cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1422081.v1
title: First occurrence of a mawsoniid coelacanth in the Early Jurassic of Europe

description: ABSTRACT—Coelacanths form a clade of sarcopterygian fishes (lobe-finned vertebrates) that today is represented by a single genus, <i>Latimeria</i>. This genus belongs to a lineage of marine coelacanths, the latimeriids, whose fossils are common in the Jurassic and the Cretaceous deposits of Europe and North America. During the same periods, another lineage of fresh/brackish water coelacanths, the mawsoniids, occurred in South America, Africa, and Madagascar. Mawsoniids are supposed to have originated during the Triassic in North America and were assumed to have subsequently dispersed to South America during the Jurassic, before reaching western Africa during the Early Cretaceous. Previous hypotheses advocated that mawsoniid coelacanths reached Europe during the Late Cretaceous, suggesting the dispersal of freshwater organisms from Africa to Europe during this period. We here reevaluate this scenario based on the reexamination of the coelacanth <i>Trachymetopon</i> from the Early Jurassic of Germany. Although this genus is known from remarkably well-preserved material, its relationships to other Mesozoic coelacanths remained unsolved. An anatomical investigation shows that <i>Trachymetopon</i> shares many common features with the Late Jurassic–Late Cretaceous mawsoniids <i>Mawsonia</i> and <i>Axelrodichthys</i> from western Gondwana, such as the absence of a descending process of the supratemporal, the presence of ossified ribs, and the skull roof and cheek bones ornamented by conspicuous coarse rugosities and ridges. A phylogenetic analysis of morphological characters places <i>Trachymetopon</i> within Mawsoniidae. We suggest that mawsoniid coelacanths were already present in Europe from the Early Jurassic onwards, challenging previous paleobiogeographic scenarios.SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1422086.v2
title: New Undescribed Lineages of Non-extremophilic Archaea Form a Homogeneous and Dominant Element Within Alpine Moonmilk Microbiomes

description: The moonmilk deposits within the alpine Hundsalm cave in Austria offered the opportunity to investigate anthropogenically uninfluenced microbiomes. Via cultivation experiments we were able to show that the communities were cold-adapted and oligotrophic. Combined qPCR, DGGE, cloning and sequencing data further highlighted that the archaeal community basically comprises a low number of species, though highly abundant. These organisms are assumed to form new lineages within the <i>Euryarchaeota</i>, while the detected <i>Thaumarchaeota</i>, closely related to ammonium oxidizers, form a second, but minor, abundant group within the moonmilk deposits. Moreover, in terms of abundance the archaeal community clearly outnumbers bacteria (e.g., genera <i>Pseudomonas, Flavobacterium</i> and <i>Rhodococcus</i>) and fungi within the investigated microbiomes. In contrast to the highly complex bacterial and fungal communities, only a low number of archaeal species form a constant and essential element within the moonmilk speleothems and other cave-internal habitats.
DOI: 10.6084/m9.figshare.1422086.v4
title: New Undescribed Lineages of Non-extremophilic Archaea Form a Homogeneous and Dominant Element Within Alpine Moonmilk Microbiomes

description: The moonmilk deposits within the alpine Hundsalm cave in Austria offered the opportunity to investigate anthropogenically uninfluenced microbiomes. Via cultivation experiments we were able to show that the communities were cold-adapted and oligotrophic. Combined qPCR, DGGE, cloning and sequencing data further highlighted that the archaeal community basically comprises a low number of species, though highly abundant. These organisms are assumed to form new lineages within the <i>Euryarchaeota</i>, while the detected <i>Thaumarchaeota</i>, closely related to ammonium oxidizers, form a second, but minor, abundant group within the moonmilk deposits. Moreover, in terms of abundance the archaeal community clearly outnumbers bacteria (e.g., genera <i>Pseudomonas, Flavobacterium</i> and <i>Rhodococcus</i>) and fungi within the investigated microbiomes. In contrast to the highly complex bacterial and fungal communities, only a low number of archaeal species form a constant and essential element within the moonmilk speleothems and other cave-internal habitats.
DOI: 10.6084/m9.figshare.1422078.v1
title: A new Late Triassic traversodontid cynodont (Therapsida, Eucynodontia) from India

description: ABSTRACT—A large traversodontid cynodont <i>Ruberodon roychowdhurii</i>, gen et. sp. nov., is described from the Late Triassic Tiki Formation of the Rewa Gondwana Basin, India, based on an ontogenetic series of five partial lower jaws. <i>Ruberodon</i> is characterized by a robust and deep dentary symphysis, lower dental formula of i3-c1-pc9, procumbent and hypertrophied first lower incisor, a large canine, long diastema between the lower canine and first postcanine, and a high coronoid process at 60° to the horizontal tooth row. With growth, the symphyseal region became relatively more slender with lengthening of the diastema. Phylogenetic analysis based on 19 taxa and 35 craniodental characters places <i>Ruberodon</i> within the clade containing <i>Gomphodontosuchus</i>, <i>Menadon</i>, <i>Protuberum</i>, <i>Scalenodontoides</i>, and the multispecific <i>Exaeretodon</i>. The new genus forms a sister taxon to <i>E. statisticae</i> and is more advanced than <i>E. riograndensis</i> and <i>E. argentinus</i> based on the presence of a strong coronoid ridge anterior to the masseteric fossa. Based on its tetrapod assemblage, the Tiki Formation may be globally correlated with other formations such as the lower part of the Maleri Formation of India, the Isalo II Beds of Madagascar, and the upper part of the Santa Maria Formation of Brazil. An early Carnian age is proposed for the Tiki Formation. http://zoobank.org/urn:lsid:zoobank.org:pub:80D363C5-D311-4788-90E2-3BE4CFC35FEESUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1422078.v2
title: A new Late Triassic traversodontid cynodont (Therapsida, Eucynodontia) from India

description: ABSTRACT—A large traversodontid cynodont <i>Ruberodon roychowdhurii</i>, gen et. sp. nov., is described from the Late Triassic Tiki Formation of the Rewa Gondwana Basin, India, based on an ontogenetic series of five partial lower jaws. <i>Ruberodon</i> is characterized by a robust and deep dentary symphysis, lower dental formula of i3-c1-pc9, procumbent and hypertrophied first lower incisor, a large canine, long diastema between the lower canine and first postcanine, and a high coronoid process at 60° to the horizontal tooth row. With growth, the symphyseal region became relatively more slender with lengthening of the diastema. Phylogenetic analysis based on 19 taxa and 35 craniodental characters places <i>Ruberodon</i> within the clade containing <i>Gomphodontosuchus</i>, <i>Menadon</i>, <i>Protuberum</i>, <i>Scalenodontoides</i>, and the multispecific <i>Exaeretodon</i>. The new genus forms a sister taxon to <i>E. statisticae</i> and is more advanced than <i>E. riograndensis</i> and <i>E. argentinus</i> based on the presence of a strong coronoid ridge anterior to the masseteric fossa. Based on its tetrapod assemblage, the Tiki Formation may be globally correlated with other formations such as the lower part of the Maleri Formation of India, the Isalo II Beds of Madagascar, and the upper part of the Santa Maria Formation of Brazil. An early Carnian age is proposed for the Tiki Formation. http://zoobank.org/urn:lsid:zoobank.org:pub:80D363C5-D311-4788-90E2-3BE4CFC35FEESUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP
DOI: 10.6084/m9.figshare.1422086.v3
title: New Undescribed Lineages of Non-extremophilic Archaea Form a Homogeneous and Dominant Element Within Alpine Moonmilk Microbiomes

description: The moonmilk deposits within the alpine Hundsalm cave in Austria offered the opportunity to investigate anthropogenically uninfluenced microbiomes. Via cultivation experiments we were able to show that the communities were cold-adapted and oligotrophic. Combined qPCR, DGGE, cloning and sequencing data further highlighted that the archaeal community basically comprises a low number of species, though highly abundant. These organisms are assumed to form new lineages within the <i>Euryarchaeota</i>, while the detected <i>Thaumarchaeota</i>, closely related to ammonium oxidizers, form a second, but minor, abundant group within the moonmilk deposits. Moreover, in terms of abundance the archaeal community clearly outnumbers bacteria (e.g., genera <i>Pseudomonas, Flavobacterium</i> and <i>Rhodococcus</i>) and fungi within the investigated microbiomes. In contrast to the highly complex bacterial and fungal communities, only a low number of archaeal species form a constant and essential element within the moonmilk speleothems and other cave-internal habitats.
DOI: 10.6084/m9.figshare.1422074
title: OXCYSnr

description: Dataset containing disulfide bond annotations for proteins with no homologs in the PDBCYS and SPX datasets.
DOI: 10.6084/m9.figshare.1422073
title: OXCYS15

description: Dataset extracted from the April 2015 version of PDB. It contains disulfide bonds annotations collected from PDB structures released after June 2010
DOI: 10.6084/m9.figshare.1422073.v1
title: OXCYS15

description: Dataset extracted from the April 2015 version of PDB. It contains disulfide bonds annotations collected from PDB structures released after June 2010
DOI: 10.6084/m9.figshare.1422074.v1
title: OXCYSnr

description: Dataset containing disulfide bond annotations for proteins with no homologs in the PDBCYS and SPX datasets.
DOI: 10.6084/m9.figshare.1422054
title: Macroautophagy is essential for killing of intracellular <i>Burkholderia pseudomallei</i> in human neutrophils

description: Neutrophils play a key role in the control of <i>Burkholderia pseudomallei</i>, the pathogen that causes melioidosis. Here, we show that survival of intracellular <i>B. pseudomallei</i> was significantly increased in the presence of 3-methyladenine or lysosomal cathepsin inhibitors. The LC3-flux was increased in <i>B. pseudomallei</i>-infected neutrophils. Concordant with this result, confocal microscopy analyses using anti-LC3 antibodies revealed that <i>B. pseudomallei</i>-containing phagosomes partially overlapped with LC3-positive signal at 3 and 6 h postinfection. Electron microscopic analyses of <i>B. pseudomallei</i>-infected neutrophils at 3 h revealed <i>B. pseudomallei</i>-containing phagosomes that occasionally fused with phagophores or autophagosomes. Following infection with a <i>B. pseudomallei</i> mutant lacking the <i>Burkholderia</i> secretion apparatus Bsa Type III secretion system, neither this characteristic structure nor bacterial escape into the cytosol were observed. These findings indicate that human neutrophils are able to recruit autophagic machinery adjacent to <i>B. pseudomallei</i>-containing phagosomes in a Type III secretion system-dependent manner.
DOI: 10.6084/m9.figshare.1422058
title: Subject_1_1 from Appelgren and Bengtsson, Feedback on Trait or Action Impacts on Caudate and Paracingulum Activity, Plos one 2015

description: Subject1 session Task from Appelgren and Bengtsson, Feedback on Trait or Action Impacts on Caudate and Paracingulum Activity, Plos one 2015
DOI: 10.34740/kaggle/dsv/1463479
title: Vietnam SARS-CoV-2 | COVID-19 Data
DOI: 10.6084/m9.figshare.1422058.v2
title: Subject_1_1 from Appelgren and Bengtsson, Feedback on Trait or Action Impacts on Caudate and Paracingulum Activity, Plos one 2015

description: Subject1 session Task from Appelgren and Bengtsson, Feedback on Trait or Action Impacts on Caudate and Paracingulum Activity, Plos one 2015
DOI: 10.6084/m9.figshare.1422054.v1
title: Macroautophagy is essential for killing of intracellular <i>Burkholderia pseudomallei</i> in human neutrophils

description: Neutrophils play a key role in the control of <i>Burkholderia pseudomallei</i>, the pathogen that causes melioidosis. Here, we show that survival of intracellular <i>B. pseudomallei</i> was significantly increased in the presence of 3-methyladenine or lysosomal cathepsin inhibitors. The LC3-flux was increased in <i>B. pseudomallei</i>-infected neutrophils. Concordant with this result, confocal microscopy analyses using anti-LC3 antibodies revealed that <i>B. pseudomallei</i>-containing phagosomes partially overlapped with LC3-positive signal at 3 and 6 h postinfection. Electron microscopic analyses of <i>B. pseudomallei</i>-infected neutrophils at 3 h revealed <i>B. pseudomallei</i>-containing phagosomes that occasionally fused with phagophores or autophagosomes. Following infection with a <i>B. pseudomallei</i> mutant lacking the <i>Burkholderia</i> secretion apparatus Bsa Type III secretion system, neither this characteristic structure nor bacterial escape into the cytosol were observed. These findings indicate that human neutrophils are able to recruit autophagic machinery adjacent to <i>B. pseudomallei</i>-containing phagosomes in a Type III secretion system-dependent manner.
DOI: 10.6084/m9.figshare.1422058.v1
title: S1_1

description: Subject1 session Task from Appelgren and Bengtsson, Feedback on Trait or Action Impacts on Caudate and Paracingulum Activity, Plos one 2015
DOI: 10.6084/m9.figshare.1422052
title: Human Protein Atlas Connexin Cx annotation

description: Search of Human Protein Database carried out on 21 May 2015 with search term "connexin". Removed data for proteins CNST, CAV3, CXADR.
DOI: 10.6084/m9.figshare.1422054.v2
title: Macroautophagy is essential for killing of intracellular <i>Burkholderia pseudomallei</i> in human neutrophils

description: Neutrophils play a key role in the control of <i>Burkholderia pseudomallei</i>, the pathogen that causes melioidosis. Here, we show that survival of intracellular <i>B. pseudomallei</i> was significantly increased in the presence of 3-methyladenine or lysosomal cathepsin inhibitors. The LC3-flux was increased in <i>B. pseudomallei</i>-infected neutrophils. Concordant with this result, confocal microscopy analyses using anti-LC3 antibodies revealed that <i>B. pseudomallei</i>-containing phagosomes partially overlapped with LC3-positive signal at 3 and 6 h postinfection. Electron microscopic analyses of <i>B. pseudomallei</i>-infected neutrophils at 3 h revealed <i>B. pseudomallei</i>-containing phagosomes that occasionally fused with phagophores or autophagosomes. Following infection with a <i>B. pseudomallei</i> mutant lacking the <i>Burkholderia</i> secretion apparatus Bsa Type III secretion system, neither this characteristic structure nor bacterial escape into the cytosol were observed. These findings indicate that human neutrophils are able to recruit autophagic machinery adjacent to <i>B. pseudomallei</i>-containing phagosomes in a Type III secretion system-dependent manner.
DOI: 10.6084/m9.figshare.1422052.v1
title: Human Protein Atlas Connexin Cx annotation

description: Search of Human Protein Database carried out on 21 May 2015 with search term "connexin". Removed data for proteins CNST, CAV3, CXADR.
DOI: 10.6084/m9.figshare.1422054.v4
title: Macroautophagy is essential for killing of intracellular <i>Burkholderia pseudomallei</i> in human neutrophils

description: Neutrophils play a key role in the control of <i>Burkholderia pseudomallei</i>, the pathogen that causes melioidosis. Here, we show that survival of intracellular <i>B. pseudomallei</i> was significantly increased in the presence of 3-methyladenine or lysosomal cathepsin inhibitors. The LC3-flux was increased in <i>B. pseudomallei</i>-infected neutrophils. Concordant with this result, confocal microscopy analyses using anti-LC3 antibodies revealed that <i>B. pseudomallei</i>-containing phagosomes partially overlapped with LC3-positive signal at 3 and 6 h postinfection. Electron microscopic analyses of <i>B. pseudomallei</i>-infected neutrophils at 3 h revealed <i>B. pseudomallei</i>-containing phagosomes that occasionally fused with phagophores or autophagosomes. Following infection with a <i>B. pseudomallei</i> mutant lacking the <i>Burkholderia</i> secretion apparatus Bsa Type III secretion system, neither this characteristic structure nor bacterial escape into the cytosol were observed. These findings indicate that human neutrophils are able to recruit autophagic machinery adjacent to <i>B. pseudomallei</i>-containing phagosomes in a Type III secretion system-dependent manner.
DOI: 10.6084/m9.figshare.1422045
title: TipC and the chorea-acanthocytosis protein VPS13A regulate autophagy in <i>Dictyostelium</i> and human HeLa cells

description: Deficient autophagy causes a distinct phenotype in <i>Dictyostelium discoideum</i>, characterized by the formation of multitips at the mound stage. This led us to analyze autophagy in a number of multitipped mutants described previously (<i>tipA</i><sup>−</sup>, <i>tipB</i><sup>−</sup>, <i>tipC</i><sup>−</sup>, and <i>tipD</i><sup>−</sup>). We found a clear autophagic dysfunction in <i>tipC</i><sup>−</sup> and <i>tipD</i><sup>−</sup> while the others showed no defects. <i>tipD</i> codes for a homolog of Atg16, which confirms the role of this protein in <i>Dictyostelium</i> autophagy and validates our approach. The <i>tipC</i>-encoded protein is highly similar to human VPS13A (also known as chorein), whose mutations cause the chorea-acanthocytosis syndrome. No member of the VPS13 protein family has been previously related to autophagy despite the presence of a region of similarity to Atg2 at the C terminus. This region also contains the conserved domain of unknown function DUF1162. Of interest, the expression of the TipC C-terminal coding sequence containing these 2 motifs largely complemented the mutant phenotype. <i>Dictyostelium</i> cells lacking TipC displayed a reduced number of autophagosomes visualized with the markers GFP-Atg18 and GFP-Atg8 and an impaired autophagic degradation as determined by a proteolytic cleavage assay. Downregulation of human <i>VPS13A</i> in HeLa cells by RNA interference confirmed the participation of the human protein in autophagy. VPS13A-depleted cells showed accumulation of autophagic markers and impaired autophagic flux.
DOI: 10.6084/m9.figshare.1422054.v3
title: Macroautophagy is essential for killing of intracellular <i>Burkholderia pseudomallei</i> in human neutrophils

description: Neutrophils play a key role in the control of <i>Burkholderia pseudomallei</i>, the pathogen that causes melioidosis. Here, we show that survival of intracellular <i>B. pseudomallei</i> was significantly increased in the presence of 3-methyladenine or lysosomal cathepsin inhibitors. The LC3-flux was increased in <i>B. pseudomallei</i>-infected neutrophils. Concordant with this result, confocal microscopy analyses using anti-LC3 antibodies revealed that <i>B. pseudomallei</i>-containing phagosomes partially overlapped with LC3-positive signal at 3 and 6 h postinfection. Electron microscopic analyses of <i>B. pseudomallei</i>-infected neutrophils at 3 h revealed <i>B. pseudomallei</i>-containing phagosomes that occasionally fused with phagophores or autophagosomes. Following infection with a <i>B. pseudomallei</i> mutant lacking the <i>Burkholderia</i> secretion apparatus Bsa Type III secretion system, neither this characteristic structure nor bacterial escape into the cytosol were observed. These findings indicate that human neutrophils are able to recruit autophagic machinery adjacent to <i>B. pseudomallei</i>-containing phagosomes in a Type III secretion system-dependent manner.
DOI: 10.6084/m9.figshare.1422040
title: Camera traps capture species replacement

description: Data relevant to:Caravaggi, A., Zaccaroni, M., Riga, F., Schai‐Braun, S. C., Dick, J. T., Montgomery, W. I., & Reid, N. (2016). An invasive‐native mammalian species replacement process captured by camera trap survey random encounter models. <i>Remote Sensing in Ecology and Conservation</i>.
DOI: 10.6084/m9.figshare.1422040.v1
title: Camera traps capture species replacement

description: Data relevant to:Caravaggi, A., Zaccaroni, M., Riga, F., Schai‐Braun, S. C., Dick, J. T., Montgomery, W. I., & Reid, N. (2016). An invasive‐native mammalian species replacement process captured by camera trap survey random encounter models. <i>Remote Sensing in Ecology and Conservation</i>.
DOI: 10.6084/m9.figshare.1422045.v2
title: TipC and the chorea-acanthocytosis protein VPS13A regulate autophagy in <i>Dictyostelium</i> and human HeLa cells

description: Deficient autophagy causes a distinct phenotype in <i>Dictyostelium discoideum</i>, characterized by the formation of multitips at the mound stage. This led us to analyze autophagy in a number of multitipped mutants described previously (<i>tipA</i><sup>−</sup>, <i>tipB</i><sup>−</sup>, <i>tipC</i><sup>−</sup>, and <i>tipD</i><sup>−</sup>). We found a clear autophagic dysfunction in <i>tipC</i><sup>−</sup> and <i>tipD</i><sup>−</sup> while the others showed no defects. <i>tipD</i> codes for a homolog of Atg16, which confirms the role of this protein in <i>Dictyostelium</i> autophagy and validates our approach. The <i>tipC</i>-encoded protein is highly similar to human VPS13A (also known as chorein), whose mutations cause the chorea-acanthocytosis syndrome. No member of the VPS13 protein family has been previously related to autophagy despite the presence of a region of similarity to Atg2 at the C terminus. This region also contains the conserved domain of unknown function DUF1162. Of interest, the expression of the TipC C-terminal coding sequence containing these 2 motifs largely complemented the mutant phenotype. <i>Dictyostelium</i> cells lacking TipC displayed a reduced number of autophagosomes visualized with the markers GFP-Atg18 and GFP-Atg8 and an impaired autophagic degradation as determined by a proteolytic cleavage assay. Downregulation of human <i>VPS13A</i> in HeLa cells by RNA interference confirmed the participation of the human protein in autophagy. VPS13A-depleted cells showed accumulation of autophagic markers and impaired autophagic flux.
DOI: 10.6084/m9.figshare.1422045.v1
title: TipC and the chorea-acanthocytosis protein VPS13A regulate autophagy in <i>Dictyostelium</i> and human HeLa cells

description: Deficient autophagy causes a distinct phenotype in <i>Dictyostelium discoideum</i>, characterized by the formation of multitips at the mound stage. This led us to analyze autophagy in a number of multitipped mutants described previously (<i>tipA</i><sup>−</sup>, <i>tipB</i><sup>−</sup>, <i>tipC</i><sup>−</sup>, and <i>tipD</i><sup>−</sup>). We found a clear autophagic dysfunction in <i>tipC</i><sup>−</sup> and <i>tipD</i><sup>−</sup> while the others showed no defects. <i>tipD</i> codes for a homolog of Atg16, which confirms the role of this protein in <i>Dictyostelium</i> autophagy and validates our approach. The <i>tipC-</i>encoded protein is highly similar to human VPS13A (also known as Chorein), whose mutations cause the chorea-acanthocytosis syndrome. No member of the VPS13 protein family has been previously related to autophagy despite the presence of a region of similarity to Atg2 at the C terminus. This region also contains the conserved domain of unknown function DUF1162. Of interest, the expression of the TipC C-terminal coding sequence containing these 2 motifs largely complemented the mutant phenotype. <i>Dictyostelium</i> cells lacking TipC displayed a reduced number of autophagosomes visualized with the markers GFP-Atg18 and GFP-Atg8 and an impaired autophagic degradation as determined by a proteolytic cleavage assay. Downregulation of human <i>VPS13A</i> in HeLa cells by RNA interference confirmed the participation of the human protein in autophagy. VPS13A-depleted cells showed accumulation of autophagic markers and impaired autophagic flux.