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340 results for “plasmid”
Data from: A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea
<p><span>Conjugative plasmids (CP) are self-transmissible mobile genetic elements which transfer DNA between host cells via Type IV Secretion Systems (T4SS). While T4SS-mediated conjugation has been well-studied in bacteria, information is sparse in Archaea and known representatives exist only in the Sulfolobales order of Crenarchaeota. Here we present the first self-transmissible plasmid identified in a Euryarchaeon, Thermococcus sp. 33-3. The 103 kbp plasmid, pT33-3, is seen in CRISPR-spacers throughout the Thermococcales order. We demonstrate that pT33-3 is a bona fide conjugative plasmid that requires cell-to-cell contact, and is dependent upon canonical, plasmid-encoded T4SS-like genes. Under laboratory conditions pT33-3 transfers to various Thermococcales, and transconjugants propagate at 100°C. Using pT33-3, we developed a genetic toolkit which allows modification of phylogenetically diverse Archaeal genomes. We demonstrate pT33-3–mediated plasmid mobilization and subsequent targeted genome modification in previously untransformable Thermococcales species, and extend this process to interphylum transfer to a Crenarchaeon.</span></p>
Complete bacterial assemblies for 'Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK'
<p>Complete bacterial assemblies from the journal article 'Matlock, William, et al. "<em>Enterobacterales</em> plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK." <em>Elife</em> 12 (2023): e85302.'</p> <p>'assemblies.zip' contains assemblies for <em>n</em>=1,458 isolates with circularised chromosomes and <em>n</em>=3,697 circularised plasmids.</p> <p><strong>If you use this data please cite the journal article <em>and</em> the Zenodo DOI. </strong></p>
Read coverage information for analysis missing plasmid sequences
<p>This file contains two directories: read_coverage, and read_coverage_contigs. This directories should be decompressed and located within ecoli-binary-classifier/2021_11_missing_sequences_analysis/results/ in order to reproduce results described the in the mansucript.</p>
Biofilm formation and plasmid-mediated quinolone resistance genes at varying quinolone inhibitory concentrations in quinolone-resistant bacteria superinfecting COVID-19 inpatients
<p>The likelihood of treatment failure in COVID-19 patients with bacterial superinfection stems from phenotypic, viz., biofilms, and genotypic mechanisms. This cross-sectional study aimed to determine the inhibitory concentrations of quinolones—nalidixic acid, norfloxacin, ciprofloxacin, ofloxacin, and levofloxacin—in biofilm formers [minimum biofilm inhibitory concentration (MBIC)] and non-formers [minimum inhibitory concentration (MIC)] as well as correlate the quinolones' folds with the presence of plasmid-mediated quinolone-resistance (PMQR) genes in quinolone-resistant bacteria isolated from COVID-19 inpatients. Quinolone-resistant isolates (n=193), verified through disc diffusion, were tested for quinolone inhibitory concentrations and biofilm formation with broth microdilution and microtiter plate methods, respectively. Polymerase chain reaction was used to detect PMQR genes. MIC to MBIC median increase in folds for ciprofloxacin, ofloxacin, and levofloxacin was 128 (2-8,192), 64 (4-1,024), and 32 (4-512) in gram-positive cocci (GPC), respectively, while it was 32 (4-8,192), 32 (4-2,048), and 16 (2-1,024) in fermentative-gram-negative bacilli (F-GNB), and 16 (4-4,096), 64 (2-64), and 16 (8-512) in non-fermentative-gram-negative bacilli (NF-GNB). Biofilm-forming F-GNB (32/126) and NF-GNB (10/24) harbored <em>qnrB</em> [11/32 versus (vs.) 3/10], <em>aac(6')-Ib-cr </em>(10/32 vs. 4/10), and <em>qnrS</em> (9/32 vs. 0/10) genes, respectively. A 32-fold median increase in ciprofloxacin was significantly associated with <em>qnrA</em> and <em>qnrS</em> in F-GNB and NF-GNB, respectively. F-GNB and NF-GNB biofilms were significantly associated with <em>aac(6')-Ib-cr</em> and <em>qnrS</em> genes, respectively. Nearly one-third of the superinfecting bacteria in COVID-19 patients formed biofilms, and had at least one PMQR gene, increasing the need for quinolone inhibitory concentrations.</p>
Data from: Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro
<div> <div> <div> <p>Antimicrobial resistance (AR) mechanisms encoded on plasmids can affect other phenotypic traits in bacteria, including biofilm formation. These effects may be important contributors to the spread of AR and the evolutionary success of plasmids, but it is not yet clear how common such effects are for clinical plasmids/bacteria, and how they vary among different plasmids and host strains. Here, we used a combinatorial approach to test the effects of clinical AR plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains. In most of the 25 plasmid-bacterium combinations tested, we observed no significant change in biofilm formation upon plasmid introduction, contrary to the notion that plasmids frequently alter biofilm formation. In a few cases we detected altered biofilm formation, and these effects were specific to particular plasmid-bacterium combinations. By contrast, we found a relatively strong effect of a chromosomal streptomycin-resistance mutation (in rpsL) on biofilm formation. Further supporting weak and host-strain- dependent effects of clinical plasmids on bacterial phenotypes in the combinations we tested, we found growth costs associated with plasmid carriage (measured in the absence of antibiotics) were moderate and varied among bacterial strains. These findings suggest some key clinical resistance plasmids cause only mild phenotypic disruption to their host bacteria, which may contribute to the persistence of plasmids in the absence of antibiotics.</p> </div> </div> </div>
Machine learning suggests small size is a key determinant of plasmid host range
<p>Plasmids mediate gene exchange across taxonomic barriers through conjugation, shaping bacterial evolution for billions of years. While plasmid mobility can be harnessed for genetic engineering and drug-delivery applications, rapid plasmid-mediated spread of resistance genes has rendered most clinical antibiotics useless, posing an existential threat to human society. To solve this urgent problem, we must understand how plasmids spread across bacterial communities. Here, we applied machine-learning models to identify features that determine plasmid host range. We assembled an up-to-date dataset of more than thirty thousand bacterial plasmids, separated them into 1125 clusters, and assigned a distribution possibility score, which takes host distribution of each taxonomic rank and the sampling bias of the existing sequencing data into account, for each cluster. Using this score and an optimized plasmid feature pool, we built a model stack consisting of DecisionTreeRegressor, EvoTreeRegressor, and LGBMRegressor as base models and LinearRegressor as a meta-learner. Our analysis reveals that a short sequence length is most important for successful plasmid spread, followed by P-loop NTPases, mobility factors, and <span>β</span>-lactamases. Ours and other recent results suggest that small plasmids broaden their range by evading host defenses and using alternative modes of transfer instead of autonomous conjugation.</p>
Study of Hepatocyte Growth Factor (HGF) Via Plasmid Vector to Improve Perfusion in Critical Limb Ischemia Patients With Peripheral Ischemic Ulcers
ClinicalTrials.gov study NCT00189540. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Safety and Effectiveness of HIV-1 DNA Plasmid Vaccine and HIV-1 Recombinant Adenoviral Vector Vaccine in HIV-Uninfected, Circumcised Men and Male-to-Female (MTF) Transgender Persons Who Have Sex With
ClinicalTrials.gov study NCT00865566. IPD Sharing: Not stated. Countries: 1. Publications: 4.
NY-ESO-1 Plasmid DNA (pPJV7611) Cancer Vaccine
ClinicalTrials.gov study NCT00199849. IPD Sharing: NO. Countries: 1. Publications: 1.
Safety and Efficacy of Injectable Klotho Plasmid Gene Therapy in Humans
ClinicalTrials.gov study NCT07216781. IPD Sharing: YES. Countries: 2. Publications: 14.
Intracellular competition shapes plasmid population dynamics
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A streamlined approach for fluorescence labelling of low copy-number plasmids for determination of conjugation frequency by flow cytometry
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Machine learning suggests that small size helps broaden plasmid host range
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Data from: Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli
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Data from: A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea
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Data from: Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro
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Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans
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Off-target integron activity leads to rapid plasmid compensatory evolution in response to antibiotic selection pressure
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.bam alignment files of Illumina and ONT sequencing of pREF plasmid
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Spatial structure and benefits to hosts allow plasmids with and without post-segregational killing (PSK) systems to coexist
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International Brain Laboratory public data
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OpenNeuro
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