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153 results for “bacteriophage”
Codes and parameter datasets for the "Bacteriophage self-counting in the presence of viral replication"
<p>Matlab codes and datasets used for modeling in the paper "Bacteriophage self-counting in the presence of viral replication" PNAS 2021 Vol. 118 No. 51 e2104163118 https://doi.org/10.1073/pnas.2104163118 </p>
Bacteriophage genomes in the Japanese 4D microbiome project
<p>4,709 bacteriophage genomes constructed from the metagenomic dataset in the Japanese 4D microbiome project</p>
Stop-codon recoding in bacteriophages may regulate translation of lytic genes
<p><strong>This has some basic datasets for bacteriophages that use alternative genetic codes, and their close standard code relatives. </strong></p> <p>I have included the following:</p> <p>- Genomes for all alternatively coded phages and their relatives</p> <p>- Predicted proteins all alternatively coded phages and their relatives</p> <p>- A sheet with some basic information about these phages</p> <p>- Terminase treefile (Figure 2A) </p> <p>- Genomes for crAss-like phages used in the alternative code bias analysis (Figure 4)</p> <p>- Genomes for Agate phages used in the alternative code bias analysis (Figure 4) as well as the ANI analysis (Figure 3A)</p> <p>- Untrimmed lysogenic contigs for prophages (Like those shown in Figure 5)</p> <p> </p>
Bacteriophage genomes that potentially infect PDAC-associated species
<p>58 bacteriophage genomes that were predicted to infect PDAC-associated species.</p>
Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage ΦD5 results in fitness tradeoffs for the bacterium during infection - microscopic dataset
<p>Microscopic datasets (TEM, SEM and AFM) supporting the manuscript entitled: <strong>Resistance of </strong><em><strong>Dickeya solani</strong></em><strong> strain IPO 2222 to lytic bacteriophage </strong><strong>Φ</strong><strong>D5 results in fitness tradeoffs for the bacterium during infection.</strong></p>
Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage ΦD5 results in fitness tradeoffs for the bacterium during infection - mutants genomes dataset
<p>Raw genome sequence (genomes of the phage-resistant D. solani Tn5 mutants) dataset supporting the manuscript entitled: <strong>Resistance of </strong><em><strong>Dickeya solani</strong></em><strong> strain IPO 2222 to lytic bacteriophage </strong><strong>Φ</strong><strong>D5 results in fitness tradeoffs for the bacterium during infection.</strong></p>
Resistance to bacteriophage incurs a cost to virulence in drug resistant Acinetobacter baumannii
<p>Introduction<em>: Acinetobacter baumannii</em> is a critical priority pathogen (World Health Organisation) because of the rise in nosocomial<em> </em>infections and its ability to evolve resistance to last resort antibiotics, which makes <em>A. baumannii</em> a priority target for phage therapy. Two strains of a novel, lytic bacteriophage (LemonAid and Tonic) able to infect carbapenem-resistant <em>A. baumannii</em> (strain NCTC 13420), were isolated from environmental water samples collected through a citizen science program.</p> <p>Methods: <em>In vitro </em>and <em>in vivo</em> assays, genomics and microscopy techniques were used to characterise the phages, determine mechanisms of phage resistance and the efficacy of the phages against <em>A. baumannii</em>.</p> <p>Results: <em>A. baumannii </em>developed resistance to both viruses, LemonAid and Tonic. Resistance came at a cost to virulence, with the resistant variants causing significantly reduced mortality in a <em>Galleria mellonella </em>larval <em>in vivo</em> model. A replicated 8bp insertion increased in frequency (~40% higher frequency than in the wildtype) within phage-resistant <em>A. baumannii </em>mutants, putatively resulting in early truncation of a protein of unknown function. Evidence from comparative genomics and an adsorption assay suggests this protein acts as a novel phage receptor site in <em>A. baumannii</em>. We find no evidence linking resistance to changes in capsule structure, a known virulence factor. LemonAid efficiently suppressed growth of <em>A. baumanni</em> <em>in vitro</em> across a wide range of titres. However, <em>in vivo</em>, while survival of <em>A. baumannii</em> infected larvae significantly increased with both remedial and prophylactic treatment with LemonAid (10<sup>7 </sup>PFU/mL), the effect was weak and not sufficient to save larvae from morbidity and mortality.</p> <p>Conclusion: While LemonAid and Tonic did not prove effective as a treatment in a <em>Galleria </em>larvae model, there is potential to harness their ability to attenuate virulence in drug-resistant <em>A. baumannii</em>.</p>
Virus – calcium carbonate composites: Possible mechanisms of bacteriophage-induced vaterite formation - Dataset
<p>Raw data (optical microscopy, electron microscopy, X-ray diffraction) from carbonate precipitation experiments in the presence of bacterial viruses.</p>
Data from: More evolvable bacteriophages better suppress their host
<p>The number of multidrug-resistant strains of bacteria is increasing rapidly, while the number of new antibiotic discoveries has stagnated. This trend has caused a surge in interest in bacteriophages as anti-bacterial therapeutics, in part because there is near limitless diversity of phages to harness. While this diversity provides an opportunity, it also creates the dilemma of having to decide which criteria to use to select phages. Here we test whether a phage's ability to coevolve with its host (evolvability) should be considered and how this property compares to two previously proposed criteria: fast reproduction and thermostability. To do this, we compared the suppressiveness of three phages that vary by a single amino acid yet differ in these traits such that each strain maximized two of three characteristics. Our studies revealed that both evolvability and reproductive rate are independently important. The phage most able to suppress bacterial populations was the strain with high evolvability and reproductive rate, yet this phage was unstable. Phages varied due to differences in the types of resistance evolved against them and their ability to counteract resistance. When conditions were shifted to exaggerate the importance of thermostability, one of the stable phages was most suppressive in the short-term, but not over the long-term. Our results demonstrate the utility of biological therapeutics' capacities to evolve and adjust in action to resolve complications like resistance evolution. Furthermore, evolvability is a property that can be engineered into phage therapeutics to enhance their effectiveness.</p>
Transfer of bacteriophages between the fingers of volunteers and water or saliva
<p>Data sets on the percentage of virus transferred between fingers and water or saliva. Transfer with saliva is for both wet hands (where the virus inoculum was not allowed to appreciably dry before transfer) and for dry hands (where the virus inoculum was allowed to dry before transfer). The data were collected, analyzed, and reported within the following publication:</p> <p>Pitol, A. K., Bischel, H. N., Kohn, T., & Julian, T. R. (2017). Virus Transfer at the Skin–Liquid Interface. Environmental Science & Technology, 51(24), 14417-14425. <a href="https://doi.org/10.1021/acs.est.7b04949">https://doi.org/10.1021/acs.est.7b04949</a>]</p>
Data for: Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes
<p>Bacteriophages are versatile mobile genetic elements that play key roles in driving the evolution of their bacterial hosts through horizontal gene transfer. Phages co-evolve with their bacterial hosts and have plastic genomes with extensive mosaicism. In this study, we present bioinformatic and experimental evidence that temperate and virulent (lytic) phages carry integrons, including integron-integrase genes, attC/attI recombination sites and gene cassettes. Integrons are normally found in Bacteria, where they capture, express and re-arrange mobile gene cassettes via integron-integrase activity. We demonstrate experimentally that a panel of attC sites carried in virulent phage can be recognized by the bacterial class 1 integron-integrase (IntI1) and then integrated into the paradigmatic attI1 recombination site using an attC x attI recombination assay. With an increasing number of phage genomes projected to become available, more phage-associated integrons and their components will likely be identified in the future. The discovery of integron components in bacteriophages establishes a new route for lateral transfer of these elements and their cargo genes between bacterial host cells.</p>
Data from: Heteroaggregation of virions with microplastics reduces the number of active bacteriophages in aqueous environments
<p>The objective of this study is to explore the effects of microplastics on the viability of the bacteriophages in an aqueous environment. Bacteriophages (phages), i.e., viruses of bacteria, are essential in homeostasis. It is estimated that phages cause up to 40% of the death of all bacteria daily. Any factor affecting phage activity is vital for the whole food chain and the ecology of numerous niches. We hypothesize that the number of active phages decreases due to the virions' adsorption on microplastic particles or by the released leachables from additives used in the production of plastic, e.g., stabilizers, plasticizers, colorants, and reinforcements. We exposed three diverse phages, namely T4 (tailed), MS2 (icosahedral), and M13 (filamentous), to 1 mg/mL suspension of twelve industrial-grade plastics [acrylonitrile butadiene styrene (ABS), high-impact polystyrene (HIPS), poly-ε-caproamide (PA6), polycarbonate (PC), polyethylene (PE), polyethylene terephthalate (PET), poly(methyl methacrylate) (PMMA), polypropylene (PP), polystyrene (PS), polytetrafluoroethylene (PTFE), polyurethane (PUR), polyvinyl chloride (PVC)] shredded to obtain microparticles of radius ranging from 2 to 50 µm. The effect of leachables was measured upon exposure of phages not to particles themselves but to the buffer pre-incubated with microplastics. A double-overlay plaque counting method was used to assess phage titers. We employed a classical linear regression model to verify which physicochemical parameters (65 variables were tested) govern the decrease of phage titers. The key finding is that adsorption mechanisms result in up to complete scavenging of virions, whereas leachables deactivate up to 50% of phages. This study reveals microplastic pollution's plausible and unforeseen ecotoxicological effect causing phage deactivation. Also, phage transmission through adsorption can alter the balance of the food chain in the new environment. The effect depends mainly on the zeta potentials of the polymers and the phage type.</p>
Resistance to bacteriophage incurs a cost to virulence in drug resistant Acinetobacter baumannii
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Data from: Heteroaggregation of virions with microplastics reduces the number of active bacteriophages in aqueous environments
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Personalized inhaled bacteriophage therapy for treatment of multidrug-resistant Pseudomonas aeruginosa in cystic fibrosis
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Data from: Bacteriophage infection and killing of intracellular Mycobacterium abscessus
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Data from: More evolvable bacteriophages better suppress their host
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Data for: Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes
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high-resolution data set of esterase vb_24B_21 from Shiga toxin-encoding bacteriophage phi24B; PDB id is 6YP6
<p>high-resolution data set of esterase vb_24B_21 from Shiga toxin-encoding bacteriophage phi24B; PDB id is 6YP6</p> <p>Data were collected at Diamond I04 on February 8, 2012 using an ADSC detector.</p>
medium resolution data set of esterase vb_24B_21 from Shiga toxin-encoding bacteriophage phi24B; PDB id 6YP6
<p>medium resolution data set of esterase vb_24B_21 from Shiga toxin-encoding bacteriophage phi24B; PDB id 6YP6</p> <p>Data were collected at Diamond I04-1 on February 6, 2012</p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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