cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7910/dvn/debtui/oay1bu
title: 1-41.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886532.v1
title: <i>In silico</i> design of a novel chimeric <i>shigella</i> IpaB fused to C terminal of <i>clostridium perfringens</i> enterotoxin as a vaccine candidate

description: This study aimed to design a novel chimeric protein <i>in silico</i> to serve as a serotype-independent vaccine candidate against <i>Shigella</i>. The chimera contains amino acid residues 240–460 of <i>Shigella</i> invasion plasmid antigen B (IpaB) and the C-terminus of <i>Clostridium perfringens</i> enterotoxin (C-CPE). Amino acid sequences of 537 peptide linkers were obtained from two protein linker databases. 3D structures of IpaB-CPE<sub>290–319</sub>, IpaB-CPE<sub>184–319</sub>, IpaB-CPE<sub>194–319</sub> and 537 newly designed IpaB-linker-CPE<sub>290–319</sub> constructs with varying linker regions were predicted. These predicted 3D structures were merged with the 3D structures of native IpaB<sub>240–460</sub>, CPE<sub>194–319</sub>, CPE<sub>184–319</sub> and CPE<sub>290–319</sub> to select the structure most similar to native IpaB and C-CPE. Several <i>in silico</i> tools were used to determine the suitability of the selected IpaB-C-CPE structure as a vaccine candidate. None of the 537 linkers was capable of preserving the native structure of CPE<sub>290–319</sub> within the IpaB-linker-CPE<sub>290–319</sub> structure. <i>In silico</i> analysis determined that the IpaB-CPE<sub>194–319</sub> 3D structure was the most similar to the 3D structure of the respective native CPE domain and that it was a stable chimeric protein exposing multiple B-cell epitopes. IpaB-CPE<sub>194–319</sub> was designed for its capability to bind to human intestinal epithelial and M cells and to accumulate on these cells. The predicted B-cell epitopes are likely to be capable of inducing a mucosal antibody response in the human intestine against <i>Shigella</i> IpaB. This study also showed that the higher binding affinities of CPE<sub>184–319</sub> and CPE<sub>194–319</sub> to claudin molecules than those of CPE<sub>290–319</sub> is the result of preserving the 3D structures of CPE<sub>184–319</sub> and CPE<sub>194–319</sub> when they are linked to the C-termini of other proteins.
DOI: 10.6084/m9.figshare.6886535
title: Comprehensive identification of <i>Vibrio vulnificus</i> genes required for growth in human serum

description: <i>Vibrio vulnificus</i> can be a highly invasive pathogen capable of spreading from an infection site to the bloodstream, causing sepsis and death. To survive and proliferate in blood, the pathogen requires mechanisms to overcome the innate immune defenses and metabolic limitations of this host niche. We created a high-density transposon mutant library in YJ016, a strain representative of the most virulent <i>V. vulnificus</i> lineage (or phylogroup) and used transposon insertion sequencing (TIS) screens to identify loci that enable the pathogen to survive and proliferate in human serum. Initially, genes underrepresented for insertions were used to estimate the <i>V. vulnificus</i> essential gene set; comparisons of these genes with similar TIS-based classification of underrepresented genes in other vibrios enabled the compilation of a common <i>Vibrio</i> essential gene set. Analysis of the relative abundance of insertion mutants in the library after exposure to serum suggested that genes involved in capsule biogenesis are critical for YJ016 complement resistance. Notably, homologues of two genes required for YJ016 serum-resistance and capsule biogenesis were not previously linked to capsule biogenesis and are largely absent from other <i>V. vulnificus</i> strains. The relative abundance of mutants after exposure to heat inactivated serum was compared with the findings from the serum screen. These comparisons suggest that in both conditions the pathogen relies on its Na<sup>+</sup> transporting NADH-ubiquinone reductase (NQR) complex and type II secretion system to survive/proliferate within the metabolic constraints of serum. Collectively, our findings reveal the potency of comparative TIS screens to provide knowledge of how a pathogen overcomes the diverse limitations to growth imposed by serum.
DOI: 10.6084/m9.figshare.6886529
title: Discovery of a <i>mcr-1-</i>bearing plasmid in commensal colistin-resistant <i>Escherichia coli</i> from healthy broilers in Faisalabad, Pakistan

description: Discovery of a <i>mcr-1-</i>bearing plasmid in commensal colistin-resistant <i>Escherichia coli</i> from healthy broilers in Faisalabad, Pakistan
DOI: 10.6084/m9.figshare.6886535.v1
title: Comprehensive identification of <i>Vibrio vulnificus</i> genes required for growth in human serum

description: <i>Vibrio vulnificus</i> can be a highly invasive pathogen capable of spreading from an infection site to the bloodstream, causing sepsis and death. To survive and proliferate in blood, the pathogen requires mechanisms to overcome the innate immune defenses and metabolic limitations of this host niche. We created a high-density transposon mutant library in YJ016, a strain representative of the most virulent <i>V. vulnificus</i> lineage (or phylogroup) and used transposon insertion sequencing (TIS) screens to identify loci that enable the pathogen to survive and proliferate in human serum. Initially, genes underrepresented for insertions were used to estimate the <i>V. vulnificus</i> essential gene set; comparisons of these genes with similar TIS-based classification of underrepresented genes in other vibrios enabled the compilation of a common <i>Vibrio</i> essential gene set. Analysis of the relative abundance of insertion mutants in the library after exposure to serum suggested that genes involved in capsule biogenesis are critical for YJ016 complement resistance. Notably, homologues of two genes required for YJ016 serum-resistance and capsule biogenesis were not previously linked to capsule biogenesis and are largely absent from other <i>V. vulnificus</i> strains. The relative abundance of mutants after exposure to heat inactivated serum was compared with the findings from the serum screen. These comparisons suggest that in both conditions the pathogen relies on its Na<sup>+</sup> transporting NADH-ubiquinone reductase (NQR) complex and type II secretion system to survive/proliferate within the metabolic constraints of serum. Collectively, our findings reveal the potency of comparative TIS screens to provide knowledge of how a pathogen overcomes the diverse limitations to growth imposed by serum.
DOI: 10.7910/dvn/debtui/vwi1kc
title: 1-3.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886529.v1
title: Discovery of a <i>mcr-1-</i>bearing plasmid in commensal colistin-resistant <i>Escherichia coli</i> from healthy broilers in Faisalabad, Pakistan

description: Discovery of a <i>mcr-1-</i>bearing plasmid in commensal colistin-resistant <i>Escherichia coli</i> from healthy broilers in Faisalabad, Pakistan
DOI: 10.7910/dvn/debtui/s9qgwz
title: 1-52.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886520
title: The diversity of <i>Trichoderma</i> species from soil in South Africa, with five new additions

description: Fourteen <i>Trichoderma</i> (Hypocreales) species were identified during a survey of the genus in South Africa. These include <i>T. afroharzianum, T. asperelloides, T. asperellum, T. atrobrunneum, T. atroviride, T. camerunense, T. gamsii, T. hamatum, T. koningii, T. koningiopsis, T. saturnisporum, T. spirale, T. virens</i>, and <i>T. viride</i>. Ten of these species were not known to occur in South Africa prior to this investigation. Five additional species were novel and are described here as <i>T. beinartii, T. caeruleimontis, T. chetii, T. restrictum</i>, and <i>T. undulatum</i>. These novel <i>Trichoderma</i> species display morphological traits that are typical of the genus. Based on molecular identification using calmodulin, endochitinase, nuc rDNA internal transcribed spacers (ITS1-5.8S-ITS2), RNA polymerase II subunit B, and translation elongation factor 1-α gene sequence data, <i>T. beinartii, T. caeruleimontis</i>, and <i>T. chetii</i> were found to belong to the <i>Longibrachiatum</i> clade, whereas <i>T. restrictum</i> is a member of the <i>Hamatum</i> clade. <i>Trichoderma undulatum</i> occupies a distinct lineage distantly related to other <i>Trichoderma</i> species. Strains of <i>T. beinartii</i> and <i>T. chetii</i> were isolated previously in Hawaii and Israel; however, <i>T. caeruleimontis, T. restrictum</i>, and <i>T. undulatum</i> are so far known only from South Africa.
DOI: 10.6084/m9.figshare.6886523
title: Isolation source matters: sclerotia and ectomycorrhizal roots provide different views of genetic diversity in <i>Cenococcum geophilum</i>

description: <i>Cenococcum geophilum</i> forms sclerotia and ectomycorrhizas with host plants in forest soils. We demonstrated the differences in genetic diversity of <i>C. geophilum</i> between cultured isolates from sclerotia and those from ectomycorrhizal roots in the same 73 soil samples based on glyceraldehyde-3-phosphate dehydrogenase (<i>GAPDH</i>) gene sequences and newly developed microsatellite markers. Based on <i>GAPDH</i> sequences, 759 cultured isolates (553 from sclerotia and 206 from ectomycorrhizas) were classified into 107 “genotypes” with sequence variation of up to 8.6%. The total number of <i>GAPDH</i> genotypes per soil sample ranged from 1 to 9, but genotypes that were shared between sclerotia and ectomycorrhizas were uncommon (0–3 per soil sample). More than 50% of <i>GAPDH</i> genotypes were unique to one source in most soil samples. Unique <i>GAPDH</i> genotypes were detected from either scleotia or ectomycorrhizal roots in most of the soil samples. Multilocus analysis using nine microsatellite markers provided additional resolution to differentiate fungal individuals and supported the results of <i>GAPDH</i> genotyping. The results indicated that sampling both sclerotia and ectomycorrhizal roots maximizes the detection of diversity at the soil core scale. On the other hand, when all isolates were viewed together, 82 <i>GAPDH</i> genotypes were unique to sclerotia whereas only 6 <i>GAPDH</i> genotypes were unique to ectomycorrhizas. Rarefaction analysis indicated that <i>GAPDH</i> genotypic diversity is significantly higher in sclerotia than ectomycorrhizal roots and the diversity within sclerotia is nearly the same as that of both sclerotia and ectomycorrhizas together. These findings suggest that sampling sclerotia alone is likely to detect the majority of <i>GAPDH</i> genotypes in <i>Cenococcum</i> at the regional scale. When deciding whether to sample sclerotia, ectomycorrhizas, or both types of tissues from <i>Cenococcum</i>, it is critical to consider the spatial scale and also the main questions and hypotheses of the study.
DOI: 10.6084/m9.figshare.6886523.v1
title: Isolation source matters: sclerotia and ectomycorrhizal roots provide different views of genetic diversity in <i>Cenococcum geophilum</i>

description: <i>Cenococcum geophilum</i> forms sclerotia and ectomycorrhizas with host plants in forest soils. We demonstrated the differences in genetic diversity of <i>C. geophilum</i> between cultured isolates from sclerotia and those from ectomycorrhizal roots in the same 73 soil samples based on glyceraldehyde-3-phosphate dehydrogenase (<i>GAPDH</i>) gene sequences and newly developed microsatellite markers. Based on <i>GAPDH</i> sequences, 759 cultured isolates (553 from sclerotia and 206 from ectomycorrhizas) were classified into 107 “genotypes” with sequence variation of up to 8.6%. The total number of <i>GAPDH</i> genotypes per soil sample ranged from 1 to 9, but genotypes that were shared between sclerotia and ectomycorrhizas were uncommon (0–3 per soil sample). More than 50% of <i>GAPDH</i> genotypes were unique to one source in most soil samples. Unique <i>GAPDH</i> genotypes were detected from either scleotia or ectomycorrhizal roots in most of the soil samples. Multilocus analysis using nine microsatellite markers provided additional resolution to differentiate fungal individuals and supported the results of <i>GAPDH</i> genotyping. The results indicated that sampling both sclerotia and ectomycorrhizal roots maximizes the detection of diversity at the soil core scale. On the other hand, when all isolates were viewed together, 82 <i>GAPDH</i> genotypes were unique to sclerotia whereas only 6 <i>GAPDH</i> genotypes were unique to ectomycorrhizas. Rarefaction analysis indicated that <i>GAPDH</i> genotypic diversity is significantly higher in sclerotia than ectomycorrhizal roots and the diversity within sclerotia is nearly the same as that of both sclerotia and ectomycorrhizas together. These findings suggest that sampling sclerotia alone is likely to detect the majority of <i>GAPDH</i> genotypes in <i>Cenococcum</i> at the regional scale. When deciding whether to sample sclerotia, ectomycorrhizas, or both types of tissues from <i>Cenococcum</i>, it is critical to consider the spatial scale and also the main questions and hypotheses of the study.
DOI: 10.7910/dvn/debtui/yuomvs
title: 1-47.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/dudg0c
title: 1-2.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.7910/dvn/debtui/0nspk3
title: 1-5.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886511
title: Where are the Pink and White Terraces of Lake Rotomahana?

description: In 2018, Bunn and Nolden published a paper purporting to have established the true position of the Pink and White Terraces of Lake Rotomahana using forensic cartography, ‘reverse engineering’ an 1859 compass survey of Ferdinand von Hochstetter. Their results suggest that the terraces are buried partly on land, near the present-day lake shore. Sightlines constructed using an 1881 Charles Spencer photograph overlooking the White Terraces towards distant Maungaongaonga and Maungakakaramea, and replicated by us, show the location of the White Terraces by Bunn and Nolden to be untenable. Fitting the pre-1886 eruption outline map of Lake Rotomahana of Keam (2016. The Tarawera eruption, Lake Rotomahana, and the origin of the Pink and White Terraces. <i>Journal of Volcanology and Geothermal Research</i> 314:10–38.) to our high-resolution bathymetry shows a remarkable fit of the shoreline around the Pink Terraces area to distinct bathymetric features. Side-scan sonar images of inferred tiers of Pink Terraces (de Ronde CEJ, Scott BJ, Leonard GS, Calvert AT. 2016a. Evolution of the sublacustrine geothermal system of Lake Rotomahana, New Zealand: effects of the 1886 Mt. Tarawera eruption—an introduction. <i>Journal of Volcanology and Geothermal Research</i> 314:1–9.) show they sit where the map of Keam would have them lie.
DOI: 10.7910/dvn/debtui/bkrtjy
title: 1-17.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886505
title: Quantifying beetle-macrofungal associations in a temperate biodiversity hot spot

description: Beetles (Coleoptera) are often among the most abundant and diverse insects that feed on sporocarps of macrofungi, but little is known regarding their relative specialism or generalism in most communities. We surveyed &gt;9000 sporocarps in montane hardwood forest in the Appalachian Mountains (USA) to characterize associations of mycophagous beetles and macrofungi. We used traditional metrics and network analyses to quantify relationships between sporocarp traits (mass, age, persistence, and toughness) and assemblages of adult beetles, drawing from &gt;50 000 beetles collected over two survey years. Strict-sense specificity was rare in these associations: most beetle species were found on multiple fungal genera, and most fungi hosted multiple beetle species. Sporocarp age and fresh mass were positively associated with beetle diversity in fungi with ephemeral sporocarps (here including 12 genera of Agaricales and Russulales), but sporocarp persistence was not. In Polyporales, beetle diversity was greater in softer sporocarps than in tough or woody sporocarps. The increase of beetle diversity in aging sporocarps could not be attributed to increases in sporocarp mass or sampling point in the growing season, suggesting that age-related changes in chemistry or structure may support increasingly diverse beetle communities. Interaction networks differed as a function of sporocarp age, revealing that community-wide measures of generalism (i.e., network connectance) and evenness (i.e., variance in normalized degree) change as sporocarps mature and senesce. Beetles observed on Agaricales and Russulales with more persistent sporocarps had narrower interaction breadth (i.e., were more host-specific) than those on less persistent sporocarps, and beetles on Polyporales with tougher sporocarps had narrower interaction breadth than those on soft sporocarps. In addition to providing a large-scale evaluation of sporocarp use by adult beetles in this temperate biodiversity hot spot, this study shows that characteristics of food organisms are associated with specialism and generalism in interactions relevant to fungal and forest ecology.
DOI: 10.7910/dvn/debtui/ta05nh
title: 1-49.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886505.v1
title: Quantifying beetle-macrofungal associations in a temperate biodiversity hot spot

description: Beetles (Coleoptera) are often among the most abundant and diverse insects that feed on sporocarps of macrofungi, but little is known regarding their relative specialism or generalism in most communities. We surveyed &gt;9000 sporocarps in montane hardwood forest in the Appalachian Mountains (USA) to characterize associations of mycophagous beetles and macrofungi. We used traditional metrics and network analyses to quantify relationships between sporocarp traits (mass, age, persistence, and toughness) and assemblages of adult beetles, drawing from &gt;50 000 beetles collected over two survey years. Strict-sense specificity was rare in these associations: most beetle species were found on multiple fungal genera, and most fungi hosted multiple beetle species. Sporocarp age and fresh mass were positively associated with beetle diversity in fungi with ephemeral sporocarps (here including 12 genera of Agaricales and Russulales), but sporocarp persistence was not. In Polyporales, beetle diversity was greater in softer sporocarps than in tough or woody sporocarps. The increase of beetle diversity in aging sporocarps could not be attributed to increases in sporocarp mass or sampling point in the growing season, suggesting that age-related changes in chemistry or structure may support increasingly diverse beetle communities. Interaction networks differed as a function of sporocarp age, revealing that community-wide measures of generalism (i.e., network connectance) and evenness (i.e., variance in normalized degree) change as sporocarps mature and senesce. Beetles observed on Agaricales and Russulales with more persistent sporocarps had narrower interaction breadth (i.e., were more host-specific) than those on less persistent sporocarps, and beetles on Polyporales with tougher sporocarps had narrower interaction breadth than those on soft sporocarps. In addition to providing a large-scale evaluation of sporocarp use by adult beetles in this temperate biodiversity hot spot, this study shows that characteristics of food organisms are associated with specialism and generalism in interactions relevant to fungal and forest ecology.
DOI: 10.7910/dvn/debtui/stozbi
title: 1-45.5V

description: sigma=1.5Volts; This is a FITS file with 1 (primary) HDU. The following recognized metadata keys have been found in the FITS file: NAXIS2; NAXIS; NAXIS1; NAXIS0;
DOI: 10.6084/m9.figshare.6886499
title: Underexplored regions of Pakistan yield five new species of <i>Leucoagaricus</i>

description: The large genus <i>Leucoagaricus</i> (Basidiomycota) is poorly studied in Pakistan, where the northern parts of the country are considered hot spots for biodiversity. Based on morphological and molecular data, five new species are described: <i>Leucoagaricus badius, L. lahorensiformis, L. pakistaniensis, L. sultanii</i>, and <i>L. umbonatus</i>. Descriptions and illustrations are given for the new taxa. A phylogeny based on morphology and four DNA regions, including the internal transcribed spacers (ITS1-5.8S-ITS2 = ITS) and D1–D2 domains of the 28S gene of the nuc rDNA, the gene for RNA polymerase II second largest subunit (<i>RPB2</i>), and the translation elongation factor 1-α gene (<i>TEF1-α</i>), shows that the new taxa are clustered in a clade representing <i>Leucoagaricus</i> section <i>Rubrotincti</i> subgenus <i>Sericeomyces</i>.
DOI: 10.6084/m9.figshare.6886496
title: Growth medium and incubation temperature alter the <i>Pseudogymnoascus destructans</i> transcriptome: implications in identifying virulence factors

description: <i>Pseudogymnoascus destructans</i> is the causal agent of bat white-nose syndrome (WNS), which is devastating some North American bat populations. Previous transcriptome studies provided insight regarding the molecular mechanisms involved in WNS; however, it is unclear how different environmental parameters could influence pathogenicity. This information could be useful in developing management strategies to mitigate the negative impacts of <i>P. destructans</i> on bats. We cultured three <i>P. destructans</i> isolates from Atlantic Canada on two growth media (potato dextrose agar and Sabouraud dextrose agar) that differ in their nitrogen source, and at two separate incubation temperatures (4 C and 15 C) that approximate the temperature range of bat hibernacula during the winter and a temperature within its optimal mycelial growth range. We conducted RNA sequencing to determine transcript levels in each sample and performed differential gene expression (DGE) analyses to test the influence of growth medium and incubation temperature on gene expression. We also compared our in vitro results with previous RNA-sequencing data sets generated from <i>P. destructans</i> growing on the wings of a susceptible host, <i>Myotis lucifugus</i>. Our findings point to a critical role for substrate and incubation temperature in influencing the <i>P. destructans</i> transcriptome. DGE analyses suggested that growth medium plays a larger role than temperature in determining <i>P. destructans</i> gene expression and that although the psychrophilic fungus responds to different nitrogen sources, it may have evolved for continued growth at a broad range of low temperatures. Further, our data suggest that down-regulation of the RNA-interference pathway and increased fatty acid metabolism are involved in the <i>P. destructans</i>–bat interaction. Finally, we speculate that to reduce the activation of host defense responses, <i>P. destructans</i> minimizes changes in the expression of genes encoding secreted proteins during bat colonization.