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Bacteriophage

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https://www.readbyqxmd.com/read/27932642/complete-genome-sequence-of-vb_ecom-ufv13-a-new-bacteriophage-able-to-disrupt-trueperella-pyogenes-biofilm
#1
Vinícius S Duarte, Roberto S Dias, Andrew M Kropinski, Pedro M P Vidigal, Flávia O Sousa, André S Xavier, Cynthia C Silva, Sergio O de Paula
vB_EcoM-UFV13, a member of the T4virus genus, shows lytic activity against Escherichia coli and effectiveness in controlling the biofilm formed by Trueperella pyogenes, which qualifies it as a promising component of phage cocktails for mastitis and metritis control.
December 8, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27932636/complete-genome-sequence-of-bacteriophage-ma12-which-infects-both-campylobacter-jejuni-and-salmonella-enterica-serovar-enteritidis
#2
Sunjin Lee, Taesoo Kwon, Su-Jin Chae, Jong-Hyun Kim, Yeon Ho Kang, Gyung Tae Chung, Dae-Won Kim, Deog-Yong Lee
Here, we announce the complete genome sequence of Salmonella enterica serovar Enteritidis (S Enteritidis) bacteriophage MA12, a 41-Kb chromosome. The strain can infect both Campylobacter jejuni (C. jejuni) and S Enteritidis and can be used in phage therapy experiments with poultry and poultry meat.
December 8, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27932635/genome-sequence-of-bacteriophage-gg32-which-can-infect-both-salmonella-enterica-serovar-typhimurium-and-escherichia-coli-o157-h7
#3
Su-Jin Chae, Taesoo Kwon, Sunjin Lee, Yeon Ho Kang, Gyung Tae Chung, Dae-Won Kim, Deog-Yong Lee
We report here a new virulent Salmonella enterica serovar Typhimurium (S Typhimurium) bacteriophage, GG32, which was isolated from the Guem River in the Republic of Korea. The strain can infect both S Typhimurium and Escherichia coli (E. coli) O157:H7 and may be a good candidate for a bio-control agent.
December 8, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27924926/identification-of-protein-structural-elements-responsible-for-the-diversity-of-sequence-preferences-among-mini-iii-rnases
#4
Dawid Głów, Małgorzata Kurkowska, Justyna Czarnecka, Krzysztof Szczepaniak, Dariusz Pianka, Verena Kappert, Janusz M Bujnicki, Krzysztof J Skowronek
Many known endoribonucleases select their substrates based on the presence of one or a few specific nucleotides at or near the cleavage site. In some cases, selectivity is also determined by the structural features of the substrate. We recently described the sequence-specific cleavage of double-stranded RNA by Mini-III RNase from Bacillus subtilis in vitro. Here, we characterized the sequence specificity of eight other members of the Mini-III RNase family from different bacterial species. High-throughput analysis of the cleavage products of Φ6 bacteriophage dsRNA indicated subtle differences in sequence preference between these RNases, which were confirmed and characterized by systematic analysis of the cleavage kinetics of a set of short dsRNA substrates...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27923995/homologous-recombination-in-budding-yeast-expressing-the-human-rad52-gene-reveals-a-rad51-independent-mechanism-of-conservative-double-strand-break-repair
#5
Glenn M Manthey, Alissa D Clear, Lauren C Liddell, Maria C Negritto, Adam M Bailis
RAD52 is a homologous recombination (HR) protein that is conserved from bacteriophage to humans. Simultaneously attenuating expression of both the RAD52 gene, and the HR and tumor suppressor gene, BRCA2, in human cells synergistically reduces HR - indicating that RAD52 and BRCA2 control independent mechanisms of HR. We have expressed the human RAD52 gene (HsRAD52) in budding yeast strains lacking the endogenous RAD52 gene and found that HsRAD52 supports repair of DNA double-strand breaks (DSB) by a mechanism of HR that conserves genome structure...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27920385/sublethal-streptomycin-concentrations-and-lytic-bacteriophage-together-promote-resistance-evolution
#6
Johannes Cairns, Lutz Becks, Matti Jalasvuori, Teppo Hiltunen
Sub-minimum inhibiting concentrations (sub-MICs) of antibiotics frequently occur in natural environments owing to wide-spread antibiotic leakage by human action. Even though the concentrations are very low, these sub-MICs have recently been shown to alter bacterial populations by selecting for antibiotic resistance and increasing the rate of adaptive evolution. However, studies are lacking on how these effects reverberate into key ecological interactions, such as bacteria-phage interactions. Previously, co-selection of bacteria by phages and antibiotic concentrations exceeding MICs has been hypothesized to decrease the rate of resistance evolution because of fitness costs associated with resistance mutations...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27919889/study-of-intracellular-staphylococcus-aureus-control-by-virulent-bacteriophage-within-mac-t-bovine-mammary-epithelial-cells
#7
Lili Zhang, Lichang Sun, Ruicheng Wei, Qiang Gao, Tao He, Cunfa Xu, Xianjin Liu, Ran Wang
Bacteriophages (phages) are known to effectively kill extracellular multiplying bacteria. The present study demonstrated that phages penetrated bovine mammary epithelial cells and cleared intracellular Staphylococcus aureus, in a time-dependent manner. In particular, phage vB_SauM_JS25 reached the nucleus within the 3 h post-incubation. The phages had an endocytotic efficiency of 12%. This ability to kill intracellular host bacteria suggests the utility of phage-based therapies, and may protect from recurrent infection and treatment failure...
December 5, 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27917795/lytic-activity-of-various-phage-cocktails-on-multidrug-resistant-bacteria
#8
I Ozkan, E Akturk, N Yeshenkulov, S Atmaca, N Rahmanov, H I Atabay
PURPOSE: A bacteriophage is a virus that infects and replicates within a bacterium following the injection of phage genome into the bacterial cytoplasm. They are seen as a possible therapy for multi-drug-resistant strains of many bacteria. The aim of this study is to evaluate the lytic activity of the Pyo, Intesti and Fersisi bacteriophage cocktails on P. aeruginosa and S. aureus. METHODS: Ten different S. aureus and P. aeruginosa strains, which were isolated from hospitalized patients in Turkey, were used in the study...
December 1, 2016: Clinical and Investigative Medicine. Médecine Clinique et Experimentale
https://www.readbyqxmd.com/read/27917733/evaluation-of-an-ethanol-based-spray-disinfectant-for-decontamination-of-cover-gowns-prior-to-removal
#9
Sreelatha Koganti, Heba Alhmidi, Myreen E Tomas, Jennifer L Cadnum, Christopher Sass, Annette L Jencson, Curtis J Donskey
An ethanol-based spray disinfectant significantly reduced bacteriophage MS2 contamination on material from gowns meeting ASTM standard 1671 for resistance to blood and viral penetration and on a cover gown worn by personnel. Effectiveness of disinfection was affected by the type of gown material and the correctness of fit. Infect Control Hosp Epidemiol 2016;1-3.
December 5, 2016: Infection Control and Hospital Epidemiology
https://www.readbyqxmd.com/read/27915247/genomic-diversity-of-bacteriophages-infecting-the-fish-pathogen-flavobacterium-psychrophilum
#10
Daniel Castillo, Mathias Middelboe
Bacteriophages infecting the fish pathogen Flavobacterium psychrophilum can potentially be used to prevent and control outbreaks of this bacterium in salmonid aquaculture. However, application of bacteriophages in disease control requires detailed knowledge on their genetic composition. To explore the diversity of F. pyschrophilum bacteriophages we have analyzed the complete genome sequences of 17 phages isolated from two distant geographic areas (Denmark and Chile), including the previously characterized temperate bacteriophage 6H...
December 2, 2016: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/27913133/a-comparative-study-of-different-strategies-for-removal-of-endotoxins-from-bacteriophage-preparations
#11
Jonas D Van Belleghem, Maya Merabishvili, Bjorn Vergauwen, Rob Lavigne, Mario Vaneechoutte
Bacterial endotoxins have high immunogenicity. Phage biology studies as well as therapeutic phage applications necessitate highly purified phage particles. In this study, we compared combinations of seven different endotoxin removal strategies and validated their endotoxin removal efficacy for five different phages (i.e. four Pseudomonas aeruginosa phages and one Staphylococcus aureus phage). These purification strategies included Endotrap HD column purification and/or CsCl density centrifugation in combination with Endotrap purification, followed by organic solvent (1-octanol), detergent (Triton X-100), enzymatic inactivation of the endotoxin using alkaline phosphatase and CIM monolytic anion exchange chromatography...
November 29, 2016: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/27912785/transmission-of-viruses-via-our-microbiomes
#12
Melissa Ly, Marcus B Jones, Shira R Abeles, Tasha M Santiago-Rodriguez, Jonathan Gao, Ivan C Chan, Chandrabali Ghose, David T Pride
BACKGROUND: Bacteria inhabiting the human body have important roles in a number of physiological processes and are known to be shared amongst genetically-related individuals. Far less is known about viruses inhabiting the human body, but their ecology suggests they may be shared between close contacts. RESULTS: Here, we report the ecology of viruses in the guts and mouths of a cohort and demonstrate that substantial numbers of gut and oral viruses were shared amongst genetically unrelated, cohabitating individuals...
December 2, 2016: Microbiome
https://www.readbyqxmd.com/read/27912769/three-novel-bacteriophages-isolated-from-the-east-african-rift-valley-soda-lakes
#13
Leonardo Joaquim van Zyl, Shonisani Nemavhulani, James Cass, Donald Arthur Cowan, Marla Trindade
BACKGROUND: Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour. Although well studied with respect to their microbial composition, their viral compositions have not, and consequently few bacteriophages that infect bacteria from haloalkaline environments have been described. METHODS: Bacteria were isolated from sediment samples of lakes Magadi and Shala. Three phages were isolated on two different Bacillus species and one Paracoccus species using agar overlays...
December 3, 2016: Virology Journal
https://www.readbyqxmd.com/read/27910929/novel-groups-and-unique-distribution-of-phage-phoh-genes-in-paddy-waters-in-northeast-china
#14
Xinzhen Wang, Junjie Liu, Zhenhua Yu, Jian Jin, Xiaobing Liu, Guanghua Wang
Although bacteriophages are ubiquitous in various environments, their genetic diversity is primarily investigated in pelagic marine environments. Corresponding studies in terrestrial environments are few. In this study, we conducted the first survey of phage diversity in the paddy ecosystem by targeting a new viral biomarker gene, phoH. A total of 424 phoH sequences were obtained from four paddy waters generated from a pot experiment with different soils collected from open paddy fields in northeast China. The majority of phoH sequences in paddy waters were novel, with the highest identity of ≤70% with known phoH sequences...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27908758/thermally-triggered-release-of-the-bacteriophage-endolysin-chapk-and-the-bacteriocin-lysostaphin-for-the-control-of-methicillin-resistant-staphylococcus-aureus-mrsa
#15
Hollie Hathaway, Jude Ajuebor, Liam Stephens, Aidan Coffey, Ursula Potter, J Mark Sutton, A Toby A Jenkins
Staphylococcus aureus infections of the skin and soft tissue pose a major concern to public health, largely owing to the steadily increasing prevalence of drug resistant isolates. As an alternative mode of treatment both bacteriophage endolysins and bacteriocins have been shown to possess antimicrobial efficacy against multiple species of bacteria including otherwise drug resistant strains. Despite this, the administration and exposure of such antimicrobials should be restricted until required in order to discourage the continued evolution of bacterial resistance, whilst maintaining the activity and stability of such proteinaceous structures...
November 28, 2016: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/27908235/pentatricopeptide-motifs-in-the-n-terminal-extension-domain-of-yeast-mitochondrial-rna-polymerase-rpo41p-are-not-essential-for-its-function
#16
J Kruszewski, P Golik
The core mitochondrial RNA polymerase is a single-subunit enzyme that in yeast Saccharomyces cerevisiae is encoded by the nuclear RPO41 gene. It is an evolutionary descendant of the bacteriophage RNA polymerases, but it includes an additional unconserved N-terminal extension (NTE) domain that is unique to the organellar enzymes. This domain mediates interactions between the polymerase and accessory regulatory factors, such as yeast Sls1p and Nam1p. Previous studies demonstrated that deletion of the entire NTE domain results only in a temperature-dependent respiratory deficiency...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27904467/isolation-and-characterization-of-a-bacteriophage-preying-an-antifungal-bacterium
#17
Aryan Rahimi-Midani, Kyoung-Ho Kim, Seon-Woo Lee, Sang Bong Jung, Tae-Jin Choi
Several Bacillus species were isolated from rice field soils, and 16S rRNA gene sequence analysis showed that Bacillus cereus was the most abundant. A strain named BC1 showed antifungal activity against Rhizoctonia solani. Bacteriophages infecting strain BC1 were isolated from the same soil sample. The isolated phage PK16 had an icosahedral head of 100 ± 5 nm and tail of 200 ± 5 nm, indicating that it belonged to the family Myoviridae. Analysis of the complete linear dsDNA genome revealed a 158,127-bp genome with G + C content of 39...
December 2016: Plant Pathology Journal
https://www.readbyqxmd.com/read/27903913/functional-rnas-combined-assembly-and-packaging-in-vlps
#18
Po-Yu Fang, Lizzette M Gómez Ramos, Stefany Y Holguin, Chiaolong Hsiao, Jessica C Bowman, Hung-Wei Yang, Loren Dean Williams
We describe here a one pot RNA production, packaging and delivery system based on bacteriophage Qβ. We demonstrate a method for production of a novel RNAi scaffold, packaged within Qβ virus-like particles (VLPs). The RNAi scaffold is a general utility chimera that contains a functional RNA duplex with paired silencing and carrier sequences stabilized by a miR-30 stem-loop. The Qβ hairpin on the 5' end confers affinity for the Qβ coat protein (CP). Silencing sequences can include mature miRNAs and siRNAs, and can target essentially any desired mRNA...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902329/abundance-of-antibiotic-resistance-genes-in-environmental-bacteriophages
#19
Taruna Anand, Bidhan Ch Bera, Rajesh K Vaid, Sanjay Barua, Thachamvally Riyesh, Nitin Virmani, Mubarik Hussain, Raj K Singh, Bhupendra N Tripathi
The ecosystem is continuously exposed to a wide variety of antimicrobials through waste effluents, agricultural runoffs, animal related and anthropogenic activities, which contribute to spread of antibiotic resistance genes (ARGs). The contamination of ecosystems with ARGs may create increased opportunities for their transfer to naive microbes and eventually lead to entry into the human food chain. Transduction is a significant mechanism of horizontal gene transfer in natural environments, which has traditionally been underestimated as compared to transformation...
October 21, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27899557/alignment-free-d_2-oligonucleotide-frequency-dissimilarity-measure-improves-prediction-of-hosts-from-metagenomically-derived-viral-sequences
#20
Nathan A Ahlgren, Jie Ren, Yang Young Lu, Jed A Fuhrman, Fengzhu Sun
Viruses and their host genomes often share similar oligonucleotide frequency (ONF) patterns, which can be used to predict the host of a given virus by finding the host with the greatest ONF similarity. We comprehensively compared 11 ONF metrics using several k-mer lengths for predicting host taxonomy from among ∼32 000 prokaryotic genomes for 1427 virus isolate genomes whose true hosts are known. The background-subtracting measure [Formula: see text] at k = 6 gave the highest host prediction accuracy (33%, genus level) with reasonable computational times...
November 28, 2016: Nucleic Acids Research
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