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729 results for “Streptococcus”
Identification and characterization of the cell division protein MapZ of Streptococcus suis
<p>Supplementary data and code related to the manuscript "Identification and characterization of the cell division protein MapZ of <em>Streptococcus suis</em>".</p>
Supplemental material of the Streptococcus pyogenes whole genome MLST schema deposited in Chewie-NS
<p>This supplemental material includes the lists of accession numbers for the Blackwell et al. and NCBI RefSeq assemblies used to populate the whole genome MLST schema for <em>Streptococcus pyogenes</em>, the UniProt identifiers of the reference proteomes used for schema annotation and the set of complete genomes, and associated metadata, used for schema creation.</p> <p>The wgMLST schema was created with <a href="https://github.com/B-UMMI/chewBBACA">chewBBACA</a> and is publicly available at <a href="https://chewbbaca.online/species/1/schemas/1">chewie-NS</a>, where a more detailed description of schema creation, annotation and curation can be found.</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>
Code for generating figures and analyzing amplicon sequencing of human mRNA and reporter mRNA targeted with type III-A CRISPR complex from Streptococcus thermophiles
<p>This dataset contains code for analyzing amplicon sequencing data and generating figures in the manuscript by Anna Nemudraia, Artem Nemudryi, and Blake Wiedenheft (2024), "Repair of CRISPR-guided RNA breaks enables site-specific RNA excision in human cells." </p> <p>Amplicon sequencing data has been deposited to NCBI Sequence Read Archive (SRA) under BioProject PRJNA1099688. The description of read files deposited to SRA can be found in the spreadsheet ./code_for_sequencing_data_analysis/SRA_read_files_description.xlsx</p> <p>The code for analyzing amplicon sequencing data can be found in the archive "code_for_sequencing_data_analysis.tar.gz." Output files from this analysis were used to generate figures. Figures were generated using the ggplot2 package in R and finalized in CorelDRAW.</p> <p>Code for generating figures can be found in the archive "code_for_generating_figures.tar.gz". </p> <p>Any questions or requests regarding the data or the code should be addressed to Dr. Artem Nemudryi at artem.nemudryi@gmail.com.</p>
Data and code for: Dihydrothiazolo ring-fused 2-pyridone antimicrobial compounds effectively treat Streptococcus pyogenes skin and soft tissue infection
<p>We have developed GmPcides from a peptidomimetic dihydrothiazolo ring-fused 2-pyridone scaffold that have antimicrobial activities against a broad-spectrum of Gram-positive pathogens. Here we examine the treatment efficacy of GmPcides using skin and soft tissue infection (SSTI) and biofilm formation models by <em>Streptococcus pyogenes</em>. Screening our compound library for minimal inhibitory (MIC) and minimal bactericidal (MBC) concentrations identified GmPcide PS757 as highly active against <em>S. pyogenes</em> . Treatment of <em>S. pyogenes</em> biofilm with PS757 revealed robust efficacy against all phases of biofilm formation by preventing initial biofilm development, ceasing biofilm maturation and eradicating mature biofilm. In a murine model of <em>S. pyogenes</em> SSTI, subcutaneous delivery of PS757 resulted in reduced levels of tissue damage, decreased bacterial burdens and accelerated rates of wound-healing, which were associated with down-regulation of key virulence factors, including M protein and the SpeB cysteine protease. These data demonstrate that GmPcides show considerable promise for treating <em>S. pyogenes</em> infections.</p>
Input data for running a GWAS on penicillin resistance in Streptococcus pneumoniae
<p>Results from running the pyseer tutorial at https://pyseer.readthedocs.io/en/master/tutorial.html</p>
Supplemental material of "An annotated whole-genome multilocus sequence typing schema for scalable high resolution typing of Streptococcus pyogenes"
<p>This supplemental material includes the genome assemblies, associated metadata and analysis results for five datasets used to define a publicly available annotated wgMLST schema for <em>S. pyogenes</em> and to evaluate its suitability for high resolution typing. A brief description for each file in the dataset is available in the included README file. Raw sequencing data and sample metadata for the 265 isolates included in Dataset1 have been deposited in the European Nucleotide Archive (ENA) under Project <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB49967?show=reads">PRJEB49967</a>.</p> <p>The wgMLST schema was created with <a href="https://github.com/B-UMMI/chewBBACA">chewBBACA</a> and is publicly available at <a href="https://chewbbaca.online/species/1/schemas/1">chewie-NS</a>, where a more detailed description of schema creation, annotation and curation can be found.</p>
Data and code for: Dihydrothiazolo ring-fused 2-pyridone antimicrobial compounds effectively treat Streptococcus pyogenes skin and soft tissue infection
Open the record for dataset details and reuse information.
Data for: Pangenome evaluation of gene essentiality in Streptococcus pyogenes
<p>This is the raw output files of analyses using methods within the <a href="https://transit.readthedocs.io/en/latest/">Transit</a> toolkit on <em>Streptococcus pyogenes</em> transposons sequencing datasets. In total there are nine datasets of both Tn5-like and Himar1-like transposons.</p> <p>Information about read handling and analysis of the data can be found in the publication: https://doi.org/10.1101/2023.08.29.555273 </p>
Supplementary Movies: "Probing the dynamics of Streptococcus pyogenes Cas9 endonuclease bound to sgRNA complex using hydrogen-deuterium exchange mass spectrometry"
<p>Movies related to the article "Probing the dynamics of Streptococcus pyogenes Cas9 endonuclease bound to sgRNA complex using hydrogen-deuterium exchange mass spectrometry" in the International Journal of Molecular Science. "MD_Movie_Cas9_sgRNA_DNA" is the video of SpCas9-sgRNA-DNA complex behavior during 50 ns molecular dynamics simulation. In this movie, SpCas9 protein domains are shown in the following colors: REC lobe (green), CTD (blue), RuvC (pink), L-I-II (yellow), Arg (violet), and HNH (orange). RNA presented in cyan, and DNA -in dark blue.</p> <p>Movies "SpCas9_HeatMap" and "SpCas9-sgRNA_HeatMap" show the hydrogen exchange levels superimposed onto the protein structure obtained from MD trajectories. Relative uptake level presented at the time points of 10 s, 30 s, 1 min, 2 min, 5 min, 10 min, 30 min, 60 min, 120 min, 240 min, 360 min, and 480 min. The exchange scale is shown in a rainbow color scheme, where blue corresponds to the minimum uptake, while red corresponds to the highest observed uptake.</p>
Streptococcus iniae DC-313 RASTtk Annotation
<p>Whole genome annotation of Streptococcus iniae DC-313 strain isolated from the tilapia brain.</p> <p>The sequence was annotated using the RAST tool kit available throughout BV-BRC. <span>The whole genome sequence has been deposited to Sequence Read Archive (SRA) with the Accession number </span><a href="https://www.ncbi.nlm.nih.gov/sra/?term=SRR28967390"><span>SRR28967390</span></a><span>, available through the National Center for Biotechnology Information. The WGS Accession number is </span><a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN39963917"><span>SAMN39963917</span></a><span>. The </span><span>WGS project ID is </span><a href="https://www.ncbi.nlm.nih.gov/nuccore/JBAJMQ000000000.1"><span>JBAJMQ01</span></a><span>.</span></p>
Figure 1 in Colonization by Streptococcus pneumoniae among children in Porto Velho, Rondônia, Western Brazilian Amazon
Figure 1. Location of the study area.
DivIVA controls the dynamics of septum splitting and cell elongation in Streptococcus pneumoniae
<ul> <li>Raw phase contrast and fluorescence images to analyze the localization of DivIVA-HT in <em>Streptococcus pneumoniae</em>.</li> <li>Raw phase contrast and fluorescence images to analyze the localization of GFP-aPBP1a in <em>Streptococcus pneumoniae </em>wild-type and D<em>divIVA</em> cells.<em><br></em></li> <li>Raw phase contrast and fluorescence images to analyze the localization of GFP-aPBP2a in <em>Streptococcus pneumoniae </em>wild-type and D<em>divIVA</em> cells.</li> <li>Raw bright field (BF), diffraction-limited (DL) and reconstructed dSTORM images to analyze peptidoglycan synthesis in <em>S. pneumoniae </em>wild-type and mutant cells (D<em>divIVA</em>, D<em>pbp1a, </em>D<em>pbp2a, </em>D<em>pbp2b mltG(Y488D)</em>.</li> </ul>
Streptococcus pyogenes pharyngitis elicits diverse antibody responses to key vaccine antigens influenced by the imprint of past infections.
<p>Here you will find the raw data (RawData.RData) and code (CHIVAS_SEROLOGY_Code.Rmd, an R Markdown file) for generating the analysis and figures for the following publication:</p> <p><strong><em>Streptococcus pyogenes</em> pharyngitis elicits diverse antibody responses to key vaccine antigens influenced by the imprint of past infections.</strong></p> <p>Joshua Osowicki1,2,3 #, Hannah R Frost1 #, Kristy I Azzopardi1, Alana L Whitcombe4, Reuben McGregor4, Lauren H. Carlton4, Ciara Baker1, Loraine Fabri1,5,6, Manisha Pandey7, Michael F Good7, Jonathan R. Carapetis8,9,10, Mark J Walker11,12,13, Pierre R Smeesters1,2,5,6, Paul V Licciardi2,14, Nicole J Moreland4 *, Danika L Hill15 *, Andrew C Steer1,2,3 *</p> <p>Provided in the RData file are the following items: </p> <p><strong>Dataframes: </strong></p> <p>"outcome" : clinical variables associated with human challenge for each participant</p> <p>"data" : ELISA and functional antibody responses for human challenge participants. Each timepoint and isotype for each antigen as seperate column)</p> <p>"data_long": Data equivalent to "data" file but in long format, i.e. One column for each antigen, timepoint and isotype as factors. </p> <p>"data.melt" : Data equivalent to "data" file but in longer format , i.e. timepoint, isotype and antigen as factors, 'value' as ELISA AU. </p> <p>"luminex" : IgG responses to 6 antigens analysed by luminex bead-based assay in human challenge participants.</p> <p>"luminex.children" : IgG responses to 6 antigen analysed by luminex bead-based assay in children</p> <p><strong>Vectors:</strong></p> <p>"pharyngitis" : participant "id" for the 19 individuals that developed pharyngitis. </p> <p>"Antigen.Order" : relates to "Main" antigen classification used in Figure 2</p> <p>'additional" : relates to "Additional </p> <p><strong>Function: </strong></p> <p>"custom_theme" : used as a theme when using ggplot to graph. </p> <p>Adobe Illustrator or Inkscape were used to generate the final image files for publication, with some graph editing to axes labels, font size, adding p-values etc. </p> <p> </p> <p><em><strong>Additional files: </strong></em></p> <p> 3 .csv files have been included for download</p> <p>"ELISA_data_wide_format.csv", a wide format data table of 25 human challenge individuals and 219 variables. Equivalent to the 'data' dataframe in the RData file</p> <p>"CHIVAS_luminex.csv", a long format data table of 25 human challenge participants at 1 week, 1 month, and 3 months. Equivalent to the 'luminex' dataframe in the RData file. </p> <p>"Luminex.children.csv", a datatable of 6 luminex variables for 39 children (healthy and post pharyngitis). Equivalent to the 'luminex.children' dataframe in the RData file. </p> <p> </p>
Nasopharyngeal Carriage, Antimicrobial Resistance, and Serotype Distribution of Streptococcus pneumoniae in Children Under Five in Lebanon: Baseline Data Prior to PCV13 Introduction
<p>Dataset and R Code Script</p>
Supplementary dataset to publication: Whole-genome sequencing of Streptococcus uberis isolated from cows with mastitis in Thuringia
<p><span><strong>Introduction</strong>.</span> <em><span>Streptococcus uberis</span></em> is a common cause of mastitis in cattle, leading to significant economic losses. The widespread use of antimicrobials has contributed to the emergence of resistance, which poses a severe challenge in controlling <em><span>S. uberis</span></em> infection.</p> <p><span><strong>Aim</strong>.</span> The objective of this study was to gain insights into the antimicrobial resistance (AMR) and epidemiological typing of <em><span>S. uberis</span></em> isolated from milk collected from bovine mastitis on dairy farms in Thuringia.</p> <p><span><strong>Methodology</strong>.</span> In this study, 84 <em><span>S. uberis</span></em> isolates were obtained from cattle with clinical mastitis in Thuringia, their phenotypic and genotypic AMR were analyzed and their phylogenetic relationship was explored using whole-genome sequencing.</p> <p><span><strong>Results</strong>.</span> Genetically heterogeneous strains were found on the farms, but clusters of highly similar strains also circulated within the same farms. All isolates were sensitive to ampicillin, penicillin, ceftiofur, and vancomycin. However, 42.9%, 42.9%, 22.6%, 19.0%, and 13.0% were resistant to tetracycline, doxycycline, clindamycin, pirlimycin, and erythromycin, respectively. Thirty-nine strains were phenotypically resistant to two or more tested antibiotics. We identified a plasmid associated with macrolide and lincosamide resistance in 12% of the strains.</p> <p><span><strong>Conclusion</strong>.</span> The emergence of <em><span>S. uberis</span></em> strains resistant to multiple antibiotics highlights the importance of <em><span>S. uberis</span></em> surveillance and the prudent use of antimicrobials.</p>
dSTORM imaging of Streptococcus pneumoniae using fluorescent d-amino acids
<p>Please see more details in the readme file.</p>
AGPT test results in pregnant goats sensitized to Streptococcus mutans antigen
<p>The appearance of precipitation lines during the AGPT examination proved the formation of anti-S. mutans antibodies.</p>
Epithelial Micro-Invasion Events by Streptococcus pneumoniae Drives Unique Epithelial Cell Responses
<p>RNA Sequencing dataset for Weight et al Manuscript.</p>
Safety and Immunogenicity of a Group B Streptococcus Vaccine in Non Pregnant and Pregnant Women 18-40 Years of Age
ClinicalTrials.gov study NCT01193920. IPD Sharing: Not stated. Countries: 1. Publications: 3.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.