cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9779246.v1
title: Table S5 from Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes

description: Giant viruses have remarkable genomic repertoires—blurring the line with cellular life—and act as top-down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four ‘PacV’ partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate three of the new viruses span a clade with deep-branching members of giant <i>Mimiviridae</i>, incorporating the <i>Cafeteria roenbergensis</i> virus, the uncultivated, terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421 is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (<i>e</i>-value −5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the Ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In a co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence–absence patterns across PacV and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs.This article is part of the discussion meeting issue ‘Single cell ecology’.
DOI: 10.5281/zenodo.4090997
title: Alteration of gut microbiota with rifampicin does not impair maternal care in the European earwig

description: Dataset, R script and detailed bioinformatic pipelines used in the publication "Alteration of gut microbiota with rifampicin does not impair maternal care in the European earwig"
description: This research has been supported by a research grant from the French Ministry of Research (to S.V.M.) and a research grant from the ANR (project MicroSoc to J.M.)
DOI: 10.6084/m9.figshare.9779234.v2
title: Table S1 from Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes.

description: Giant viruses have remarkable genomic repertoires—blurring the line with cellular life—and act as top–down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four ‘PacV’ partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate that three of the new viruses span a clade with deep-branching members of giant <i>Mimiviridae</i>, incorporating the <i>Cafeteria roenbergensis</i> virus, the uncultivated terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421, is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (<i>e</i>-value −5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the Ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence–absence patterns across the PacVs and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs.This article is part of the discussion meeting issue ‘Single cell ecology’.
DOI: 10.6084/m9.figshare.9779234.v1
title: Table S1 from Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes

description: Giant viruses have remarkable genomic repertoires—blurring the line with cellular life—and act as top-down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four ‘PacV’ partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate three of the new viruses span a clade with deep-branching members of giant <i>Mimiviridae</i>, incorporating the <i>Cafeteria roenbergensis</i> virus, the uncultivated, terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421 is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (<i>e</i>-value −5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the Ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In a co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence–absence patterns across PacV and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs.This article is part of the discussion meeting issue ‘Single cell ecology’.
DOI: 10.6084/m9.figshare.9782879
title: Supplementary Data 1 from Low connectivity between shallow, mesophotic and rariphotic zone benthos.

description: Presence-absence and abundance data for all morphotypes identified in this study.
DOI: 10.6084/m9.figshare.9782876
title: Supplementary Data 2 from Low connectivity between shallow, mesophotic and rariphotic zone benthos.

description: Substratum and environmental characteristics for all transects conducted in this study.
DOI: 10.6084/m9.figshare.9782879.v2
title: Supplementary Data 1 from Low connectivity between shallow, mesophotic and rariphotic zone benthos.

description: Presence-absence and abundance data for all morphotypes identified in this study.
DOI: 10.6084/m9.figshare.9782873
title: Supplementary Data 3 from Low connectivity between shallow, mesophotic and rariphotic zone benthos.

description: SIMPER results using presence-absence data (entire benthic community) and abundance data (all corals and some countable sponges).
DOI: 10.6084/m9.figshare.9782879.v1
title: Supplementary Data 1 from Low connectivity between shallow, mesophotic and rariphotic zone benthos

description: Presence-absence and abundance data for all morphotypes identified in this study.
DOI: 10.6084/m9.figshare.9782876.v2
title: Supplementary Data 2 from Low connectivity between shallow, mesophotic and rariphotic zone benthos.

description: Substratum and environmental characteristics for all transects conducted in this study.
DOI: 10.6084/m9.figshare.9782873.v2
title: Supplementary Data 3 from Low connectivity between shallow, mesophotic and rariphotic zone benthos.

description: SIMPER results using presence-absence data (entire benthic community) and abundance data (all corals and some countable sponges).
DOI: 10.6084/m9.figshare.9782876.v1
title: Supplementary Data 2 from Low connectivity between shallow, mesophotic and rariphotic zone benthos

description: Substratum and environmental characteristics for all transects conducted in this study.
DOI: 10.6084/m9.figshare.9782873.v1
title: Supplementary Data 3 from Low connectivity between shallow, mesophotic and rariphotic zone benthos

description: SIMPER results using presence-absence data (entire benthic community) and abundance data (all corals and some countable sponges).
DOI: 10.6084/m9.figshare.9783065
title: Raw data of Study 2 from Synaesthetic colour associations for Japanese Kanji characters: from the perspective of grapheme learning.

description: One of the fundamental questions about grapheme–colour synaesthesia is how specific associations between the graphemes and colours are formed. We addressed this question by focusing on the determinants of synaesthetic colours for Japanese Kanji characters (logographic characters) using a psycholinguistic approach. Study 1 explored the influence meaning has on synaesthetic colours for Kanji characters representing abstract meanings by examining synaesthetic colours for antonym pairs (i.e. characters with meanings opposed to each other) in Japanese synaesthetes. Results showed that semantic relations influenced the grapheme–colour associations for characters representing abstract meanings in the early stages of learning abstract Kanji, while the influence was reduced in the grapheme–colour associations for those learned later. Study 2 examined the effect that learning new sounds or meanings of graphemes has on synaesthetic colours for those graphemes. Japanese synaesthetes were taught new sounds or new meanings for familiar Kanji characters. Results indicated that acquiring new information for graphemes slightly but significantly reduced the test–retest grapheme–colour association consistency, suggesting that synaesthetic colours can be modulated to reflect the synaesthete's latest knowledge about graphemes. Implications of these findings are discussed from the perspective of the relationship between synaesthesia and grapheme learning.This article is part of the discussion meeting issue ‘Bridging senses: new developments in synaesthesia’.
DOI: 10.6084/m9.figshare.9783065.v2
title: Raw data of Study 2 from Synaesthetic colour associations for Japanese Kanji characters: from the perspective of grapheme learning.

description: One of the fundamental questions about grapheme–colour synaesthesia is how specific associations between the graphemes and colours are formed. We addressed this question by focusing on the determinants of synaesthetic colours for Japanese Kanji characters (logographic characters) using a psycholinguistic approach. Study 1 explored the influence meaning has on synaesthetic colours for Kanji characters representing abstract meanings by examining synaesthetic colours for antonym pairs (i.e. characters with meanings opposed to each other) in Japanese synaesthetes. Results showed that semantic relations influenced the grapheme–colour associations for characters representing abstract meanings in the early stages of learning abstract Kanji, while the influence was reduced in the grapheme–colour associations for those learned later. Study 2 examined the effect that learning new sounds or meanings of graphemes has on synaesthetic colours for those graphemes. Japanese synaesthetes were taught new sounds or new meanings for familiar Kanji characters. Results indicated that acquiring new information for graphemes slightly but significantly reduced the test–retest grapheme–colour association consistency, suggesting that synaesthetic colours can be modulated to reflect the synaesthete's latest knowledge about graphemes. Implications of these findings are discussed from the perspective of the relationship between synaesthesia and grapheme learning.This article is part of the discussion meeting issue ‘Bridging senses: new developments in synaesthesia’.
DOI: 10.6084/m9.figshare.9783068
title: Raw data of Study 1 from Synaesthetic colour associations for Japanese Kanji characters: from the perspective of grapheme learning.

description: One of the fundamental questions about grapheme–colour synaesthesia is how specific associations between the graphemes and colours are formed. We addressed this question by focusing on the determinants of synaesthetic colours for Japanese Kanji characters (logographic characters) using a psycholinguistic approach. Study 1 explored the influence meaning has on synaesthetic colours for Kanji characters representing abstract meanings by examining synaesthetic colours for antonym pairs (i.e. characters with meanings opposed to each other) in Japanese synaesthetes. Results showed that semantic relations influenced the grapheme–colour associations for characters representing abstract meanings in the early stages of learning abstract Kanji, while the influence was reduced in the grapheme–colour associations for those learned later. Study 2 examined the effect that learning new sounds or meanings of graphemes has on synaesthetic colours for those graphemes. Japanese synaesthetes were taught new sounds or new meanings for familiar Kanji characters. Results indicated that acquiring new information for graphemes slightly but significantly reduced the test–retest grapheme–colour association consistency, suggesting that synaesthetic colours can be modulated to reflect the synaesthete's latest knowledge about graphemes. Implications of these findings are discussed from the perspective of the relationship between synaesthesia and grapheme learning.This article is part of the discussion meeting issue ‘Bridging senses: new developments in synaesthesia’.
DOI: 10.6084/m9.figshare.9783065.v1
title: Raw data of Study 2 from Synaesthetic colour associations for Japanese kanji characters: from the perspective of grapheme learning

description: One of the fundamental questions about grapheme–colour synaesthesia is how specific associations between the graphemes and colours are formed. We addressed this question by focusing on the determinants of synaesthetic colours for Japanese Kanji characters (logographic characters) using a psycholinguistic approach. Study 1 explored the influence meaning has on synaesthetic colours for Kanji characters representing abstract meanings by examining synaesthetic colours for antonym pairs (i.e. characters with meanings opposed to each other) in Japanese synaesthetes. Results showed that semantic relations influenced the grapheme–colour associations for characters representing abstract meanings in the early stages of learning abstract Kanji, while the influence was reduced in the grapheme–colour associations for those learned later. Study 2 examined the effect that learning new sounds or meanings of graphemes has on synaesthetic colours for those graphemes. Japanese synaesthetes were taught new sounds or new meanings for familiar Kanji characters. Results indicated that acquiring new information for graphemes slightly but significantly reduced the test–retest grapheme–colour association consistency, suggesting that synaesthetic colours can be modulated to reflect the synaesthete's latest knowledge about graphemes. Implications of these findings are discussed from the perspective of the relationship between synaesthesia and grapheme learning.This article is part of the discussion meeting issue ‘Bridging senses: new developments in synaesthesia’.
DOI: 10.6084/m9.figshare.9783068.v2
title: Raw data of Study 1 from Synaesthetic colour associations for Japanese Kanji characters: from the perspective of grapheme learning.

description: One of the fundamental questions about grapheme–colour synaesthesia is how specific associations between the graphemes and colours are formed. We addressed this question by focusing on the determinants of synaesthetic colours for Japanese Kanji characters (logographic characters) using a psycholinguistic approach. Study 1 explored the influence meaning has on synaesthetic colours for Kanji characters representing abstract meanings by examining synaesthetic colours for antonym pairs (i.e. characters with meanings opposed to each other) in Japanese synaesthetes. Results showed that semantic relations influenced the grapheme–colour associations for characters representing abstract meanings in the early stages of learning abstract Kanji, while the influence was reduced in the grapheme–colour associations for those learned later. Study 2 examined the effect that learning new sounds or meanings of graphemes has on synaesthetic colours for those graphemes. Japanese synaesthetes were taught new sounds or new meanings for familiar Kanji characters. Results indicated that acquiring new information for graphemes slightly but significantly reduced the test–retest grapheme–colour association consistency, suggesting that synaesthetic colours can be modulated to reflect the synaesthete's latest knowledge about graphemes. Implications of these findings are discussed from the perspective of the relationship between synaesthesia and grapheme learning.This article is part of the discussion meeting issue ‘Bridging senses: new developments in synaesthesia’.
DOI: 10.6084/m9.figshare.9783068.v1
title: Raw data of Study 1 from Synaesthetic colour associations for Japanese kanji characters: from the perspective of grapheme learning

description: One of the fundamental questions about grapheme–colour synaesthesia is how specific associations between the graphemes and colours are formed. We addressed this question by focusing on the determinants of synaesthetic colours for Japanese Kanji characters (logographic characters) using a psycholinguistic approach. Study 1 explored the influence meaning has on synaesthetic colours for Kanji characters representing abstract meanings by examining synaesthetic colours for antonym pairs (i.e. characters with meanings opposed to each other) in Japanese synaesthetes. Results showed that semantic relations influenced the grapheme–colour associations for characters representing abstract meanings in the early stages of learning abstract Kanji, while the influence was reduced in the grapheme–colour associations for those learned later. Study 2 examined the effect that learning new sounds or meanings of graphemes has on synaesthetic colours for those graphemes. Japanese synaesthetes were taught new sounds or new meanings for familiar Kanji characters. Results indicated that acquiring new information for graphemes slightly but significantly reduced the test–retest grapheme–colour association consistency, suggesting that synaesthetic colours can be modulated to reflect the synaesthete's latest knowledge about graphemes. Implications of these findings are discussed from the perspective of the relationship between synaesthesia and grapheme learning.This article is part of the discussion meeting issue ‘Bridging senses: new developments in synaesthesia’.
DOI: 10.6084/m9.figshare.9785339
title: Experiment 1: Raw Data from Do synaesthesia and mental imagery tap into similar cross-modal processes?.

description: Raw Data set from Experiment 1
DOI: 10.6084/m9.figshare.9785342
title: Experiment 2: Raw Data from Do synaesthesia and mental imagery tap into similar cross-modal processes?.

description: Raw Data set from Experiment 2
DOI: 10.6084/m9.figshare.9785339.v2
title: Experiment 1: Raw Data from Do synaesthesia and mental imagery tap into similar cross-modal processes?.

description: Raw Data set from Experiment 1
DOI: 10.6084/m9.figshare.9785339.v1
title: Experiment 1: Raw Data from Do synaesthesia and mental imagery tap into similar cross-modal processes?

description: Raw Data set from Experiment 1
DOI: 10.6084/m9.figshare.9785342.v2
title: Experiment 2: Raw Data from Do synaesthesia and mental imagery tap into similar cross-modal processes?.

description: Raw Data set from Experiment 2
DOI: 10.6084/m9.figshare.9785342.v1
title: Experiment 2: Raw Data from Do synaesthesia and mental imagery tap into similar cross-modal processes?

description: Raw Data set from Experiment 2
DOI: 10.6084/m9.figshare.9785564
title: Phyre 2 structures from Zinc binding proteome of a phytopathogen <i>Xanthomonas translucens</i> pv. <i>undulosa</i>.

description: <i>Xanthomonas translucens</i> pv. <i>undulosa</i> (<i>Xtu</i>) is a proteobacteria which causes bacterial leaf streak (BLS) or bacterial chaff disease in wheat and barley. The constant competition for zinc (Zn) metal nutrients contributes significantly in plant–pathogen interactions. In this study, we have employed a systematic <i>in silico</i> approach to study the Zn-binding proteins of <i>Xtu.</i> From the whole proteome of <i>Xtu</i>, we have identified ̴approximately 7.9% of proteins having Zn-binding sequence and structural motifs<i>.</i> Further, 115 proteins were found homologous to plant–pathogen interaction database. Among these 115 proteins, 11 were predicted as putative secretory proteins. The functional diversity in Zn-binding proteins was revealed by functional domain, gene ontology and subcellular localization analysis. The roles of Zn-binding proteins were found to be varied in the range from metabolism, proteolysis, protein biosynthesis, transport, cell signalling, protein folding, transcription regulation, DNA repair, response to oxidative stress, RNA processing, antimicrobial resistance, DNA replication and DNA integration. This study provides preliminary information on putative Zn-binding proteins of <i>Xtu</i> which may further help in designing new metal-based antimicrobial agents for controlling BLS and bacterial chaff infections on staple crops.