryonic stage and 1d after birth were generated through Illumina paired-end sequencing, and their mapping rates were 89.82 and 90.99%, respectively. Moreover, 4517 DEGs and 648 DELs were identified, and 4784 lncRNA-mRNA targeting relationships were predicted. Gene function annotation results showed that 4101 DEGs were significantly enriched to 1098 GO terms, and 2014 DEGs were significantly enriched to 40 KEGG pathways, including many GO terms and pathways related to muscle development, such as cell differentiation and Wnt signaling pathway. Then, 10 DELs and 20 DEGs were randomly selected for RT-qPCR verification, and the agreement rate between the verification and RNA-Seq results was 90%, indicating the high reliability of the RNA-Seq data analysis. In conclusion, this study obtained several mRNAs and lncRNAs related to the muscle development of Dazu black goats and identified several targeted regulatory pairs of lncRNA–mRNA. This study may serve as a reference to understand the genetic basis and molecular mechanism of muscle development in goats.
DOI: 10.6084/m9.figshare.17900820.v1
title: Identification of differentially expressed long non-coding RNAs and messenger RNAs involved with muscle development in Dazu black goats through RNA sequencing

description: This study aimed to explore the genetic basis of muscle development in goats. The transcriptome dataset for differentially expressed lncRNAs (DELs) and differentially expressed genes (DEGs) of goat muscle at different developmental stages were obtained using RNA-Seq. A total of 447,806,481 and 587,559,465 clean reads in the longissimus dorsi muscle of Dazu black goats between 75d embryonic stage and 1d after birth were generated through Illumina paired-end sequencing, and their mapping rates were 89.82 and 90.99%, respectively. Moreover, 4517 DEGs and 648 DELs were identified, and 4784 lncRNA-mRNA targeting relationships were predicted. Gene function annotation results showed that 4101 DEGs were significantly enriched to 1098 GO terms, and 2014 DEGs were significantly enriched to 40 KEGG pathways, including many GO terms and pathways related to muscle development, such as cell differentiation and Wnt signaling pathway. Then, 10 DELs and 20 DEGs were randomly selected for RT-qPCR verification, and the agreement rate between the verification and RNA-Seq results was 90%, indicating the high reliability of the RNA-Seq data analysis. In conclusion, this study obtained several mRNAs and lncRNAs related to the muscle development of Dazu black goats and identified several targeted regulatory pairs of lncRNA–mRNA. This study may serve as a reference to understand the genetic basis and molecular mechanism of muscle development in goats.
DOI: 10.6084/m9.figshare.16989733.v1
title: Assessing genomic diversity and selective pressures in Bashan cattle by whole-genome sequencing data

description: Specific ecological environments and domestication have continuously influenced the physiological characteristics of Chinese indigenous cattle. Among them, Bashan cattle belongs to one of the indigenous breeds. However, the genomic diversity of Bashan cattle is still unknown. Published whole-genome sequencing (WGS) data of 13 Bashan cattle and 48 worldwide cattle were used to investigate the genetic composition and selection characteristics of Bashan cattle. The population structure analysis revealed that Bashan cattle harbored ancestries with East Asian taurine and Chinese indicine. Genetic diversity analysis implied the relatively high genomic diversity in Bashan cattle. Through the identification of containing &gt;5 nsSNPs or frameshift mutations genes in Bashan cattle, a large number of pathways related to sensory perception were discovered. CLR, θπ ratio, <i>F</i><sub>ST</sub>, and XP-EHH methods were used to detect the candidate signatures of positive selection in Bashan cattle. Among the identified genes, most of the enriched signal pathways were related to environmental information processing, biological systems, and metabolism. We mainly reported genes related to the nervous system (<i>HCN1</i>, <i>KATNA1</i>, <i>FSTL1</i>, <i>GRIK2</i>, and <i>CPLX2</i>), immune (<i>CD244</i>, <i>SLAMF1</i>, <i>LY9</i>, and <i>CD48</i>), and reproduction (<i>AKR1C1</i>, <i>AKR1C3</i>, <i>AKR1C4</i>, and <i>TUSC3</i>). Our findings will be significant in understanding the molecular basis underlying phenotypic variation of breed-related traits and improving productivity in Bashan cattle.
DOI: 10.6084/m9.figshare.19134726
title: Coat score. A possible explanation for the zebuine selective sweep located on bovine chromosome 5: 47,670,001–48,100,000 bp

description: Over 65% of the world's cattle population resides in warm areas where heat stress conditions limit the breed of European taurine cattle. Composite breeds were developed to retain the main traits of both parental breeds. The skin plays a central role in animal response to heat stress. Research on the genetic architecture of skin traits has identified genes and regions related to warm resistance skin features. The aim of this study was to determine whether the indicine proportion accounted for coat type or whether there were genes of large effect segregating in Brangus. Bulls (<i>n</i><b> </b>=<b> </b>108) were genotyped using microarrays and their coat score and hair length were evaluated. Indicine-taurine genome-wide composition was estimated and GWAS was performed. Although significant correlations between indicine proportion and traits were not observed, four windows of SNPs on BTA4 and BTA5 explained more than 2% of the trait variance. The GWAS for coat score in summer showed the main peak on BTA5:46,941,446–48,030,219<b> </b>bp, accounting for 4.65% of the variance. Our results suggest that the variation in coat score and undercoat hair length in Argentinian Brangus bulls is associated with the presence of some particular gene variants, rather than with the whole indicine genetic content.
DOI: 10.6084/m9.figshare.19134726.v1
title: Coat score. A possible explanation for the zebuine selective sweep located on bovine chromosome 5: 47,670,001–48,100,000 bp

description: Over 65% of the world's cattle population resides in warm areas where heat stress conditions limit the breed of European taurine cattle. Composite breeds were developed to retain the main traits of both parental breeds. The skin plays a central role in animal response to heat stress. Research on the genetic architecture of skin traits has identified genes and regions related to warm resistance skin features. The aim of this study was to determine whether the indicine proportion accounted for coat type or whether there were genes of large effect segregating in Brangus. Bulls (<i>n</i><b> </b>=<b> </b>108) were genotyped using microarrays and their coat score and hair length were evaluated. Indicine-taurine genome-wide composition was estimated and GWAS was performed. Although significant correlations between indicine proportion and traits were not observed, four windows of SNPs on BTA4 and BTA5 explained more than 2% of the trait variance. The GWAS for coat score in summer showed the main peak on BTA5:46,941,446–48,030,219<b> </b>bp, accounting for 4.65% of the variance. Our results suggest that the variation in coat score and undercoat hair length in Argentinian Brangus bulls is associated with the presence of some particular gene variants, rather than with the whole indicine genetic content.