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290 results for “phage”
De novo sequencing of phages T4 and T7
<p>Raw data and assemblies of the <em>de novo </em>sequencing of the "model" phages T4 and T7, performed with Illumina NextSeq 2x150 and Oxford Nanopore, generated for the "Phage Annotation Workshop" held online on November 2021:</p> <p>https://github.com/quadram-institute-bioscience/phage-annotation-workshop/</p>
Phage defence loci of Streptococcus thermophilus
<p><span>We describe the systematic identification and functional analysis of the phage resistome of <em>S. thermophilus </em>using a collection of 27 strains as representatives of the species. In addition to CRISPR-Cas and R/M systems, we uncover nine distinct phage-resistance systems including homologues of Kiwa, Gabija, Dodola, defence-associated sirtuins and abortive infection systems. The genes encoding several of these newly identified systems are located in proximity to the genetic determinants of CRISPR-Cas systems thus constituting apparent Phage Defence Islands. Other phage-resistance systems whose encoding genes are not co-located with genes specifying CRISPR-Cas systems may represent anchors to identify additional Defence Islands harbouring, as yet, uncharacterised phage defence systems. Remarkably, we estimate that up to 2.5 % of the genetic material of the analysed strains is dedicated to phage defence, highlighting that phage-host antagonism plays an important role in driving the evolution and shaping the composition of dairy streptococcal genomes.</span></p>
Supplementary phylogenetic data for Rouïl et. al. 2020 "The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals"
<p>Supplementary phylogenetic data for Rouïl <em>et. al.</em> 2020 "The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals"</p> <p> </p> <p>The data set consists of the following sub-directories:</p> <p>1) "APSE_conserved_proteins_alns": Single-copy conserved genes codon sequences and alignments in FASTA format.</p> <p>2) "APSE_phylogeny": Files used for APSE phylogenetic and recombination analyses.</p> <p>3) "APSE_reannotations": GenBank-formatted files of the assemblies and re-annotations of APSE phages. Newly-sequenced phages deposited at the European nucleotide Archive are also included. ***New in this version***</p> <p>4) "APSE_toxin_lyzozyme": Files used for APSE toxin-cassette and lyzozyme-related gene phylogenies.</p> <p>5) "Arsenophonus_PHASTER": PHASTER phage annotation output files organised by organisim and contig/scaffold.</p> <p>6) "Hamiltonella_drafts": Newly-sequenced low-coverage draft <em>Hamiltonella</em> genomes in FASTA format.</p> <p>7) "Hamiltonella_phylogeny": files used for <em>Hamiltonella</em> phylogenetic analysis.</p> <p> </p> <p>See enclosed README.txt file for more details.</p> <p> </p> <p>* ver. 1.1.1: Updated annotations for APSE genomes including inteins missing in previous annotation files.</p>
Phage selection drives resistance-virulence trade-offs in Ralstonia solanacearum plant pathogenic bacterium irrespective of the growth temperature
<p><span>While temperature has been shown to affect the survival and growth of bacteria and their phage parasites, it is unclear if trade-offs between phage resistance and other bacterial traits depend on the temperature. Here, we experimentally compared the evolution of phage resistance-virulence trade-offs and underlying molecular mechanisms in phytopathogenic <em>Ralstonia</em> <em>solanacearum</em> bacterium at 25 °C and 35 °C temperature environments. We found that experimental growth conditions selected for small colony variants (SCVs) with increased growth rate and mutations in the quorum-sensing (QS) signalling receptor gene, <em>phcS</em>. Interestingly, SCVs were also phage-resistant and reached higher frequencies in the presence of phages in both temperature environments. Evolving phage resistance was costly in terms of reduced carrying capacity, biofilm formation and reduced virulence i<em>n planta</em> possibly due to loss of QS-mediated expression of key virulence genes. We also observed mucoid phage-resistant colonies that showed loss of virulence and reduced twitching motility likely due to parallel mutations in prepilin peptidase gene pilD. Moreover, phage-resistant SCVs from 35 °C-phage treatment had parallel mutations in genes encoding type II secretion system (T2SS) genes (<em>gspE</em> and <em>gspF</em>), indicating that defects in pseudopilus made bacterium resistant to the phage. Additional transcriptomic analysis revealed upregulation of CBASS and type Ⅰ restriction-modification phage defence systems in response to phage exposure, which coincided with reduced expression of motility and virulence-associated genes, including <em>pilD</em> and type II and III secretion systems. Together, these results suggest that phage resistance-virulence trade-offs are not affected by the growth temperature but can be mediated through both pre- and post-infection phage resistance mechanisms.</span></p>
Plaque assay images from the article "Predicting phage-bacteria interactions at the strain level from genomes"
<p>This dataset contains the plaque assay images for (i) the construction of the 403 bacteria * 96 phages interaction matrix and (ii) the "cocktails" experiment (100 E. coli strains challenged with recommended cocktails vs. a baseline). </p>
Phage RBP detection data
<p>These datasets contain the filtered <em>RBP </em>and <em>Other</em> sequences utilized in our manuscript in submission for the special issue 'Virus Bioinformatics 2022' in <em>Viruses</em>: "Identification of phage receptor-binding protein sequences with hidden Markov models and an extreme gradient boosting classifier". These datasets enable to fully reproduce our analyses.</p>
Alternatively_coded_phage_proteomics
<p>Genomes for 2 alternatively coded phages in our proteomics study, and a .tsv with accession numbers for associated datasets. </p>
Profiling phage-host interactions between Skunavirus receptor binding proteins and lactococcal cell wall polysaccharide structures
Open the record for dataset details and reuse information.
Fig. 5 in Molecular Identification of a Phage-infected Protochlamydia Strain Naturally Harboured by Non-Encysting Naegleria
Fig. 5. Detail of electron microscopy of Naegleria clarki infected by Pcb, showing three enlarged RBs containing filled and empty phages. A normal-size wrinkled EB is also visible. Scale bar: 0.5 µm.
Datasets for Evaluating Metagenomic Phage Detection Tools
<p>These datasets include sequences that can be used for evaluating computational tools that detect bacteriophage in metagenomes.</p> <p>Datasheets are supplied for each dataset, and a README describes how to extract each dataset. Once the directories are extracted, there is a README in each directory describing the individual dataset.</p>
Refseq tailed phages
<p>5172 tailed phage genomes downloaded from Genbank on 10 May 2023 </p>
Supplement: Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities
<p>Background<br> Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments.</p> <p>Results<br> We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles.</p> <p>Conclusions<br> Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry.</p>
Data from Matrishin et al. "Phages are important unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis"
<p>Data files associated with Matrishin et al. "Phages are important unrecognized players in the ecology of the oral pathogen <em>Porphyromonas gingivalis</em>".</p> <p><strong>Please see the table in 00.README.xlsx for key information regarding nomenclature</strong>. We caution that the same locus tag identifiers refer to different genes in the Zenodo files than in NCBI. This difference resulted from use of the same Locus Tag Prefixes for in house gene calls using Bakta for the manuscript analyses as for the PGAP analyses ultimately performed upon submission of the assemblies to GenBank. Unlike the Supplementary Data Files submitted with the manuscript, see below, it was not possible to readily update all the Zenodo-deposited files to their updated final GCA and distinct locus tag identifiers because of the complexity of some of the included filetypes, therefore all files in the Zenodo set were left unchanged from the nomenclature used in the original in house analyses based on Bakta.</p> <table align="left"> <thead> <tr> <th scope="col">Directory</th> <th scope="col">Contents</th> </tr> </thead> <tbody> <tr> <td><strong>00.README</strong></td> <td>Important information regarding nomenclature differences across data types.</td> </tr> <tr> <td><strong>01.bax.bakta</strong></td> <td>Results of Bakta annotation of 88 <em>Pg</em> genomes.</td> </tr> <tr> <td><strong>02.bax.ppanggolin</strong></td> <td>Results of PPanGGOLiN pangenome analysis of 88 <em>Pg</em> genomes.</td> </tr> <tr> <td><strong>03.bax.combo</strong></td> <td>Results of multiple analyses used to inform identification and curation of prophages in <em>Pg</em> genomes, provided as bacterial genome fastas and gff files that can be uploaded together to genome viewer tools (e.g. Geneious) and visualized as tracks. Note, these do not include final prophage calls.</td> </tr> <tr> <td><strong>04.phage.genomes</strong></td> <td><em>Pg</em> phage genomes in fasta format.</td> </tr> <tr> <td><strong>05.phage.prots</strong></td> <td><em>Pg</em> phage proteins in fasta format, clipped proteins at the beginnings and ends of genomes are excluded.</td> </tr> <tr> <td><strong>06.phage.gbs</strong></td> <td><em>Pg</em> phage information in GenBank format, clipped proteins at the beginnings and ends of genomes are excluded.</td> </tr> <tr> <td><strong>07.phage.families.virclust</strong></td> <td>Results of VirClust analysis used to inform resolution family-level units.</td> </tr> <tr> <td><strong>08.phage.families.victor</strong></td> <td>Results of VICTOR analysis used to inform resolution of family-level units.</td> </tr> </tbody> </table> <p> </p>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Visualizing phage infection
<p>We staged infections at four multiplicities of infection (MOI 0, 0.01, 0.1, and 1), and took snapshots every ten minutes over a 40-minute period. We designed FISH probes targeting the non-coding strand of the <em>gp34</em> gene, which encodes a tail fiber protein and quantified cells with 5 or more MGE spots, less than 5 spots, and no spots</p>
Cell-free synthesis of infective phages from in vitro assembled phage genomes for efficient phage engineering and production of large phage libraries
<p>Upload of relevant sequencing data for the paper "<strong>Cell-free synthesis of infective phages from <em>in vitro</em> assembled phage genomes for efficient phage engineering and production of large phage libraries"</strong></p>
“Tear down that wall” – updating the vocabulary of phage and bacterial lytic proteins
Open the record for dataset details and reuse information.
Phage selection drives resistance-virulence trade-offs in Ralstonia solanacearum plant pathogenic bacterium irrespective of the growth temperature
Open the record for dataset details and reuse information.
Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics
Open the record for dataset details and reuse information.
The complete genome sequence and comparative genomic analyses of four phages (NJ-P3, NB-P21, NC-P34 and NN-P42)
<p>We downloaded and reanalyzed the raw data of four phages genomes (NJ-P3, NB-P21, NC-P34, NN-P42). This is the reassembled whole genomes and comparative genomic analyses of four phages.</p>
Simulations For: Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa
<p>Coordinate, simulation input and simulation output files for atomistic molecular dynamics simulations in Biophysical basis of filamentous phage tactoid-mediated antibiotic tolerance in P. aeruginosa. </p><p> </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.