cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6886412
title: Hinge action versus grip in translocation by RNA polymerase

description: Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were observed to close. Hinges within the bridge helix and trigger loop supported generation of translocation force against the RNA–DNA hybrid resulting in opening of the furthest upstream i−8 RNA–DNA bp, establishing conditions for RNAP sliding. The β flap tip helix and the most N-terminal β′ Zn finger engage the RNA, indicating a path of RNA threading out of the exit channel. Because the β flap tip connects to the RNAP active site through the β subunit double-Ψ–β-barrel and the associated sandwich barrel hybrid motif (also called the flap domain), the RNAP active site is coupled to the RNA exit channel and to the translocation of RNA–DNA. Using an exonuclease III assay to monitor translocation of RNAP elongation complexes, we show that K<sup>+</sup> and Mg<sup>2+</sup> and also an RNA 3′-OH or a 3′-H<sub>2</sub> affect RNAP sliding. Because RNAP grip to template suggests a sticky translocation mechanism, and because grip is enhanced by increasing K<sup>+</sup> and Mg<sup>2+</sup>concentration, biochemical assays are consistent with a conformational change that drives forward translocation as observed in simulations. Mutational analysis of the bridge helix indicates that 778-GARKGL-783 (<i>Escherichia coli</i> numbering) is a homeostatic hinge that undergoes multiple bends to compensate for complex conformational dynamics during phosphodiester bond formation and translocation.
DOI: 10.7910/dvn/debtui/aenvid
title: 1-43.5V

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.6886412.v1
title: Hinge action versus grip in translocation by RNA polymerase

description: Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were observed to close. Hinges within the bridge helix and trigger loop supported generation of translocation force against the RNA–DNA hybrid resulting in opening of the furthest upstream i−8 RNA–DNA bp, establishing conditions for RNAP sliding. The β flap tip helix and the most N-terminal β′ Zn finger engage the RNA, indicating a path of RNA threading out of the exit channel. Because the β flap tip connects to the RNAP active site through the β subunit double-Ψ–β-barrel and the associated sandwich barrel hybrid motif (also called the flap domain), the RNAP active site is coupled to the RNA exit channel and to the translocation of RNA–DNA. Using an exonuclease III assay to monitor translocation of RNAP elongation complexes, we show that K<sup>+</sup> and Mg<sup>2+</sup> and also an RNA 3′-OH or a 3′-H<sub>2</sub> affect RNAP sliding. Because RNAP grip to template suggests a sticky translocation mechanism, and because grip is enhanced by increasing K<sup>+</sup> and Mg<sup>2+</sup>concentration, biochemical assays are consistent with a conformational change that drives forward translocation as observed in simulations. Mutational analysis of the bridge helix indicates that 778-GARKGL-783 (<i>Escherichia coli</i> numbering) is a homeostatic hinge that undergoes multiple bends to compensate for complex conformational dynamics during phosphodiester bond formation and translocation.
DOI: 10.6084/m9.figshare.6886409
title: <i>linc00673 (ERRLR01)</i> is a prognostic indicator of overall survival in breast cancer

description: LncRNAs are novel noncoding RNAs involved in the epigenetic regulation of gene expression by recruiting ribonucleoprotein complexes to specific genomic loci to initiate histone methylation and/or other chromatin modifications. LncRNAs themselves function as tumor suppressors or oncogenes, depending on the gene regulatory networks they govern. We identified lnc00673 (<i>ERRLR01</i>) as a marker of overall survival (OS) in breast cancer patients. Specifically, <i>ERRLR01</i> levels were elevated in triple-negative breast cancer (TNBC) as compared with Luminal-A, Luminal-B, and HER2 breast cancer subtypes. <i>ERRLR01</i> levels were also inversely correlated with breast cancer survival across all breast cancer patients. Upon stratification, OS in ERα<sup>−</sup> tumors correlated with negative overall survival, while in ERα<sup>+</sup> tumors, <i>ERRLR01</i> correlated with positive outcomes. This suggests <i>ERRLR01</i> is modulated by hormone signaling in breast cancer. Gene-network analysis revealed <i>ERRLR01</i> correlated with distinct pathways including “epithelial development” and “cellular differentiation.” These data suggest <i>ERRLR01</i> operates as an oncogene in TNBC, as well as a biomarker in breast cancer patients.
DOI: 10.7910/dvn/debtui/adadt1
title: 1-16.5V

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.6886406
title: SOD1 stimulates lamellipodial protrusions in Neuro 2A cell lines

description: We here investigated the effects of overexpressed superoxide dismutase (SOD)1 and amyotrophic lateral sclerosis (ALS)-linked SOD1 mutants G93A and G147S in Neuro 2A (N2A) cell lines, and found a three-fold increase in lamellipodia either in cells cultured under differentiated or undifferentiated growth conditions. In undifferentiated N2A cells, SOD1 constructs promoted lamellipodial protrusions to similar extent as the overexpression of Rac1, and SOD1-mediated lamellipodia were prevented by coexpression of the N17 dominant-negative form of Rac1, or shRNA for a downstream effector of Rac1, the insulin receptor tyrosine kinase substrate p53 (IRSp53) or its binding partner LIN7. Moreover, no additive effect was measured by coexpression of the SOD1 constructs with Rac1, IRSp53 or LIN7. Collectively these data support a role for SOD1 in the regulation of Rac1-mediated lamellipodia pathway, a property fully retained by the two SOD1 mutants.
DOI: 10.6084/m9.figshare.6886409.v1
title: <i>linc00673 (ERRLR01)</i> is a prognostic indicator of overall survival in breast cancer

description: LncRNAs are novel noncoding RNAs involved in the epigenetic regulation of gene expression by recruiting ribonucleoprotein complexes to specific genomic loci to initiate histone methylation and/or other chromatin modifications. LncRNAs themselves function as tumor suppressors or oncogenes, depending on the gene regulatory networks they govern. We identified lnc00673 (<i>ERRLR01</i>) as a marker of overall survival (OS) in breast cancer patients. Specifically, <i>ERRLR01</i> levels were elevated in triple-negative breast cancer (TNBC) as compared with Luminal-A, Luminal-B, and HER2 breast cancer subtypes. <i>ERRLR01</i> levels were also inversely correlated with breast cancer survival across all breast cancer patients. Upon stratification, OS in ERα<sup>−</sup> tumors correlated with negative overall survival, while in ERα<sup>+</sup> tumors, <i>ERRLR01</i> correlated with positive outcomes. This suggests <i>ERRLR01</i> is modulated by hormone signaling in breast cancer. Gene-network analysis revealed <i>ERRLR01</i> correlated with distinct pathways including “epithelial development” and “cellular differentiation.” These data suggest <i>ERRLR01</i> operates as an oncogene in TNBC, as well as a biomarker in breast cancer patients.
DOI: 10.7910/dvn/debtui/t7c854
title: 1-4.5V

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.6886406.v1
title: SOD1 stimulates lamellipodial protrusions in Neuro 2A cell lines

description: We here investigated the effects of overexpressed superoxide dismutase (SOD)1 and amyotrophic lateral sclerosis (ALS)-linked SOD1 mutants G93A and G147S in Neuro 2A (N2A) cell lines, and found a three-fold increase in lamellipodia either in cells cultured under differentiated or undifferentiated growth conditions. In undifferentiated N2A cells, SOD1 constructs promoted lamellipodial protrusions to similar extent as the overexpression of Rac1, and SOD1-mediated lamellipodia were prevented by coexpression of the N17 dominant-negative form of Rac1, or shRNA for a downstream effector of Rac1, the insulin receptor tyrosine kinase substrate p53 (IRSp53) or its binding partner LIN7. Moreover, no additive effect was measured by coexpression of the SOD1 constructs with Rac1, IRSp53 or LIN7. Collectively these data support a role for SOD1 in the regulation of Rac1-mediated lamellipodia pathway, a property fully retained by the two SOD1 mutants.
DOI: 10.7910/dvn/debtui/xrttpi
title: 1-9.5V

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.6886400
title: Glycine is able to induce both a motility speed in- and decrease during zebrafish neuronal migration

description: Various neurotransmitters influence neuronal migration in the developing zebrafish hindbrain. Migrating tegmental hindbrain nuclei neurons (THNs) are governed by depolarizing neurotransmitters (acetylcholine and glutamate), and glycine. In mature neurons, glycine binds to its receptor to hyperpolarize cells. This effect depends on the co-expression of the solute carrier KCC2. Immature precursors, however, typically express NKCC1 instead of KCC2, leading to membrane depolarization upon glycine receptor activation. As neuronal migration occurs in neurons after leaving the cell cycle and before terminal differentiation, we hypothesized that the switch from NKCC1 to KCC2 expression could alter the effect of glycine on THN migration. We tested this notion using in vivo cell tracking, overexpression of glycine receptor mutations and whole mount in situ hybridization. We summarize our findings in a speculative model, combining developmental age, glycine receptor strength and solute carrier expression to describe the effect of glycine on the migration of THNs.
DOI: 10.7910/dvn/debtui/dd9i2f
title: 1-22.5V

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.6886397
title: Molecular identification and characterization of endophytes from uncultivated barley

description: <i>Epichloë</i> species (Clavicipitaceae, Ascomycota) are endophytic symbionts of many cool-season grasses. Many interactions between <i>Epichloë</i> and their host grasses contribute to plant growth promotion, protection from many pathogens and insect pests, and tolerance to drought stress. Resistance to insect herbivores by endophytes associated with <i>Hordeum</i> species has been previously shown to vary depending on the endophyte-grass-insect combination. We explored the genetic and chemotypic diversity of endophytes present in wild <i>Hordeum</i> species. We analyzed seeds of <i>Hordeum bogdanii, H. brevisubulatum</i>, and <i>H. comosum</i> obtained from the US Department of Agriculture’s (USDA) National Plant Germplasm System (NPGS), of which some have been reported as endophyte-infected. Using polymerase chain reaction (PCR) with primers specific to <i>Epichloë</i> species, we were able to identify endophytes in seeds from 17 of the 56 Plant Introduction (PI) lines, of which only 9 lines yielded viable seed. Phylogenetic analyses of housekeeping, alkaloid biosynthesis, and mating type genes suggest that the endophytes of the infected PI lines separate into five taxa: <i>Epichloë bromicola, Epichloë tembladerae</i>, and three unnamed interspecific hybrid species. One PI line contained an endophyte that is considered a new taxonomic group, <i>Epichloë</i> sp. HboTG-3 (<i>H. bogdanii</i> Taxonomic Group 3). Phylogenetic analyses of the interspecific hybrid endophytes from <i>H. bogdanii</i> and <i>H. brevisubulatum</i> indicate that these taxa all have an <i>E. bromicola</i> allele but the second allele varies. We verified in planta alkaloid production from the five genotypes yielding viable seed. Morphological characteristics of the isolates from the viable <i>Hordeum</i> species were analyzed for their features in culture and in planta. In the latter, we observed epiphyllous growth and in some cases sporulation on leaves of infected plants.
DOI: 10.6084/m9.figshare.6886400.v2
title: Glycine is able to induce both a motility speed in- and decrease during zebrafish neuronal migration

description: Various neurotransmitters influence neuronal migration in the developing zebrafish hindbrain. Migrating tegmental hindbrain nuclei neurons (THNs) are governed by depolarizing neurotransmitters (acetylcholine and glutamate), and glycine. In mature neurons, glycine binds to its receptor to hyperpolarize cells. This effect depends on the co-expression of the solute carrier KCC2. Immature precursors, however, typically express NKCC1 instead of KCC2, leading to membrane depolarization upon glycine receptor activation. As neuronal migration occurs in neurons after leaving the cell cycle and before terminal differentiation, we hypothesized that the switch from NKCC1 to KCC2 expression could alter the effect of glycine on THN migration. We tested this notion using in vivo cell tracking, overexpression of glycine receptor mutations and whole mount in situ hybridization. We summarize our findings in a speculative model, combining developmental age, glycine receptor strength and solute carrier expression to describe the effect of glycine on the migration of THNs.
DOI: 10.6084/m9.figshare.6886397.v1
title: Molecular identification and characterization of endophytes from uncultivated barley

description: <i>Epichloë</i> species (Clavicipitaceae, Ascomycota) are endophytic symbionts of many cool-season grasses. Many interactions between <i>Epichloë</i> and their host grasses contribute to plant growth promotion, protection from many pathogens and insect pests, and tolerance to drought stress. Resistance to insect herbivores by endophytes associated with <i>Hordeum</i> species has been previously shown to vary depending on the endophyte-grass-insect combination. We explored the genetic and chemotypic diversity of endophytes present in wild <i>Hordeum</i> species. We analyzed seeds of <i>Hordeum bogdanii, H. brevisubulatum</i>, and <i>H. comosum</i> obtained from the US Department of Agriculture’s (USDA) National Plant Germplasm System (NPGS), of which some have been reported as endophyte-infected. Using polymerase chain reaction (PCR) with primers specific to <i>Epichloë</i> species, we were able to identify endophytes in seeds from 17 of the 56 Plant Introduction (PI) lines, of which only 9 lines yielded viable seed. Phylogenetic analyses of housekeeping, alkaloid biosynthesis, and mating type genes suggest that the endophytes of the infected PI lines separate into five taxa: <i>Epichloë bromicola, Epichloë tembladerae</i>, and three unnamed interspecific hybrid species. One PI line contained an endophyte that is considered a new taxonomic group, <i>Epichloë</i> sp. HboTG-3 (<i>H. bogdanii</i> Taxonomic Group 3). Phylogenetic analyses of the interspecific hybrid endophytes from <i>H. bogdanii</i> and <i>H. brevisubulatum</i> indicate that these taxa all have an <i>E. bromicola</i> allele but the second allele varies. We verified in planta alkaloid production from the five genotypes yielding viable seed. Morphological characteristics of the isolates from the viable <i>Hordeum</i> species were analyzed for their features in culture and in planta. In the latter, we observed epiphyllous growth and in some cases sporulation on leaves of infected plants.
DOI: 10.6084/m9.figshare.6886400.v1
title: Glycine is able to induce both a motility speed in- and decrease during zebrafish neuronal migration

description: Various neurotransmitters influence neuronal migration in the developing zebrafish hindbrain. Migrating tegmental hindbrain nuclei neurons (THNs) are governed by depolarizing neurotransmitters (acetylcholine and glutamate), and glycine. in mature neurons, glycine binds to its receptor to hyperpolarize cells. This effect depends on the co-expression of the solute carrier KCC2. Immature precursors, however, typically express NKCC1 instead of KCC2, leading to membrane depolarization upon glycine receptor activation. As neuronal migration occurs in neurons after leaving the cell cycle and before terminal differentiation, we hypothesized that the switch from NKCC1 to KCC2 expression could alter the effect of glycine on THN migration. We tested this notion using in vivo cell tracking, overexpression of glycine receptor mutations and whole mount in situ hybridization. We summarize our findings in a speculative model, combining developmental age, glycine receptor strength and solute carrier expression to describe the effect of glycine on the migration of THNs. Addendum to Ulrike Theisen, Christian D. Hennig, Tobias Ring, Ralf Schnabel, and Reinhard W. Köster: “Neurotransmitter-mediated activity spatially controls neuronal migration in the zebrafish cerebellum”, PLoS Biology, 16(1): e2002226. https://doi.org/10.1371/journal.pbio.2002226
DOI: 10.7910/dvn/debtui/c3sobw
title: 1-1.5V

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.6886391
title: Cathelicidin peptide rescues <i>G. mellonella</i> infected with <i>B. anthracis</i>

description: Cathelicidin peptide rescues <i>G. mellonella</i> infected with <i>B. anthracis</i>
DOI: 10.6084/m9.figshare.6886391.v1
title: Cathelicidin peptide rescues <i>G. mellonella</i> infected with <i>B. anthracis</i>

description: Cathelicidin peptide rescues <i>G. mellonella</i> infected with <i>B. anthracis</i>
DOI: 10.7910/dvn/debtui/huihnp
title: 1-6.5V

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/e1cke1
title: 1-37.5V

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.6886382
title: Identifying and naming the currently known diversity of the genus <i>Hydnum</i>, with an emphasis on European and North American taxa

description: In this study, 49 species of <i>Hydnum</i> are recognized worldwide. Twenty-two of them are described here as new species. Epitypes are proposed for <i>H. repandum</i> and <i>H. rufescens</i>. The majority of the species are currently known only from a single continent. The barcodes produced in this study are deposited in the RefSeq database and used as a basis to name species hypotheses in UNITE. Eleven infrageneric clades recovered in a phylogenetic analysis are supported by morphological characteristics and formally recognized: subgenera <i>Alba, Hydnum, Pallida</i>, and <i>Rufescentia</i>; sections <i>Hydnum, Olympica, Magnorufescentia</i>, and <i>Rufescentia</i>; and subsections <i>Mulsicoloria, Rufescentia</i>, and <i>Tenuiformia</i>.
DOI: 10.6084/m9.figshare.6886385
title: Taxonomy, phylogeny, and divergence time estimation for <i>Apiosphaeria guaranitica</i>, a Neotropical parasite on bignoniaceous hosts

description: <i>Apiosphaeria guaranitica</i>, the causal agent of brown crust disease of several bignoniaceous hosts, among them <i>Handroanthus</i> and <i>Tabebuia</i> species, has been traditionally placed in Phyllachoraceae, based exclusively on morphological studies, without supporting molecular evidence. Here, we provide molecular data for the link between sexual and asexual states of the fungus and elucidate the phylogeny of <i>A. guaranitica</i>. The multilocus phylogenetic analyses employed sequences from the 18S subunit (18S), 28S subunit (28S), and nuclear internal transcribed spacers (ITS1-5.8S-ITS2 = ITS) of the nuc rDNA, second-largest subunit of RNA polymerase II (<i>RPB2</i>), and translation elongation factor 1-α (<i>TEF1</i>) genetic loci. Estimates of the divergence time of this lineage were supported by fossil calibration (FC) and secondary calibration (SC) strategies. Our results indicate a natural placement of <i>Apiosphaeria</i> within Diaporthaceae (Diaporthales), where it represents an ancient lineage of the crown group of Diaporthaceae, diverging during the late Paleocene at 61.15 (FC) and 60.63 (SC) million years ago. This divergence time estimate within Diaporthales is based on <i>Spataporthe taylori</i>, a diaporthaceous fossil.
DOI: 10.7910/dvn/debtui/do5s7h
title: 1-44.5V

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/2rjsyx
title: 1-36.5V

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.6886385.v2
title: Taxonomy, phylogeny, and divergence time estimation for <i>Apiosphaeria guaranitica</i>, a Neotropical parasite on bignoniaceous hosts

description: <i>Apiosphaeria guaranitica</i>, the causal agent of brown crust disease of several bignoniaceous hosts, among them <i>Handroanthus</i> and <i>Tabebuia</i> species, has been traditionally placed in Phyllachoraceae, based exclusively on morphological studies, without supporting molecular evidence. Here, we provide molecular data for the link between sexual and asexual states of the fungus and elucidate the phylogeny of <i>A. guaranitica</i>. The multilocus phylogenetic analyses employed sequences from the 18S subunit (18S), 28S subunit (28S), and nuclear internal transcribed spacers (ITS1-5.8S-ITS2 = ITS) of the nuc rDNA, second-largest subunit of RNA polymerase II (<i>RPB2</i>), and translation elongation factor 1-α (<i>TEF1</i>) genetic loci. Estimates of the divergence time of this lineage were supported by fossil calibration (FC) and secondary calibration (SC) strategies. Our results indicate a natural placement of <i>Apiosphaeria</i> within Diaporthaceae (Diaporthales), where it represents an ancient lineage of the crown group of Diaporthaceae, diverging during the late Paleocene at 61.15 (FC) and 60.63 (SC) million years ago. This divergence time estimate within Diaporthales is based on <i>Spataporthe taylori</i>, a diaporthaceous fossil.