cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30001319
title: Single-cell transcriptomic atlas of blood and lung from mice infected with SARS-CoV-2 revealing distinct virulence characteristics between prototype and Omicron BA.1 strain

description: The markedly reduced pathogenicity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron variant in comparison to earlier strains has raised critical questions regarding its underlying mechanisms. To elucidate the host immune responses driving these differences, we performed single-cell transcriptomic profiling of lung and blood samples from human angiotensin-converting enzyme 2 (hACE2) transgenic mice infected with either the SARS-CoV-2 prototype strain or the Omicron BA.1 variant at 5 days post-inoculation. Both strains induced a reduction in lung cell numbers, with capillary endothelial cells showing the highest number of differentially expressed genes (DEGs). Shared transcriptional responses included upregulation of chemokine (e.g. <i>Gnaq</i>, <i>Lyn</i>, <i>Ccl5</i>) and IL-17 signaling pathways. Notably, Omicron BA.1 infection resulted in downregulation of <i>Txnip</i>, a key gene involved in oxidative stress responses. Genes associated with neutrophil granules and pro-inflammatory functions (<i>Mmp8</i>, <i>S100a8</i>, <i>S100a9</i>) were also downregulated, whereas wound healing pathways were upregulated in immature neutrophils. Additionally, Omicron BA.1 altered gene expression associated with neutrophil migration from blood to lung, and decreased the activation of cell chemotaxis, cytokine-mediated signaling, IL-17 and NF-κB pathways in pro-inflammatory monocytes and pulmonary interstitial macrophages. These findings highlight distinct immunological signatures contributing to the attenuated pathogenicity of Omicron BA.1, particularly through the modulation of neutrophil and monocyte-macrophage responses.
DOI: 10.6084/m9.figshare.30001319.v1
title: Single-cell transcriptomic atlas of blood and lung from mice infected with SARS-CoV-2 revealing distinct virulence characteristics between prototype and Omicron BA.1 strain

description: The markedly reduced pathogenicity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron variant in comparison to earlier strains has raised critical questions regarding its underlying mechanisms. To elucidate the host immune responses driving these differences, we performed single-cell transcriptomic profiling of lung and blood samples from human angiotensin-converting enzyme 2 (hACE2) transgenic mice infected with either the SARS-CoV-2 prototype strain or the Omicron BA.1 variant at 5 days post-inoculation. Both strains induced a reduction in lung cell numbers, with capillary endothelial cells showing the highest number of differentially expressed genes (DEGs). Shared transcriptional responses included upregulation of chemokine (e.g. <i>Gnaq</i>, <i>Lyn</i>, <i>Ccl5</i>) and IL-17 signaling pathways. Notably, Omicron BA.1 infection resulted in downregulation of <i>Txnip</i>, a key gene involved in oxidative stress responses. Genes associated with neutrophil granules and pro-inflammatory functions (<i>Mmp8</i>, <i>S100a8</i>, <i>S100a9</i>) were also downregulated, whereas wound healing pathways were upregulated in immature neutrophils. Additionally, Omicron BA.1 altered gene expression associated with neutrophil migration from blood to lung, and decreased the activation of cell chemotaxis, cytokine-mediated signaling, IL-17 and NF-κB pathways in pro-inflammatory monocytes and pulmonary interstitial macrophages. These findings highlight distinct immunological signatures contributing to the attenuated pathogenicity of Omicron BA.1, particularly through the modulation of neutrophil and monocyte-macrophage responses.
DOI: 10.6084/m9.figshare.30164692
title: Temporal dynamics of macrophage activation during <i>Salmonella enterica</i> serovar Typhi infection: An integrated transcriptomic and metabolomic analysis

description: <i>Salmonella enterica</i> serovar Typhi (<i>S</i>. Typhi) is a major bacteria responsible for foodborne illnesses. Understanding the temporal dynamics of the host immune response and associated metabolic reprogramming is crucial for identifying potential therapeutic targets. This study employed an integrated transcriptomic and metabolomic approach to investigate the response of macrophages infected with <i>S</i>. Typhi over a defined stage (0 h, 2 h, 4 h, 8 h, and 24 h). RNA sequencing (RNA-seq) was used to profile gene expression changes, while untargeted metabolomics characterized metabolic shifts. Gene set enrichment and pathway analyses were conducted to identify key immune and metabolic pathways. Additionally, Convergent Cross-Mapping (CCM) analysis was applied to uncover causal relationships between gene expression and metabolite fluctuations. Transcriptomic revealed distinct temporal phases of immune activation. Early responses were dominated by interferon signaling, cytokine production, and inflammatory responses, whereas later stages involved sustained immune signaling and metabolic adaptation. Key pathways, including NF-κB, TNF, and cytokine-cytokine receptor interactions, were significantly enriched. Metabolomic profiling demonstrated a transition from glycolysis and amino acid metabolism in early infection stages to fatty acid oxidation and mitochondrial function in later stages, with glutathione metabolism playing a central role in oxidative stress regulation. CCM analysis identified critical genes (e.g. RGS4, KIF18A, RSPO1) exhibiting strong causal relationships with metabolic alterations, underscoring the tight integration between immune and metabolic responses. This study provides a comprehensive, time-resolved view of <i>S</i>. Typhi infection, highlighting dynamic immune activation and metabolic reprogramming in macrophages. These findings advance our understanding of host-pathogen interactions.
DOI: 10.6084/m9.figshare.30164692.v1
title: Temporal dynamics of macrophage activation during <i>Salmonella enterica</i> serovar Typhi infection: An integrated transcriptomic and metabolomic analysis

description: <i>Salmonella enterica</i> serovar Typhi (<i>S</i>. Typhi) is a major bacteria responsible for foodborne illnesses. Understanding the temporal dynamics of the host immune response and associated metabolic reprogramming is crucial for identifying potential therapeutic targets. This study employed an integrated transcriptomic and metabolomic approach to investigate the response of macrophages infected with <i>S</i>. Typhi over a defined stage (0 h, 2 h, 4 h, 8 h, and 24 h). RNA sequencing (RNA-seq) was used to profile gene expression changes, while untargeted metabolomics characterized metabolic shifts. Gene set enrichment and pathway analyses were conducted to identify key immune and metabolic pathways. Additionally, Convergent Cross-Mapping (CCM) analysis was applied to uncover causal relationships between gene expression and metabolite fluctuations. Transcriptomic revealed distinct temporal phases of immune activation. Early responses were dominated by interferon signaling, cytokine production, and inflammatory responses, whereas later stages involved sustained immune signaling and metabolic adaptation. Key pathways, including NF-κB, TNF, and cytokine-cytokine receptor interactions, were significantly enriched. Metabolomic profiling demonstrated a transition from glycolysis and amino acid metabolism in early infection stages to fatty acid oxidation and mitochondrial function in later stages, with glutathione metabolism playing a central role in oxidative stress regulation. CCM analysis identified critical genes (e.g. RGS4, KIF18A, RSPO1) exhibiting strong causal relationships with metabolic alterations, underscoring the tight integration between immune and metabolic responses. This study provides a comprehensive, time-resolved view of <i>S</i>. Typhi infection, highlighting dynamic immune activation and metabolic reprogramming in macrophages. These findings advance our understanding of host-pathogen interactions.
DOI: 10.6084/m9.figshare.28418160
title: The T-type voltage-gated Ca<sup>2+</sup> channel Ca<sub>V</sub>3.1 involves in the disruption of respiratory epithelial barrier induced by <i>Pasteurella multocida</i> toxin

description: <i>Pasteurella multocida</i> toxin (PMT) is an exotoxin produced by several members of the zoonotic respiratory pathogen <i>P. multocida</i>. The role of PMT in disrupting the mammalian respiratory barrier remains to be elucidated. In this study, we showed that inoculation of recombinantly expressed PMT increased the permeability of the respiratory epithelial barrier in mouse and respiratory cell models. This was evidenced by a decreased expression of tight junctions (ZO-1, occludin) and adherens junctions (β-catenin, E-cadherin), as well as enhanced cytoskeletal rearrangement. In mechanism, we demonstrated that PMT inoculation induced cytoplasmic Ca<sup>2+</sup> inflow, leading to an imbalance of cellular Ca<sup>2+</sup> homoeostasis and endoplasmic reticulum stress. This process further stimulated the RhoA/ROCK signalling, promoting cytoskeletal rearrangement and reducing the expression of tight junctions and adherens junctions. Notably, the T-type voltage-gated Ca<sup>2+</sup> channel Ca<sub>V</sub>3.1 was found to participate in PMT-induced cytoplasmic Ca<sup>2+</sup> inflow. Knocking out Ca<sub>V</sub>3.1 significantly reduced the cytotoxicity induced by PMT on swine respiratory epithelial cells and mitigated cytoplasmic Ca<sup>2+</sup> inflow stimulated by PMT. These findings suggest Ca<sub>V</sub>3.1 contributes to PMT-induced respiratory epithelial barrier disruption.
DOI: 10.6084/m9.figshare.28418160.v1
title: The T-type voltage-gated Ca<sup>2+</sup> channel Ca<sub>V</sub>.1 involves in the disruption of respiratory epithelial barrier induced by <i>Pasteurella multocida</i> toxin

description: <i>Pasteurella multocida</i> toxin (PMT) is an exotoxin produced by several members of the zoonotic respiratory pathogen <i>P. multocida</i>. The role of PMT in disrupting the mammalian respiratory barrier remains to be elucidated. In this study, we showed that inoculation of recombinantly expressed PMT increased the permeability of the respiratory epithelial barrier in mouse and respiratory cell models. This was evidenced by a decreased expression of tight junctions (ZO-1, occludin) and adherens junctions (β-catenin, E-cadherin), as well as enhanced cytoskeletal rearrangement. In mechanism, we demonstrated that PMT inoculation induced cytoplasmic Ca<sup>2+</sup> inflow, leading to an imbalance of cellular Ca<sup>2+</sup> homoeostasis and endoplasmic reticulum stress. This process further stimulated the RhoA/ROCK signalling, promoting cytoskeletal rearrangement and reducing the expression of tight junctions and adherens junctions. Notably, the T-type voltage-gated Ca<sup>2+</sup> channel Ca<sub>V</sub>3.1 was found to participate in PMT-induced cytoplasmic Ca<sup>2+</sup> inflow. Knocking out Ca<sub>V</sub>3.1 significantly reduced the cytotoxicity induced by PMT on swine respiratory epithelial cells and mitigated cytoplasmic Ca<sup>2+</sup> inflow stimulated by PMT. These findings suggest Ca<sub>V</sub>3.1 contributes to PMT-induced respiratory epithelial barrier disruption.
DOI: 10.6084/m9.figshare.28418160.v2
title: The T-type voltage-gated Ca<sup>2+</sup> channel Ca<sub>V</sub>3.1 involves in the disruption of respiratory epithelial barrier induced by <i>Pasteurella multocida</i> toxin

description: <i>Pasteurella multocida</i> toxin (PMT) is an exotoxin produced by several members of the zoonotic respiratory pathogen <i>P. multocida</i>. The role of PMT in disrupting the mammalian respiratory barrier remains to be elucidated. In this study, we showed that inoculation of recombinantly expressed PMT increased the permeability of the respiratory epithelial barrier in mouse and respiratory cell models. This was evidenced by a decreased expression of tight junctions (ZO-1, occludin) and adherens junctions (β-catenin, E-cadherin), as well as enhanced cytoskeletal rearrangement. In mechanism, we demonstrated that PMT inoculation induced cytoplasmic Ca<sup>2+</sup> inflow, leading to an imbalance of cellular Ca<sup>2+</sup> homoeostasis and endoplasmic reticulum stress. This process further stimulated the RhoA/ROCK signalling, promoting cytoskeletal rearrangement and reducing the expression of tight junctions and adherens junctions. Notably, the T-type voltage-gated Ca<sup>2+</sup> channel Ca<sub>V</sub>3.1 was found to participate in PMT-induced cytoplasmic Ca<sup>2+</sup> inflow. Knocking out Ca<sub>V</sub>3.1 significantly reduced the cytotoxicity induced by PMT on swine respiratory epithelial cells and mitigated cytoplasmic Ca<sup>2+</sup> inflow stimulated by PMT. These findings suggest Ca<sub>V</sub>3.1 contributes to PMT-induced respiratory epithelial barrier disruption.
DOI: 10.15468/dl.gztbur
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((117.607 3.136173, 117.536633 3.130604, 117.468 3.114034, 117.402794 3.086871, 117.342622 3.049786, 117.288965 3.003692, 117.243146 2.949725, 117.206293 2.889215, 117.17931 2.823653, 117.162863 2.754654, 117.157352 2.683917, 117.162914 2.613184, 117.179407 2.544196, 117.206426 2.478652, 117.243303 2.418165, 117.28913 2.364223, 117.342779 2.318154, 117.402928 2.281092, 117.468097 2.253947, 117.536684 2.237389, 117.607 2.231824, 117.677316 2.237389, 117.745903 2.253947, 117.811072 2.281092, 117.871221 2.318154, 117.92487 2.364223, 117.970697 2.418165, 118.007574 2.478652, 118.034593 2.544196, 118.051086 2.613184, 118.056648 2.683917, 118.051137 2.754654, 118.03469 2.823653, 118.007707 2.889215, 117.970854 2.949725, 117.925035 3.003692, 117.871378 3.049786, 117.811206 3.086871, 117.746 3.114034, 117.677367 3.130604, 117.607 3.136173))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003549-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30390797
title: Eukaryotic translation elongation factor 1 alpha 1 facilitates coxsackievirus B replication through interacting with PABP, viral protein 3 CD and viral RNA

description: Viral myocarditis, often caused by Coxsackievirus B (CVB), is the leading cause of dilated cardiomyopathy and heart failure. Despite extensive research, the pathogenesis of CVB infection remains incompletely understood. Our previous study found that Anisomycin inhibits CVB replication by promoting the degradation of eukaryotic translation elongation factor 1 alpha 1 (eEF1A1). However, the precise mechanism through which eEF1A1 facilitates the replication of CVB remains to be fully elucidated. Here, we demonstrated that upregulated eEF1A1 is required for CVB3 replication. <i>In vitro</i> transcription and RNA pulldown assay demonstrated that eEF1A1 binds to the 5’ cloverleaf region of CVB3 RNA. We observed that eEF1A1 interacts with double-stranded viral RNA, viral precursor protein 3 CD, and poly(A)-binding protein (PABP), which enhances its interaction with 3 CD. We show that CVB3 upregulates eEF1A1 expression by activating NF-κB. Chromosome-immunoprecipitation assay confirmed that NF-κB p65 binds to the <i>EEF1A1</i> promoter. Luciferase reporter assays validated that NF-κB up-regulates <i>EEF1A1</i> transcription. We further showed that eEF1A1 promotes CVB3 replication through interacting with viral RNA, 3 CD, and cellular protein PABP. This study highlights that eEF1A1, which is essential for cellular translation, is manipulated by CVB3 to promote viral replication. These findings suggest that targeting eEF1A1 could be a potential antiviral strategy against CVB infection.
DOI: 10.6084/m9.figshare.30390797.v1
title: Eukaryotic translation elongation factor 1 alpha 1 facilitates coxsackievirus B replication through interacting with PABP, viral protein 3 CD and viral RNA

description: Viral myocarditis, often caused by Coxsackievirus B (CVB), is the leading cause of dilated cardiomyopathy and heart failure. Despite extensive research, the pathogenesis of CVB infection remains incompletely understood. Our previous study found that Anisomycin inhibits CVB replication by promoting the degradation of eukaryotic translation elongation factor 1 alpha 1 (eEF1A1). However, the precise mechanism through which eEF1A1 facilitates the replication of CVB remains to be fully elucidated. Here, we demonstrated that upregulated eEF1A1 is required for CVB3 replication. <i>In vitro</i> transcription and RNA pulldown assay demonstrated that eEF1A1 binds to the 5’ cloverleaf region of CVB3 RNA. We observed that eEF1A1 interacts with double-stranded viral RNA, viral precursor protein 3 CD, and poly(A)-binding protein (PABP), which enhances its interaction with 3 CD. We show that CVB3 upregulates eEF1A1 expression by activating NF-κB. Chromosome-immunoprecipitation assay confirmed that NF-κB p65 binds to the <i>EEF1A1</i> promoter. Luciferase reporter assays validated that NF-κB up-regulates <i>EEF1A1</i> transcription. We further showed that eEF1A1 promotes CVB3 replication through interacting with viral RNA, 3 CD, and cellular protein PABP. This study highlights that eEF1A1, which is essential for cellular translation, is manipulated by CVB3 to promote viral replication. These findings suggest that targeting eEF1A1 could be a potential antiviral strategy against CVB infection.
DOI: 10.6073/pasta/ac701d3b0e6ca5f5201478f7224ee2cc
title: Social-Ecological Dynamics of Recreational Fishery Landscapes: Recreational angler catch and satisfaction in the Midwest, 2018 to 2024

description: The goal of this dataset is to understand angler information gathering and sharing, technology use, expectation-setting, site choice, and the factors influencing angler satisfaction in rural and urban environments. These data were collected through on-site creel surveys and instantaneous counts of fishing effort and associated angler vehicles. Traditional creel surveys are completed only at the end of an angler's fishing trip. These dual-intercept creel survey data are novel because anglers were intercepted both before and after their fishing trip. This survey design allowed us to collect unbiased estimates of anglers' expected catch. These data can be used to understand the role of angler expectations in angler satisfaction and behavior.
 Data collection were conducted in two counties in Wisconsin, USA. Vilas County is a primarily rural, forested, and glaciated region with many relatively small lakes. Dane County has a larger urban center (Madison, WI) that is surrounded by agricultural areas. Most of the Dane County lakes surveyed were part of the Yahara chain of lakes: Lakes Mendota, Monona, Wingra, Waubesa, and Kegonsa. Dane county has fewer, larger lakes with greater connectivity to each other. Vilas County was sampled in the summer of 2018, the summer of 2019, and the summer and winter of 2022. Dane County was sampled in the winter and summer of 2022.
DOI: 10.6084/m9.figshare.29627417
title: Disruption of <i>CmHmgr1</i> triggers apoptosis and causes defects in growth, conidiogenesis, and mycoparasitism of <i>Coniothyrium minitans</i>

description: <i>Coniothyrium minitans</i> is a well-known mycoparasite against <i>Sclerotinia sclerotiorum.</i> Two critical factors for the commercialization of <i>C. minitans</i> as a biocontrol agent are conidial production and parasitism. To decipher the mechanisms of conidiogenesis and mycoparasitism in <i>C. minitans</i>, a conidiation-deficient mutant, ZS-1TN5012, was isolated from a transfer DNA (T-DNA) insertional library. This mutant exhibited significantly reduced hyphal development, poor conidiation, and decreased sclerotial mycoparasitism. <i>CmHmgr1</i> encoding a 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) was disrupted by the T-DNA insertion. The colony morphology of the wild-type strain ZS-1 resembled that of the mutant ZS-1TN5012 when the HMGR inhibitor atorvastatin was added to potato dextrose agar, with the mutant showing more sensitivity to atorvastatin. Furthermore, cellular localization assays revealed that CmHmgr1 was localized in mitochondria. Gene replacement and complementation experiments confirmed that <i>CmHmgr1</i> is involved in the growth, conidiogenesis and mycoparasitism of <i>C. minitans</i>, and disruption of <i>CmHmgr1</i> triggers apoptosis.
DOI: 10.6084/m9.figshare.29627417.v1
title: Disruption of <i>CmHmgr1</i> triggers apoptosis and causes defects in growth, conidiogenesis, and mycoparasitism of <i>Coniothyrium minitans</i>

description: <i>Coniothyrium minitans</i> is a well-known mycoparasite against <i>Sclerotinia sclerotiorum.</i> Two critical factors for the commercialization of <i>C. minitans</i> as a biocontrol agent are conidial production and parasitism. To decipher the mechanisms of conidiogenesis and mycoparasitism in <i>C. minitans</i>, a conidiation-deficient mutant, ZS-1TN5012, was isolated from a transfer DNA (T-DNA) insertional library. This mutant exhibited significantly reduced hyphal development, poor conidiation, and decreased sclerotial mycoparasitism. <i>CmHmgr1</i> encoding a 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) was disrupted by the T-DNA insertion. The colony morphology of the wild-type strain ZS-1 resembled that of the mutant ZS-1TN5012 when the HMGR inhibitor atorvastatin was added to potato dextrose agar, with the mutant showing more sensitivity to atorvastatin. Furthermore, cellular localization assays revealed that CmHmgr1 was localized in mitochondria. Gene replacement and complementation experiments confirmed that <i>CmHmgr1</i> is involved in the growth, conidiogenesis and mycoparasitism of <i>C. minitans</i>, and disruption of <i>CmHmgr1</i> triggers apoptosis.
DOI: 10.6084/m9.figshare.30485597
title: Novel amino acid residues in listerolysin O drive phagosome escape and pathogenicity in <i>Listeria monocytogenes</i>

description: <i>Listeria monocytogenes</i>, a significant zoonotic foodborne intracellular pathogen, relies on its principal virulence factor, listeriolysin O (LLO), to escape from host cell phagosomes-a critical step for establishing intracellular infection and replication. LLO, composed of four structural domains with amino acids essential for its pore-forming abilities, still harbors many sites with undefined roles. We identified a critical domain within LLO (amino acids 251–255) crucial for bacterial pathogenesis and systematically investigated the individual roles of five amino acid sites within this domain. Our findings demonstrate that LLO K252 is dispensable for LLO functionality, residues F251, Q253, and Y255 are critical for LLO’s hemolytic activity and cytotoxicity. Mutation of I254 to alanine alters hemolytic activity, with effects dependent on environmental pH. Notably, alanine mutations at F251, Q253, and Y255A significantly impair bacterial proliferation in mouse organs and disruption of late phagosome membranes. In particular, mutations F251A and Y255A abolish late phagosome escape, underscoring their importance in host cell infection. This study has expanded our understanding of LLO’s role in <i>Listeria</i> pathogenicity and phagosome escape, offering new insights into the molecular mechanisms driving this pathogens’ virulence.