cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7936970
title: Comparative genomics of <i>Campylobacter concisus</i>: Analysis of clinical strains reveals genome diversity and pathogenic potential

description: In recent years, an increasing number of <i>Campylobacter</i> species have been associated with human gastrointestinal (GI) diseases including gastroenteritis, inflammatory bowel disease, and colorectal cancer. <i>Campylobacter concisus</i>, an oral commensal historically linked to gingivitis and periodontitis, has been increasingly detected in the lower GI tract. In the present study, we generated robust genome sequence data from <i>C. concisus</i> strains and undertook a comprehensive pangenome assessment to identify <i>C. concisus</i> virulence properties and to explain potential adaptations acquired while residing in specific ecological niche(s) of the GI tract. Genomes of 53 new <i>C. concisus</i> strains were sequenced, assembled, and annotated including 36 strains from gastroenteritis patients, 13 strains from Crohn’s disease patients and four strains from colitis patients (three collagenous colitis and one lymphocytic colitis). When compared with previous published sequences, strains clustered into two main groups/genomospecies (GS) with phylogenetic clustering explained neither by disease phenotype nor sample location. Paired oral/faecal isolates, from the same patient, indicated that there are few genetic differences between oral and gut isolates which suggests that gut isolates most likely reflect oral strain relocation. Type IV and VI secretion systems genes, genes known to be important for pathogenicity in the <i>Campylobacter</i> genus, were present in the genomes assemblies, with 82% containing Type VI secretion system genes. Our findings indicate that <i>C. concisus</i> strains are genetically diverse, and the variability in bacterial secretion system content may play an important role in their virulence potential.
DOI: 10.6084/m9.figshare.7936970.v2
title: Comparative genomics of <i>Campylobacter concisus</i>: Analysis of clinical strains reveals genome diversity and pathogenic potential

description: In recent years, an increasing number of <i>Campylobacter</i> species have been associated with human gastrointestinal (GI) diseases including gastroenteritis, inflammatory bowel disease, and colorectal cancer. <i>Campylobacter concisus</i>, an oral commensal historically linked to gingivitis and periodontitis, has been increasingly detected in the lower GI tract. In the present study, we generated robust genome sequence data from <i>C. concisus</i> strains and undertook a comprehensive pangenome assessment to identify <i>C. concisus</i> virulence properties and to explain potential adaptations acquired while residing in specific ecological niche(s) of the GI tract. Genomes of 53 new <i>C. concisus</i> strains were sequenced, assembled, and annotated including 36 strains from gastroenteritis patients, 13 strains from Crohn’s disease patients and four strains from colitis patients (three collagenous colitis and one lymphocytic colitis). When compared with previous published sequences, strains clustered into two main groups/genomospecies (GS) with phylogenetic clustering explained neither by disease phenotype nor sample location. Paired oral/faecal isolates, from the same patient, indicated that there are few genetic differences between oral and gut isolates which suggests that gut isolates most likely reflect oral strain relocation. Type IV and VI secretion systems genes, genes known to be important for pathogenicity in the <i>Campylobacter</i> genus, were present in the genomes assemblies, with 82% containing Type VI secretion system genes. Our findings indicate that <i>C. concisus</i> strains are genetically diverse, and the variability in bacterial secretion system content may play an important role in their virulence potential.
DOI: 10.6084/m9.figshare.7937075
title: Biodiversity of rodent anelloviruses in China

description: Biodiversity of rodent anelloviruses in China
DOI: 10.6084/m9.figshare.7937075.v1
title: Biodiversity of rodent anelloviruses in China

description: Biodiversity of rodent anelloviruses in China
DOI: 10.15468/dl.pamjqc
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cienfuegosia hitchcockii (Ulbr. ex Kearney) O.J.Blanch.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073440-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-66130
title: Redemption tidings, vol. 46, nos. 1-53, 1 Jan. - 31 Dec. 1970

description: [description english/roman)] Issued weekly.
DOI: 10.6084/m9.figshare.7936865
title: Landscape of the genome and host cell response of <i>Mycobacterium shigaense</i> reveals pathogenic features

description: A systems approach was used to explore the genome and transcriptome of <i>Mycobacterium shigaense</i>, a new opportunistic pathogen isolated from a patient with a skin infection, and the host response transcriptome was assessed using a macrophage infection model. The <i>M</i>. <i>shigaense</i> genome comprises 5,207,883 bp, with 67.2% G+C content and 5098 predicted coding genes. Evolutionarily, the bacterium belongs to a cluster in the phylogenetic tree along with three target opportunistic pathogenic strains, namely, <i>M</i>. <i>avium</i>, <i>M</i>. <i>triplex</i> and <i>M</i>. <i>simiae</i>. Potential virulence genes are indeed expressed by <i>M</i>. <i>shigaense</i> under culture conditions. Phenotypically, <i>M</i>. <i>shigaense</i> had similar infection and replication capacities in a macrophage model as the opportunistic species compared to <i>M</i>. <i>tuberculosis</i>. <i>M</i>. <i>shigaense</i> activated NF-κB, TNF, cytokines and chemokines in the host innate immune-related signaling pathways and elicited an early response shared with pathogenic bacilli except <i>M</i>. <i>tuberculosis</i>. <i>M</i>. <i>shigaense</i> upregulated specific host response genes such as <i>TLR7</i>, <i>CCL4</i> and <i>CXCL5</i>. We performed an integrated and comparative analysis of <i>M</i>. <i>shigaense</i>. Multigroup comparison indicated certain differences with typical pathogenic bacilli in terms of gene features and the macrophage response.
DOI: 10.6084/m9.figshare.7936865.v1
title: Landscape of the genome and host cell response of <i>Mycobacterium shigaense</i> reveals pathogenic features

description: A systems approach was used to explore the genome and transcriptome of <i>Mycobacterium shigaense</i>, a new opportunistic pathogen isolated from a patient with a skin infection, and the host response transcriptome was assessed using a macrophage infection model. The <i>M</i>. <i>shigaense</i> genome comprises 5,207,883 bp, with 67.2% G+C content and 5098 predicted coding genes. Evolutionarily, the bacterium belongs to a cluster in the phylogenetic tree along with three target opportunistic pathogenic strains, namely, <i>M</i>. <i>avium</i>, <i>M</i>. <i>triplex</i> and <i>M</i>. <i>simiae</i>. Potential virulence genes are indeed expressed by <i>M</i>. <i>shigaense</i> under culture conditions. Phenotypically, <i>M</i>. <i>shigaense</i> had similar infection and replication capacities in a macrophage model as the opportunistic species compared to <i>M</i>. <i>tuberculosis</i>. <i>M</i>. <i>shigaense</i> activated NF-κB, TNF, cytokines and chemokines in the host innate immune-related signaling pathways and elicited an early response shared with pathogenic bacilli except <i>M</i>. <i>tuberculosis</i>. <i>M</i>. <i>shigaense</i> upregulated specific host response genes such as <i>TLR7</i>, <i>CCL4</i> and <i>CXCL5</i>. We performed an integrated and comparative analysis of <i>M</i>. <i>shigaense</i>. Multigroup comparison indicated certain differences with typical pathogenic bacilli in terms of gene features and the macrophage response.
DOI: 10.6084/m9.figshare.7936970.v1
title: Comparative genomics of <i>Campylobacter concisus</i>: Analysis of clinical strains reveals genome diversity and pathogenic potential

description: In recent years, an increasing number of <i>Campylobacter</i> species have been associated with human gastrointestinal (GI) diseases including gastroenteritis, inflammatory bowel disease, and colorectal cancer. <i>Campylobacter concisus</i>, an oral commensal historically linked to gingivitis and periodontitis, has been increasingly detected in the lower GI tract. In the present study, we generated robust genome sequence data from <i>C. concisus</i> strains and undertook a comprehensive pangenome assessment to identify <i>C. concisus</i> virulence properties and to explain potential adaptations acquired while residing in specific ecological niche(s) of the GI tract. Genomes of 53 new <i>C. concisus</i> strains were sequenced, assembled, and annotated including 36 strains from gastroenteritis patients, 13 strains from Crohn’s disease patients and four strains from colitis patients (three collagenous colitis and one lymphocytic colitis). When compared with previous published sequences, strains clustered into two main groups/genomospecies (GS) with phylogenetic clustering explained neither by disease phenotype nor sample location. Paired oral/faecal isolates, from the same patient, indicated that there are few genetic differences between oral and gut isolates which suggests that gut isolates most likely reflect oral strain relocation. Type IV and VI secretion systems genes, genes known to be important for pathogenicity in the <i>Campylobacter</i> genus, were present in the genomes assemblies, with 82% containing Type VI secretion system genes. Our findings indicate that <i>C. concisus</i> strains are genetically diverse, and the variability in bacterial secretion system content may play an important role in their virulence potential.
DOI: 10.15468/dl.c6qdcd
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phlomoides szechuanensis (C.Y.Wu) Kamelin & Makhm."
 ]
}

 The dataset includes 17 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075135-230530130749713/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.7936868.v2
title: Phenotypic and molecular analysis of nontypeable Group B streptococci: identification of <i>cps2a</i> and hybrid <i>cps2a/cps5</i> Group B streptococcal capsule gene clusters

description: The Group B streptococcus (GBS) can express a capsular polysaccharide (CPS). There are ten recognized CPSs (Ia, Ib, and II–IX). A GBS isolate is considered nontypeable (NT) when CPS cannot be identified as one of ten types. Two groups of GBS NT isolates were studied, isolates without surface sialic acid (sia(−)) and isolates with surface sialic acid (sia(+)). The first objective was to characterize NT sia(−) isolates that failed CPS identification by an immunodiffusion antisera typing assay and a RT-PCR capsule typing assay. NT sia(−) isolates were characterized by assaying phenotypic changes and identifying <i>covR/S</i> mutations that may potentially have a role in the altered phenotypes. The second objective was to characterize NT sia(+) isolates that failed to identify as one of the ten CPS types by an immundiffusion antisera-based typing assay and a RT-PCR capsule typing assay yet expressed capsule. Fifteen NT sia(−) isolates displayed increased β hemolysis/orange pigmentation, decreased CAMP activity, inability to form biofilm, and susceptibility to phagocytosis by human blood. DNA sequence analysis of the <i>covR/S</i> genes in the sia(−) isolates found mutations in 14 of 15 isolates assayed. These mutations in the <i>covR/S</i> genes may potentially contribute to lack of expression of phenotypic traits assayed in vitro. For the three NT sia(+) isolates, whole-genome sequence analyses identified two isolates with <i>cps</i> gene clusters identical to the recently described and uncommon CPSIIa type. The third isolate possessed a hybrid cluster containing <i>cps</i> genes for both CPSIIa and CPSV suggesting recombination between these two gene clusters.
DOI: 10.6084/m9.figshare.7937138
title: Ranavirus genotypes in the Netherlands and their potential association with virulence in water frogs (<i>Pelophylax</i> spp.)

description: Ranaviruses are pathogenic viruses for poikilothermic vertebrates worldwide. The identification of a common midwife toad virus (CMTV) associated with massive die-offs in water frogs (<i>Pelophylax</i> spp.) in the Netherlands has increased awareness for emerging viruses in amphibians in the country. Complete genome sequencing of 13 ranavirus isolates collected from ten different sites in the period 2011–2016 revealed three CMTV groups present in distinct geographical areas in the Netherlands. Phylogenetic analysis showed that emerging viruses from the northern part of the Netherlands belonged to CMTV-NL group I. Group II and III viruses were derived from the animals located in the center-east and south of the country, and shared a more recent common ancestor to CMTV-amphibian associated ranaviruses reported in China, Italy, Denmark, and Switzerland. Field monitoring revealed differences in water frog host abundance at sites where distinct ranavirus groups occur; with ranavirus-associated deaths, host counts decreasing progressively, and few juveniles found in the north where CMTV-NL group I occurs but not in the south with CMTV-NL group III. Investigation of tandem repeats of coding genes gave no conclusive information about phylo-geographical clustering, while genetic analysis of the genomes revealed truncations in 17 genes across CMTV-NL groups II and III compared to group I. Further studies are needed to elucidate the contribution of these genes as well as environmental variables to explain the observed differences in host abundance.
DOI: 10.6084/m9.figshare.7937138.v1
title: Ranavirus genotypes in the Netherlands and their potential association with virulence in water frogs (<i>Pelophylax</i> spp.)

description: Ranaviruses are pathogenic viruses for poikilothermic vertebrates worldwide. The identification of a common midwife toad virus (CMTV) associated with massive die-offs in water frogs (<i>Pelophylax</i> spp.) in the Netherlands has increased awareness for emerging viruses in amphibians in the country. Complete genome sequencing of 13 ranavirus isolates collected from ten different sites in the period 2011–2016 revealed three CMTV groups present in distinct geographical areas in the Netherlands. Phylogenetic analysis showed that emerging viruses from the northern part of the Netherlands belonged to CMTV-NL group I. Group II and III viruses were derived from the animals located in the center-east and south of the country, and shared a more recent common ancestor to CMTV-amphibian associated ranaviruses reported in China, Italy, Denmark, and Switzerland. Field monitoring revealed differences in water frog host abundance at sites where distinct ranavirus groups occur; with ranavirus-associated deaths, host counts decreasing progressively, and few juveniles found in the north where CMTV-NL group I occurs but not in the south with CMTV-NL group III. Investigation of tandem repeats of coding genes gave no conclusive information about phylo-geographical clustering, while genetic analysis of the genomes revealed truncations in 17 genes across CMTV-NL groups II and III compared to group I. Further studies are needed to elucidate the contribution of these genes as well as environmental variables to explain the observed differences in host abundance.
DOI: 10.6084/m9.figshare.7937810
title: <i>TSC1</i> and <i>DEPDC5</i> regulate HIV-1 latency through the mTOR signaling pathway

description: The latent reservoir of HIV-1 presents a major barrier to viral eradication. The mechanism of the establishment and maintenance of the latent viral reservoir is not yet fully understood, which hinders the development of effective curative strategies. In this study, we identified two inhibitory genes, <i>TSC1</i> and <i>DEPDC5</i>, that maintained HIV-1 latency by suppressing the mTORC1 pathway. We first adapted a genome-wide CRISPR screening approach to identify host factors required for HIV latency in a T-cell-based latency model and discovered two inhibitory genes, <i>TSC1</i> and <i>DEPDC5</i>, which are potentially involved in HIV-1 latency. Knockout of either <i>TSC1</i> or <i>DEPDC5</i> led to enhanced HIV-1 reactivation in both a T-cell line (C11) and a monocyte cell line (U1), and this enhancement could be antagonized by the mTORC1 inhibitor rapamycin. Further evaluation of the mechanism revealed that <i>TSC1</i> suppresses AKT-mTORC1-S6 via downregulation of Rheb, whereas <i>DEPDC5</i> inhibits AKT-mTORC1-S6 through RagA. Overall, both <i>TSC1</i> and <i>DEPDC5</i> negatively regulate the AKT-mTORC1 pathway, and thus their agonists could be used in the development of new therapeutic approaches for activating HIV-1 latency.
DOI: 10.6084/m9.figshare.7937810.v1
title: <i>TSC1</i> and <i>DEPDC5</i> regulate HIV-1 latency through the mTOR signaling pathway

description: The latent reservoir of HIV-1 presents a major barrier to viral eradication. The mechanism of the establishment and maintenance of the latent viral reservoir is not yet fully understood, which hinders the development of effective curative strategies. In this study, we identified two inhibitory genes, <i>TSC1</i> and <i>DEPDC5</i>, that maintained HIV-1 latency by suppressing the mTORC1 pathway. We first adapted a genome-wide CRISPR screening approach to identify host factors required for HIV latency in a T-cell-based latency model and discovered two inhibitory genes, <i>TSC1</i> and <i>DEPDC5</i>, which are potentially involved in HIV-1 latency. Knockout of either <i>TSC1</i> or <i>DEPDC5</i> led to enhanced HIV-1 reactivation in both a T-cell line (C11) and a monocyte cell line (U1), and this enhancement could be antagonized by the mTORC1 inhibitor rapamycin. Further evaluation of the mechanism revealed that <i>TSC1</i> suppresses AKT-mTORC1-S6 via downregulation of Rheb, whereas <i>DEPDC5</i> inhibits AKT-mTORC1-S6 through RagA. Overall, both <i>TSC1</i> and <i>DEPDC5</i> negatively regulate the AKT-mTORC1 pathway, and thus their agonists could be used in the development of new therapeutic approaches for activating HIV-1 latency.
DOI: 10.6084/m9.figshare.7936868
title: Phenotypic and molecular analysis of nontypeable Group B streptococci: identification of <i>cps2a</i> and hybrid <i>cps2a/cps5</i> Group B streptococcal capsule gene clusters

description: The Group B streptococcus (GBS) can express a capsular polysaccharide (CPS). There are ten recognized CPSs (Ia, Ib, and II–IX). A GBS isolate is considered nontypeable (NT) when CPS cannot be identified as one of ten types. Two groups of GBS NT isolates were studied, isolates without surface sialic acid (sia(−)) and isolates with surface sialic acid (sia(+)). The first objective was to characterize NT sia(−) isolates that failed CPS identification by an immunodiffusion antisera typing assay and a RT-PCR capsule typing assay. NT sia(−) isolates were characterized by assaying phenotypic changes and identifying <i>covR/S</i> mutations that may potentially have a role in the altered phenotypes. The second objective was to characterize NT sia(+) isolates that failed to identify as one of the ten CPS types by an immundiffusion antisera-based typing assay and a RT-PCR capsule typing assay yet expressed capsule. Fifteen NT sia(−) isolates displayed increased β hemolysis/orange pigmentation, decreased CAMP activity, inability to form biofilm, and susceptibility to phagocytosis by human blood. DNA sequence analysis of the <i>covR/S</i> genes in the sia(−) isolates found mutations in 14 of 15 isolates assayed. These mutations in the <i>covR/S</i> genes may potentially contribute to lack of expression of phenotypic traits assayed in vitro. For the three NT sia(+) isolates, whole-genome sequence analyses identified two isolates with <i>cps</i> gene clusters identical to the recently described and uncommon CPSIIa type. The third isolate possessed a hybrid cluster containing <i>cps</i> genes for both CPSIIa and CPSV suggesting recombination between these two gene clusters.
DOI: 10.6084/m9.figshare.7936868.v1
title: Phenotypic and molecular analysis of nontypeable Group B streptococci: identification of <i>cps2a</i> and hybrid <i>cps2a/cps5</i> Group B streptococcal capsule gene clusters

description: The Group B streptococcus (GBS) can express a capsular polysaccharide (CPS). There are ten recognized CPSs (Ia, Ib, and II–IX). A GBS isolate is considered nontypeable (NT) when CPS cannot be identified as one of ten types. Two groups of GBS NT isolates were studied, isolates without surface sialic acid (sia(−)) and isolates with surface sialic acid (sia(+)). The first objective was to characterize NT sia(−) isolates that failed CPS identification by an immunodiffusion antisera typing assay and a RT-PCR capsule typing assay. NT sia(−) isolates were characterized by assaying phenotypic changes and identifying <i>covR/S</i> mutations that may potentially have a role in the altered phenotypes. The second objective was to characterize NT sia(+) isolates that failed to identify as one of the ten CPS types by an immundiffusion antisera-based typing assay and a RT-PCR capsule typing assay yet expressed capsule. Fifteen NT sia(−) isolates displayed increased β hemolysis/orange pigmentation, decreased CAMP activity, inability to form biofilm, and susceptibility to phagocytosis by human blood. DNA sequence analysis of the <i>covR/S</i> genes in the sia(−) isolates found mutations in 14 of 15 isolates assayed. These mutations in the <i>covR/S</i> genes may potentially contribute to lack of expression of phenotypic traits assayed in vitro. For the three NT sia(+) isolates, whole-genome sequence analyses identified two isolates with <i>cps</i> gene clusters identical to the recently described and uncommon CPSIIa type. The third isolate possessed a hybrid cluster containing <i>cps</i> genes for both CPSIIa and CPSV suggesting recombination between these two gene clusters.