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47 results for “Legionella pneumophila”
Acanthamoeba castellanii genome assembly and infection by Legionella pneumophila
<p>Data associated with the publication "<em>Regulation of the Acanthamoeba castellanii genome upon infection by Legionella pneumophila</em>". The record contains 4 archives, each associated with a github repository, and a "shared assets" archive, which contains processed files used by some repositories. The code from github repositories is embedded in each tarball, along with input and output data. Analyses are organized as independent snakemake pipelines for each part.</p> <p> </p> <p>For convenient reanalysis, genomes, annotations and merged contact maps used in the publication can be found in the `shared_assets.tar.gz` archive. The infection analysis results are located in the `data/output` folder of Acastellanii_legionella_infection.tar.gz.</p> <p>All archives can be downloaded at the bottom of the page.</p> <p> </p> <p><strong>Hybrid genome assembly:</strong></p> <p>Genome assembly pipeline code and output data used for the assembly of 2 <em>A. castellanii</em> strains (Neff and C3) through a hybrid pipeline combining Illumina shotgun, Hi-C and Oxford Nanopore long reads.</p> <p>Github: <a href="https://github.com/cmdoret/Acastellanii_hybrid_assembly">https://github.com/cmdoret/Acastellanii_hybrid_assembly</a></p> <p>Archive: Acastellanii_hybrid_assembly.tar.gz</p> <p> </p> <p><strong>Genome annotation:</strong></p> <p>Genome annotation pipeline used for functional annotation of <em>A. castellanii</em> strains C3 and Neff, and associated output files.</p> <p>Github: <a href="https://github.com/cmdoret/Acastellanii_genome_annotation">https://github.com/cmdoret/Acastellanii_genome_annotation</a></p> <p>Archive: Acastellanii_genome_annotation.tar.gz</p> <p> </p> <p><strong>Genome analyses:</strong></p> <p>Code and data related to general analyses of genomic properties of <em>A. castellanii</em> strains C3 and Neff.</p> <p>Github: <a href="https://github.com/cmdoret/Acastellanii_genome_analysis">https://github.com/cmdoret/Acastellanii_genome_analysis</a></p> <p>Archive: Acastellanii_genome_analysis.tar.gz</p> <p> </p> <p><strong>Infection analyses:</strong></p> <p>Code and data related to the analysis of structural changes in the <em>A. castellanii</em> C3 genome during infection by <em>L. pneumophila</em>.</p> <p>Github: <a href="https://github.com/cmdoret/Acastellanii_legionella_infection">https://github.com/cmdoret/Acastellanii_legionella_infection</a></p> <p>Archive: Acastellanii_legionella_infection.tar.gz<br> </p> <p><strong>Shared assets:</strong></p> <p>This archive contains processed files (genomes, annotations, Hi-C matrices, differential expression results) which can be useful for reanalysis, and are automatically pulled when executing the pipeline of some repositories.</p> <p>Archive: shared_assets.tar.gz</p> <p> </p> <p><strong>Supp. analyses:</strong></p> <p>Code and data related to short ad-hoc analyses on the genomic location of specific sequences in the genomes of C3 and Neff. The archive contains two subfolders: `telomere_repeats` where we analyse the distribution of TTAGGG subtelomeric repeats throughout the A. castellanii assemblies, and `C3_exclusive_regions` where we visualize the genomic distribution of C3-specific sequences (i.e. absent from Neff) along the C3 assembly.</p> <p> </p> <p>Archive: supp_analyses.tar.gz<br> </p>
New methods for the genotyping of Legionella pneumophila - Establishment, validation and implementation of a DNA-based microarray and a core genome multilocus sequence typing
<p>This data presented here are part a doctoral thesis with the focus on new genotyping methods for the human pathogen <em>Legionella pneumophila</em>. The data are partially published in articles. </p> <p>The thesis can be downloaded: update of the URL is coming soon</p>
Data from: Surface Acoustic Wave-based Lab-On-a-Chip for the fast detection of Legionella pneumophila in water
<p><span>Surface acoustic wave (SAW) -based immuno-biosensors are used for several applications, thanks to their versatility and faster response than conventional analytical methods. SAW immuno-biosensors can be usefully applied to promptly detect bacteria and prevent bacterial infections that can lead to severe diseases. Here, we present a SAW immuno-biosensor to detect <em>Legionella</em> <em>pneumophila</em> in water. Our device, working at ultra-high frequency (740 MHz), is functionalized with an anti-<em>L</em>. <em>pneumophila</em> antibody to maximize the specificity. We report the characteristic curve of the sensor, calculated measuring bacterial samples at known densities, and its related parameters. We also measure <em>L</em>. <em>pneumophila</em> samples contaminated with different Gram-positive and Gram-negative bacterial species (<em>Escherichia</em> <em>coli</em> and <em>Enterococcus</em> <em>faecium</em>) and samples diluted in mains waters. The proposed device is able to detect <em>L</em>. <em>pneumophila</em> in the range from 1</span><span>×</span><span>10<sup>6</sup> to 1</span><span>×</span><span>10<sup>8</sup> CFU/mL, with a limit of blank of 1.22</span><span>×</span><span>10<sup>6</sup> CFU/mL and a limit of detection of 2.01</span><span>×</span><span>10<sup>6</sup> CFU/mL. The nonspecific signal due to contaminant bacteria is very limited and measurements of <em>L</em>. <em>pneumophila</em> are not affected by contamination. We obtain a good detection also in mains water, representing a realistic matrix for <em>L</em>. <em>pneumophila</em>. Our results are encouraging and pave the way to the use of fast, easy-to-use, reliable and precise sensors to prevent bacterial infections in human activities.</span></p>
Data from: Surface Acoustic Wave-based Lab-On-a-Chip for the fast detection of Legionella pneumophila in water
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Data from: Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila
Pathogens deliver complex arsenals of translocated effector proteins to host cells during infection, but the extent to which these proteins are regulated once inside the eukaryotic cell remains poorly defined. Among all bacterial pathogens, Legionella pneumophila maintains the largest known set of translocated substrates, delivering over 300 proteins to the host cell via its Type IVB, Icm/Dot translocation system. Backed by a few notable examples of effector–effector regulation in L. pneumophila, we sought to define the extent of this phenomenon through a systematic analysis of effector–effector functional interaction. We used Saccharomyces cerevisiae, an established proxy for the eukaryotic host, to query > 108,000 pairwise genetic interactions between two compatible expression libraries of ~330 L. pneumophila‐translocated substrates. While capturing all known examples of effector–effector suppression, we identify fourteen novel translocated substrates that suppress the activity of other bacterial effectors and one pair with synergistic activities. In at least nine instances, this regulation is direct—a hallmark of an emerging class of proteins called metaeffectors, or "effectors of effectors". Through detailed structural and functional analysis, we show that metaeffector activity derives from a diverse range of mechanisms, shapes evolution, and can be used to reveal important aspects of each cognate effector's function. Metaeffectors, along with other, indirect, forms of effector–effector modulation, may be a common feature of many intracellular pathogens—with unrealized potential to inform our understanding of how pathogens regulate their interactions with the host cell.
Data from: Experimental evolution of Legionella pneumophila in mouse macrophages leads to strains with altered determinants of environmental survival
The Gram-negative bacterium, Legionella pneumophila, is a protozoan parasite and accidental intracellular pathogen of humans. We propose a model in which host cycling through multiple protozoan hosts in the environment holds L. pneumophila in a state of evolutionary stasis as a broad host-range pathogen. Using an experimental evolution approach, we tested this hypothesis by restricting L. pneumophila to growth within mouse macrophages for hundreds of generations. Whole-genome resequencing and high-throughput genotyping identified several parallel adaptive mutations and population dynamics that led to improved replication within macrophages. Based on these results, we provide a detailed view of the population dynamics of an experimentally evolving bacterial population, punctuated by frequent instances of transient clonal interference and selective sweeps. Non-synonymous point mutations in the flagellar regulator, fleN, resulted in increased uptake and broadly increased replication in both macrophages and amoebae. Mutations in multiple steps of the lysine biosynthesis pathway were also independently isolated, resulting in lysine auxotrophy and reduced replication in amoebae. These results demonstrate that under laboratory conditions, host restriction is sufficient to rapidly modify L. pneumophila fitness and host range. We hypothesize that, in the environment, host cycling prevents L. pneumophila host-specialization by maintaining pathways that are deleterious for growth in macrophages and other hosts.
Novel Use of a Gas Transfer Membrane Contactor Inhibits Legionella pneumophila Growth in Hot Water Systems
<p>Large Scale Hot Water Model System Measurement Data Summary</p>
Data from: Phylogenetic reconstruction of the Legionella pneumophila Philadelphia-1 laboratory strains through comparative genomics.
Open the record for dataset details and reuse information.
Data from: Experimental evolution of Legionella pneumophila in mouse macrophages leads to strains with altered determinants of environmental survival
Open the record for dataset details and reuse information.
Data from: Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen, Legionella pneumophila
Open the record for dataset details and reuse information.
small RNA profiling of human blood derived macrophages upon infection with Legionella Pneumophila
GEO Series GSE125559. Homo sapiens. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
The LetA/S two-component system is essential for the survival of Legionella pneumophila in water
GEO Series GSE98743. Legionella pneumophila subsp. pneumophila str. Philadelphia 1. 12 samples. Type: Expression profiling by array.
microRNA profiling of murine wt and MyD88-/- deficient bone marrow derived macrophages upon infection with Legionella Pneumophila
GEO Series GSE92600. Mus musculus; Rattus norvegicus. 12 samples. Type: Expression profiling by RT-PCR.
Toxin-antitoxin deletions in Legionella pneumophila reveal unusual cell death and contact-dependent survival responses during genotoxic stress [Lp_growth_phase_RNAseq]
GEO Series GSE278702. Legionella pneumophila. 8 samples. Type: Expression profiling by high throughput sequencing.
Legionella pneumophila transcriptomic response of hfq mutant during post-exponential phase
GEO Series GSE42905. Legionella pneumophila; Legionella pneumophila subsp. pneumophila str. Philadelphia 1. 6 samples. Type: Expression profiling by array.
Legionella pneumophila JR32 and rpoS- (LM1367) strains: Statinoary phase (stat) vs. Logarithmic (log) phase growth
GEO Series GSE14830. Legionella pneumophila; Legionella pneumophila subsp. pneumophila str. Philadelphia 1. 2 samples. Type: Expression profiling by array.
Genome-wide transcriptional profiling of Legionella Pneumophila-infected A549 cells transfected with siRNA against TNFAIP2
GEO Series GSE80214. Homo sapiens. 11 samples. Type: Expression profiling by array.
Strand specific sequencing illustrates the complex transcriptional response of Legionella pneumophila during infection
GEO Series GSE27232. Legionella pneumophila. 5 samples. Type: Expression profiling by high throughput sequencing.
Symbiont-mediated defense against Legionella pneumophila in amoebae
GEO Series GSE125876. Legionella pneumophila; Candidatus Protochlamydia amoebophila; Acanthamoeba castellanii. 22 samples. Type: Expression profiling by high throughput sequencing.
Translocated Legionella pneumophila small RNAs mimic eukaryotic miRNAs to dampen the host immune response
GEO Series GSE159109. Legionella pneumophila. 8 samples. Type: Expression profiling by high throughput sequencing.
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