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1,049 results for “Pseudomonas”
Lab disease outcomes data evaluating how antibiotic tolerant vs. non-tolerant cell-free supernatant from Pseudomonas aeruginosa affects the interaction between a fungal pathogen (Batrachochytrium dendrobatidis) and amphibian (Rana sylvaticus), 2022.
Microbes living on hosts and in the environment can play a key role in helping hosts to combat pathogens. However, antibiotic-induced alterations to microbial metabolite production could disrupt this dynamic. Here, we investigated whether antibiotic tolerance influences the anti-pathogenic properties of host-associated (living on the host; biofilms) and environmental (living in the soil of water column; planktonic) microbes in vitro and in vivo. For our model host and pathogen, we used the amphibian (Rana sylvatica)-Batrachochytrium dendrobatidis (Bd) system. For our model host-associated (biofilm) and environmental (planktonic) microbes, we used four strains of Pseudomonas aeruginosa that vary in their tolerance to antibiotics and their biofilm-forming capabilities: Planktonic, non-antibiotic tolerant (ΔsagS/VC); Planktonic, antibiotic tolerant (ΔsagS::sagS_L154A); Biofilm, non-antibiotic tolerant (ΔsagS::sagS_D105A); Biofilm, antibiotic tolerant (ΔsagS::sagS). We collected cell-free supernatants (CFS) from each strain to examine the effects of metabolites. We conducted four experiments. In our pathogen-only exposures to test direct effects of metabolites on Bd, we exposed Bd zoospores to each P. aeruginosa CFS at six concentrations. After 11 days of growth, we measured relative abundance of Bd across each treatment. In our host-only exposures to test effects of metabolites on host disease outcomes, we placed R. sylvatica tadpoles in individual units containing each P. aeruginosa CFS. After 48 hours, water was changed into clean well water (no CFS). Bd zoospores were immediately added to each experimental unit following the water change. After 5 days of Bd exposure, we measured snout-vent length (SVL), mass, developmental stage, and Bd quantification in the mouthparts using qPCR for each tadpole. In our host-pathogen exposures to test interactive effects of metabolites on hosts in the presence of the pathogen, we conducted the same experiment as above. However, ins
Dataset of "Single-step Purification and Characterization of Pseudomonas aeruginosa Azurin"
<p>Azurin is a small periplasmic blue copper protein. We have created a novel approach for expressing and purifying of azurin in E. coli with high yields and optimal metalation ratio. The azurin sequence was N-terminally fused with a GST tag and protein was purified by single-step affinity chromatography on a GST-trap column. The N-terminal tag was cleaved off by HRV 3C protease and sufficient metalation was endured by incubation with copper sulphate. UV-VIS absorption, mass spectroscopy, and circular dichroism analysis all validated the effective production of azurin, appropriate protein folding and the development of an active site with an associated cofactor. MD simulations verified that incorporation of the N-terminal GPLGS segment does not affect the wild-type azurin structure.</p>
Dataset: Single nucleotide switches confer bacteriophage resistance to Pseudomonas protegens
<p>Dataset containing : <br>- csv files : Output file of the SNPs identified in all the phage-resistant variants (C2, C4, C17 and C18).</p> <p>- Excel files : </p> <ul> <li>Raw and pre-analyzed data for the bacterial growth analysis. (<a href="https://zenodo.org/api/records/15696172/draft/files/Bacterial_growth.xlsx/content" target="_blank" rel="noopener noreferrer">Bacterial_growth.xlsx</a>)</li> <li>Raw and pre-analised data for the competition assays (Compatition assays.xlsx). </li> <li>Raw and pre-analised data for the fitness assays in planta (plant experiment.xlsx) </li> <li><span lang="EN-US">Raw data of the phage adsorption assay (phage adsorption assays.xlsx) </span></li> </ul> <p>- Code used for the analysis of all the data.</p> <p>- Image and data pre analysed for the spatial distribution of the bacteria during competition in vitro (drop_competition.rar)</p> <ul> <li>Images of the colonies (GFP and red channel) in bmp format</li> <li>R code used to process and analyse this data (Phage_JV_drop.Rmd)</li> </ul> <p> </p>
Dataset: Relation of pest insect-killing and soilborne pathogen-inhibition abilities to species diversification in environmental Pseudomonas protegens
<p>This dataset is related to "<em>Relation of pest insect-killing and soilborne pathogen-inhibition abilities to species diversification in environmental Pseudomonas protegens</em>" and contains all the data obtained from insect experiments and plant-pathogen inhibition assays, as well as the code used for phylogenetic and Biolog anaylsis. </p>
QTL Mapping for Resistance to Cankers Induced by Pseudomonas syringae pv. actinidiae (Psa) in a Tetraploid Actinidia chinensis Kiwifruit Population
<p>Raw Illumina R1 sequence reads for individual plants genotyped for the study entitled "QTL Mapping for Resistance to Cankers Induced by <em>Pseudomonas syringae</em> pv. <em>actinidiae</em> (Psa) in a Tetraploid <em>Actinidia chinensis</em> Kiwifruit Population" accepted in MDPI Pathogen journals, Special issue <em>"</em><em>Pseudomonas syringae</em> Species Complex"</p>
QTL Mapping for Resistance to Cankers Induced by Pseudomonas syringae pv. actinidiae (Psa) in a Tetraploid Actinidia chinensis Kiwifruit Population
<p>Raw Illumina R2 sequence reads for individual plants genotyped for the study entitled "QTL Mapping for Resistance to Cankers Induced by <em>Pseudomonas syringae</em> pv. <em>actinidiae</em> (Psa) in a Tetraploid <em>Actinidia chinensis</em> Kiwifruit Population" accepted in MDPI Pathogen journals, Special issue <em>"</em><em>Pseudomonas syringae</em> Species Complex"</p>
BIONANO-MSCA4U. Biosynthesis of AgNP from Pseudomonas N5.12 and antimicrobial effect
<p>This dataset presents the collected data corresponding to characterization of the biosynthetized AgNP with <em>Pseudomonas</em> N5.12. Listing of all the different data collected, produced, and published are available open-access for the EU-funded <strong>MSCA4Ukraine project (ID:101101923)</strong> combined in different format (in .cvs, .xlsx, .txt and .pdf versions).</p> <p><em>Abbreviation of sample names: S1-S5 – different ratio of bacterial supernatant and 1 mM AgNO3 solution: <code>S1</code> (5:1), <code>S2</code> (4:2), <code>S3</code> (3:3), <code>S4</code> (2:4), <code>S5</code> (1:5). The next letter indicates the pH of the medium (<code>7</code> or <code>9</code>) at which the samples were synthesized.</em></p>
Exploring the Exclusive Isolation of Pseudomonas syringae in Peltigera Lichens via metabolite analysis and growth assays - Appendix
<p>Lichen samples from Iceland were collected from the genera Peltigera, Cladonia, and Stereocaulon in March 2023 at Heidmork forest, Oskjuhlid hill, and the shores of Ellidaa in Arbaejarstifla. All specimens underwent morphological analysis, and corresponding vouchers have been deposited at the Icelandic Institute of Natural History.</p>
microSPLiT single-cell and bulk transcriptomes analysed with STAR - Pseudomonas putida KT2440/pKJK5
<h3>Description of the data and file structure</h3> <p>Data are displayed as 2 files</p> <p><strong>1. Bulk transcriptomics results (Bulk_STAR.csv)</strong></p> <p>STAR processed data combined in a gene x sample table</p> <p><strong>2. microSPLiT single-cell results (microSPLiT_STARsolo.xlsx)</strong></p> <p>STARsolo processed data combined as sublibraries’ gene associated transcript numbers (UMIs) per cell for the control (E1) and experiment (E2) sublibraries (F1-8) - (1 sublibrary per table).</p> <div> <p> </p> </div>
REPIN population analysis in 42 Pseudomonas chlororaphis genomes
<p>This dataset is the output of RAREFAN (http://rarefan.evolbio.mpg.de/) a webserver to identify REPIN populations across an entire bacterial species. The data was created using the following command "java -jar -Xmx10g rarefan.jar chlororaphis/in/ chlororaphis/out/ chlTAMOak81.fas 55 21 chlororaphis/in/yafM_SBW25.faa chlororaphis.nwk 1e-30 true 1"</p> <p>All input files are located in the folder chlororaphis/in/, all output data is located in chlororaphis/out/.</p> <p>The input files include the 42 fasta formatted <em>P. chlororaphis</em> genome files (*.fas) and a RAYT protein sequence called yafM_SBW25.faa.</p> <p>The output files include the following:</p> <p>A phylogenetic tree "chlororaphis.nwk" of all genomes generated with andi (<a href="http://github.com/evolbioinf/andi/">http://github.com/evolbioinf/andi/</a>) and clustDist (http://guanine.evolbio.mpg.de/problemsBook/node1.html).</p> <p>A file containing the frequencies of all 21bp long sequences found in the TAMOak81 genome: chlTAMOak81.wfr</p> <p>A file containing all 21bp long sequences that occur more frequently than 55 times in the TAMOak81 genome: chlTAMOak81.overrep</p> <p>A file containing information on the RAYTs and their cooccurrence with different REPIN populations: prox.stats</p> <p>A file containing the nucleotide sequences of all yafM_SBW25.faa relatives identified with BLAST+ in the <em>P. chlororaphis</em> species: yafM_relatives.fna</p> <p>maxREPIN_[0-5] Contains the most frequent REPIN identified for each sequence type in each <em>P. chlororaphis</em> strain.</p> <p> presAbs_[0-5].txt Contains for each strain information on the number of RAYTs, the number of REPINs, the master sequence, the number of master sequences, the entire REP/REPIN population size, the number of REPIN clusters that contain more than 10 sequences, all REPINs in the population as well as all all REPINs that differ to the master sequences in at most three nucleotides.</p> <p>rayt_[strain name].tab contains location information for each identified RAYT relative for each strain. The files can be viewed with artemis.</p> <p>results.txt contains for each strain the frequency of the six identified 21bp long seeds.</p> <p>There is one folder called groupSeedSequences, which includes the data for identifying the most common 21 bp long sequences in <em>P. chlororaphis</em> TAMOak81. All 21bp long sequences in the genome that occur more frequently than 55 times are sorted into 6 sequence groups. These sequence groups are stored in the files Group_chlTAMOak81_*.out and .out.fas. There is also a chlTAMOak81_words.tab file, which contains the locations of all overrepresented 21bp long sequences in the TAMOak81 genome. This file can be viewed in artemis (https://www.sanger.ac.uk/tool/artemis/) together with the TAMOak81 genome file. The most common sequence in each group is used as a seed sequence to determine REPIN populations across all 42 genomes.</p> <p> </p> <p>For each genome there are six output folders (ending in _0 to _5), for each sequence group one.</p> <p>Each folder contains the following files:</p> <p>*.dd: Degree distribution of the REPIN network, where each REPIN is a node. A REPIN is connected to another REPIN if they differ in exactly one position. The degree distribution is a histogram of the number of connections of all the nodes. </p> <p>*.hist For the largest sequence cluster determined by mcl that consists of REPINs (two REPs in inverted orientation) this file contains the number of REPINs in each sequence class. Sequence class 0 is the master sequence. By definition the most common REPIN in the sequence population. Sequence class 1 contains all REPINs differing in exactly one position to the master sequence. Sequence class 2 contains REPINs differing in 2 positions etc.</p> <p>*.mcl Contains the clustering output by mcl. Each line contains the member of a cluster. Lines are sorted by cluster size.</p> <p>*.mw Contains the most common 21bp long sequence and its frequency in the genome, which is the basis for identifying first all related REP sequences and from those the REPINs formed by these REP sequences.</p> <p>*.nodes The identity and frequency of all REPINs and REP sequences for either all sequences or only for the largest sequence cluster.</p> <p>*.ss Contains REPINs and REP sequences as well as their positions in fasta format. Position information starts with the location in genome fasta file (first sequence is 0...) followed by the start and end position of the entire REPIN/REP sequence. </p> <p>*.ss.REP REP sequence information in fasta format.</p> <p>*.tab Location in tab format. Can be used to display locations of REPs and REPINs in the genome via artemis.</p> <p>*_[0-9].ss Contains REPIN/REP sequence information for each subcluster separately.</p> <p>*_[0-9].tab Contains the location of REP/REPINs for each subcluster separately for viewing in artemis.</p> <p>*allSeed.nw Contains network connections between nodes of all sequences. Can be used to view network in for example R or cytoscape together with the nodes file.</p> <p>*largestCluster.nodes Information on nodes only from the largest REPIN cluster.</p> <p>*largestCluster.ss *.ss file for the largest REPIN cluster.</p> <p>*largestCluster.tab *.tab file for the largest REPIN cluster.</p> <p>*_rayt_repin_prox.txt shows which REPIN/REP cluster is in proximity to any of the RAYT genes identified in the genome (within 200bp).</p> <p>And a subfolder that contains the complete sequences (including the variable region) for all identified REPs and REPINs.</p> <p><strong>The dataset was generated using the following external tools:</strong></p> <p>andi for tree building:</p> <p>B Haubold, F Klötzl, and P Pfaffelhuber. <strong>andi: fast and accurate estimation of evolutionary distances between closely related genomes.</strong> Bioinformatics, 2015 vol. 31 (8) pp. 1169-1175.</p> <p>MCL for REPIN population clustering:</p> <p>A J Enright, S Van Dongen, and C A Ouzounis. <strong>An efficient algorithm for large-scale detection of protein families.</strong> Nucleic Acids Research, 2002 vol. 30 (7) pp. 1575-1584.</p> <p>BLAST+ for identifying RAYT relatives in the different genomes:</p> <p>C Camacho, G Coulouris, V Avagyan, N Ma, J Papadopoulos, K Bealer, and T L Madden. <strong>BLAST+: architecture and applications.</strong> BMC Bioinformatics, 2009 vol. 10 (1) pp. 421-9.</p>
Topologies and structures of the RND transporters MexB, MexF, and MexY of Pseudomonas aeruginosa.
<p>The file contains the topologies and the structures of the RND transporters MexB, MexF, and MexY of Pseudomonas aeruginosa used to identify a common recognition topology in these transporters by means of computer simulations.</p>
Dataset Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere
<p>This dataset is related to the paper "<strong>Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial <em>Pseudomonas </em>in the wheat rhizosphere</strong>" (Garrido-Sanz et al., 2023, doi: 10.1186/s40168-023-01660-5) and contains the data obtained from bacterial competition asays and plant-growth measurements.</p> <p>Sequencing data used in this study has been deposited in the NCBI Sequence Read Archive (RSA) under the BioProject accession number <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA948847">PRJNA948847</a>.</p> <p>The R script used to analyze the data generated in the paper is available at <a href="https://github.com/dgarrs/Pprotegens_proliferation_NatComs">GitHub </a>and <a href="https://doi.org/10.5281/zenodo.8322086">Zenodo</a>.</p>
PubMLST allele profiles and sequence alignments of 382 carbapenem-resistant Pseudomonas aeruginosa isolates collected from Japanese hospitals in 2019-2020
<p>This dataset provides PubMLST allele profiles, sequence alignments, and Mash distance data used in the study of "Nationwide genome surveillance of carbapenem-resistant Pseudomonas aeruginosa in Japan". </p>
Genome assemblies of 382 carbapenem-resistant Pseudomonas aeruginosa isolates collected from Japanese hospitals in 2019−2020
<p>This dataset provides genome assemblies used in the study of "Nationwide genome surveillance of carbapenem-resistant Pseudomonas aeruginosa in Japan".</p> <p> </p>
Adaptation of Pseudomonas aeruginosa to repeated invasion into a commensal competitor
<p>Sequencing data for pooled isolate samples of <em>Pseudomonas aeruginosa</em> obtained in experimental evolution project "Adaptation of <em>Pseudomonas aeruginosa</em> to repeated invasion into a commensal competitor". To generate sequencing data, the gDNA from 10 isolates for each culture condition was pooled in equimolar ratios and libraries were sequenced using the Illumina NovaSeq6000 platform using a 250 bp paired-end protocol, submitted for x510 depth sequencing. Dataset provides raw sequencing data (untrimmed) for pooled starting culture isolates, monoculture evolved lines, and coculture evolved lines.</p>
Pseudomonas sp. MYb2
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Pseudomonas sp. MYb2, a\(n\) Gammaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Pseudomonas lurida MYb22
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Pseudomonas lurida MYb22, a\(n\) Gammaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Pseudomonas_E yamanorum_A BIGb0450
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Pseudomonas_E yamanorum_A BIGb0450, a\(n\) Gammaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Pseudomonas_E vranovensis MYb187
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Pseudomonas_E vranovensis MYb187, a\(n\) Gammaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
Pseudomonas protegens JUb28
This is one of the Wormbiome database archive files.<br>This entry includes all the genome annotation files related to Pseudomonas protegens JUb28, a\(n\) Gammaproteobacteria.<br>The Wormbiome collection is an online database dedicated to centralizing all the information related to bacteria associated with C. elegans. More information on <a href="https://bitbucket.org/the-samuel-lab/wbm_scripts/src/master/DOCS/Annotations_output.md" target="_blank" rel="noopener noreferrer">the documentation page</a>.<br><br>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.