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https://www.readbyqxmd.com/read/28545254/bacterial-virus-ontology-coordinating-across-databases
#1
Chantal Hulo, Patrick Masson, Ariane Toussaint, David Osumi-Sutherland, Edouard de Castro, Andrea H Auchincloss, Sylvain Poux, Lydie Bougueleret, Ioannis Xenarios, Philippe Le Mercier
Bacterial viruses, also called bacteriophages, display a great genetic diversity and utilize unique processes for infecting and reproducing within a host cell. All these processes were investigated and indexed in the ViralZone knowledge base. To facilitate standardizing data, a simple ontology of viral life-cycle terms was developed to provide a common vocabulary for annotating data sets. New terminology was developed to address unique viral replication cycle processes, and existing terminology was modified and adapted...
May 23, 2017: Viruses
https://www.readbyqxmd.com/read/28544996/temperate-bacteriophages-as-regulators-of-host-behavior
#2
REVIEW
Tal Argov, Gil Azulay, Anna Pasechnek, Olga Stadnyuk, Shai Ran-Sapir, Ilya Borovok, Nadejda Sigal, Anat A Herskovits
Bacteriophages are ubiquitous and affect most facets of life, from evolution of bacteria, through ecology and global biochemical cycling to human health. The interactions between phages and bacteria often lead to biological novelty and an important milestone in this process is the ability of phages to regulate their host's behavior. In this review article, we will focus on newly reported cases that demonstrate how temperate phages regulate bacterial gene expression and behavior in a variety of bacterial species, pathogenic and environmental...
May 22, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28542984/applying-quantitative-molecular-tools-for-virus-transport-studies-opportunities-and-challenges
#3
Kelvin Wong, Marirosa Molina
Bacteriophages have been used in soil column studies for the last several decades as surrogates to study the fate and transport behavior of enteric viruses in groundwater. However, recent studies have shown that the transport behavior of bacteriophages and enteric viruses in porous media can be very different. The next generation of virus transport science must therefore provide more data on mobility of enteric viruses and the relationship between transport behaviors of enteric viruses and bacteriophages. To achieve this new paradigm, labor intensity devoted to enteric virus quantification method must be reduced...
May 23, 2017: Ground Water
https://www.readbyqxmd.com/read/28542913/reduction-of-escherichia-coli-o157-h7-in-biofilms-using-bacteriophage-bpeco-19
#4
Mohammad Sadekuzzaman, Sungdae Yang, Md Furkanur Rahaman Mizan, Sang-Do Ha
Biofilm formation is a growing concern in the food industry. Escherichia coli O157:H7 is one of the most important foodborne pathogens that can persists in food and food-related environments and subsequently produce biofilms. The efficacy of bacteriophage BPECO 19 was evaluated against three E. coli O157:H7 strains in biofilms. Biofilms of the three E. coli O157:H7 strains were grown on abiotic (stainless steel, rubber, and minimum biofilm eradication concentration [MBEC(TM) ] device) and biotic (lettuce) surfaces at different temperatures...
May 19, 2017: Journal of Food Science
https://www.readbyqxmd.com/read/28542496/zinc-blocks-sos-induced-antibiotic-resistance-via-inhibition-of-reca-in-escherichia-coli
#5
Bryan E Bunnell, Jillian F Escobar, Kirsten L Bair, Mark D Sutton, John K Crane
Zinc inhibits the virulence of diarrheagenic E. coli by inducing the envelope stress response and inhibiting the SOS response. The SOS response is triggered by damage to bacterial DNA. In Shiga-toxigenic E. coli, the SOS response strongly induces the production of Shiga toxins (Stx) and of the bacteriophages that encode the Stx genes. In E. coli, induction of the SOS response is accompanied by a higher mutation rate, called the mutator response, caused by a shift to error-prone DNA polymerases when DNA damage is too severe to be repaired by canonical DNA polymerases...
2017: PloS One
https://www.readbyqxmd.com/read/28539351/bacteriophage-transfer-during-faecal-microbiota-transplantation-in-clostridium-difficile-infection-is-associated-with-treatment-outcome
#6
Tao Zuo, Sunny H Wong, Kelvin Lam, Rashid Lui, Kitty Cheung, Whitney Tang, Jessica Y L Ching, Paul K S Chan, Martin C W Chan, Justin C Y Wu, Francis K L Chan, Jun Yu, Joseph J Y Sung, Siew C Ng
OBJECTIVE: Faecal microbiota transplantation (FMT) is effective for the treatment of recurrent Clostridium difficile infection (CDI). Studies have shown bacterial colonisation after FMT, but data on viral alterations in CDI are scarce. We investigated enteric virome alterations in CDI and the association between viral transfer and clinical outcome in patients with CDI. DESIGN: Ultra-deep metagenomic sequencing of virus-like particle preparations and bacterial 16S rRNA sequencing were performed on stool samples from 24 subjects with CDI and 20 healthy controls...
May 24, 2017: Gut
https://www.readbyqxmd.com/read/28538703/metagenomic-approaches-to-assess-bacteriophages-in-various-environmental-niches
#7
REVIEW
Stephen Hayes, Jennifer Mahony, Arjen Nauta, Douwe van Sinderen
Bacteriophages are ubiquitous and numerous parasites of bacteria and play a critical evolutionary role in virtually every ecosystem, yet our understanding of the extent of the diversity and role of phages remains inadequate for many ecological niches, particularly in cases in which the host is unculturable. During the past 15 years, the emergence of the field of viral metagenomics has drastically enhanced our ability to analyse the so-called viral 'dark matter' of the biosphere. Here, we review the evolution of viral metagenomic methodologies, as well as providing an overview of some of the most significant applications and findings in this field of research...
May 24, 2017: Viruses
https://www.readbyqxmd.com/read/28536572/the-bacteriophage-ef-p29-efficiently-protects-against-lethal-vancomycin-resistant-enterococcus-faecalis-and-alleviates-gut-microbiota-imbalance-in-a-murine-bacteremia-model
#8
Mengjun Cheng, Jiaming Liang, Yufeng Zhang, Liyuan Hu, Pengjuan Gong, Ruopeng Cai, Lei Zhang, Hao Zhang, Jinli Ge, Yalu Ji, Zhimin Guo, Xin Feng, Changjiang Sun, Yongjun Yang, Liancheng Lei, Wenyu Han, Jingmin Gu
Enterococcus faecalis is becoming an increasingly important opportunistic pathogen worldwide, especially because it can cause life-threatening nosocomial infections. Treating E. faecalis infections has become increasingly difficult because of the prevalence of multidrug-resistant E. faecalis strains. Because bacteriophages show specificity for their bacterial hosts, there has been a growth in interest in using phage therapies to combat the rising incidence of multidrug-resistant bacterial infections. In this study, we isolated a new lytic phage, EF-P29, which showed high efficiency and a broad host range against E...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28533535/tail-tubular-protein-a-a-dual-function-tail-protein-of-klebsiella-pneumoniae-bacteriophage-kp32
#9
Anna Pyra, Ewa Brzozowska, Krzysztof Pawlik, Andrzej Gamian, Miroslawa Dauter, Zbigniew Dauter
Tail tubular protein A (TTPA) is a structural tail protein of Klebsiella pneumoniae bacteriophage KP32, and is responsible for adhering the bacteriophage to host cells. For the first time, we found that TTPA also exhibits lytic activity towards capsular exopolysaccharide (EPS) of the multiresistant clinical strain of Klebsiella pneumoniae, PCM2713, and thus should be regarded as a dual-function macromolecule that exhibits both structural and enzymatic actions. Here, we present our crystallographic and enzymatic studies of TTPA...
May 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28532790/a-safe-and-molecular-tagged-brucella-canis-ghosts-confers-protection-against-virulent-challenge-in-mice
#10
Jing Qian, Zhaoyang Bu, Xulong Lang, Guangmou Yan, Yanling Yang, Xiuran Wang, Xinglong Wang
Canine brucellosis, caused by Brucella canis, is a persistent infectious reproductive disease in dogs. The absence of effective treatment to the intracellular pathogen and the irreversible consequence of infection makes the need of a specific vaccine urgent. Bacterial ghosts (BGs) are the empty envelopes of bacteria with no genome content inside, which emerge as a proper vaccine candidate due to its intact outer antigen. It is generally derived from a genetically engineered strain, through the expression of Bacteriophage phiX174 lysis E gene upon induction...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28531182/selection-of-a-biosafety-level-1-bsl-1-surrogate-to-evaluate-surface-disinfection-efficacy-in-ebola-outbreaks-comparison-of-four-bacteriophages
#11
Karin Gallandat, Daniele Lantagne
The 2014 West African Ebola virus disease outbreak was the largest to date, and conflicting, chlorine-based surface disinfection protocols to interrupt disease transmission were recommended. We identified only one study documenting surface disinfection efficacy against the Ebola virus, showing a >6.6 log reduction after 5-minute exposure to 0.5% sodium hypochlorite (NaOCl) based on small-scale tests (Cook et al. (2015)). In preparation for future extensive, large-scale disinfection efficacy experiments, we replicated the Cook et al...
2017: PloS One
https://www.readbyqxmd.com/read/28531104/stumbling-across-the-same-phage-comparative-genomics-of-widespread-temperate-phages-infecting-the-fish-pathogen-vibrio-anguillarum
#12
Panos G Kalatzis, Nanna Iben Rørbo, Daniel Castillo, Jesper Juel Mauritzen, Jóhanna Jørgensen, Constantina Kokkari, Faxing Zhang, Pantelis Katharios, Mathias Middelboe
Nineteen Vibrio anguillarum-specific temperate bacteriophages isolated across Europe and Chile from aquaculture and environmental sites were genome sequenced and analyzed for host range, morphology and life cycle characteristics. The phages were classified as Siphoviridae with genome sizes between 46,006 and 54,201 bp. All 19 phages showed high genetic similarity, and 13 phages were genetically identical. Apart from sporadically distributed single nucleotide polymorphisms (SNPs), genetic diversifications were located in three variable regions (VR1, VR2 and VR3) in six of the phage genomes...
May 20, 2017: Viruses
https://www.readbyqxmd.com/read/28529972/simple-and-versatile-detection-of-viruses-using-anodized-alumina-membranes
#13
Pavan Chaturvedi, Stacy D Rodriguez, Ivan Vlassiouk, Immo A Hansen, Sergei N Smirnov
A simple sensor for viral particles based on ionic conductivity through anodized alumina membranes was demonstrated using MS2 bacteriophage as an example. A facile two-point measuring scheme is geared toward realization using a computer's sound card input/output capabilities suitable for a fast and inexpensive point of care testing. The lowest detection concentration down to ~7 pfu/mL and a large dynamic range up to ~2000 pfu/mL were obtained due to physical optimization that included proper length and diameter for the pores, removing the oxide layer at the electrode, as well as the chemical optimization of covalent binding of antibodies to the pore's walls...
May 27, 2016: ACS Sensors
https://www.readbyqxmd.com/read/28527384/embracing-the-enemy-the-diversification-of-microbial-gene-repertoires-by-phage-mediated-horizontal-gene-transfer
#14
REVIEW
Marie Touchon, Jorge A Moura de Sousa, Eduardo Pc Rocha
Bacteriophages and archaeal viruses contribute, through lysogenic conversion or transduction, to the horizontal transfer of genetic material between microbial genomes. Recent genomics, metagenomics, and single cell studies have shown that lysogenic conversion is widespread and provides hosts with adaptive traits often associated with biotic interactions. The quantification of the evolutionary impact of transduction has lagged behind and requires further theoretical and experimental work. Nevertheless, recent studies suggested that generalized transduction plays a role in the transfer of antibiotic resistance genes and in the acquisition of novel genes during intra-specific bacterial competition...
May 17, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28526791/pseudomonas-chlororaphis-produces-two-distinct-r-tailocins-that-contribute-to-bacterial-competition-in-biofilms-and-on-roots
#15
Robert J Dorosky, Jun Myoung Yu, Leland S Pierson, Elizabeth A Pierson
R-type tailocins are high molecular weight bacteriocins that resemble bacteriophage tails and are encoded within the genomes of many Pseudomonas species. In this study, analysis of the P. chlororaphis 30-84 R-tailocin gene cluster revealed that it encodes the structural components to produce two R-tailocins of different ancestral origin. Two distinct R-tailocin populations differing in length were observed in UV induced lysates of P. chlororaphis 30-84 via transmission electron microscopy. Mutants defective in the production of one or both R-tailocins demonstrated that the killing spectrum of each tailocin is limited to Pseudomonas species...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28523910/dense-layer-of-bacteriophages-ordered-in-alternating-electric-field-and-immobilized-by-surface-chemical-modification-as-sensing-element-for-bacteria-detection
#16
Łukasz Richter, Krzysztof Bielec, Adam Lesniewski, Marcin Łoś, Jan Paczesny, Robert Holyst
Faster and more sensitive environmental monitoring should be developed to face the worldwide problem of bacterial infections. To remedy this issue we demonstrate bacteria sensing element, which utilizes dense and ordered layers of bacteriophages specific for given bacteria strain. We combine 1) chemical modification of the surface to increase the surface coverage of bacteriophages 2) with alternating electric field to greatly increase the number of properly oriented bacteriophages at the surface. Usually in sensing elements a random orientation of bacteriophages results in steric hindrances, which cause that no more than few percent of all receptors is available...
May 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28522818/efficient-modification-of-%C3%AE-dna-substrates-for-single-molecule-studies
#17
Yoori Kim, Armando de la Torre, Andrew A Leal, Ilya J Finkelstein
Single-molecule studies of protein-nucleic acid interactions frequently require site-specific modification of long DNA substrates. The bacteriophage λ is a convenient source of high quality long (48.5 kb) DNA. However, introducing specific sequences, tertiary structures, and chemical modifications into λ-DNA remains technically challenging. Most current approaches rely on multi-step ligations with low yields and incomplete products. Here, we describe a molecular toolkit for rapid preparation of modified λ-DNA...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28515656/isolation-and-characterization-of-listeria-phages-for-control-of-growth-of-listeria-monocytogenes-in-milk
#18
Sunhee Lee, Min Gon Kim, Hee Soo Lee, Sunhak Heo, Mirae Kwon, GeunBae Kim
In this study, two Listeria bacteriophages, LMP1 and LMP7, were isolated from chicken feces as a means of biocontrol of L. monocytogenes. Both bacteriophages had a lytic effect on L. monocytogenes ATCC 7644, 15313, 19114, and 19115. Phages LMP1 and LMP7 were able to inhibit the growth of L. monocytogenes ATCC 7644 and 19114 in tryptic soy broth at 10°C and 30°C. Nevertheless, LMP1 was more effective than LMP7 at inhibiting L. monocytogenes ATCC 19114. On the contrary, LMP7 was more effective than LMP1 at inhibiting L...
2017: Korean Journal for Food Science of Animal Resources
https://www.readbyqxmd.com/read/28514857/pathways-for-gold-nucleation-and-growth-over-protein-cages
#19
Ziyou Zhou, Gregory J Bedwell, Rui Li, Soubantika Palchoudhury, Peter E Prevelige, Arunava Gupta
Proteins are widely utilized as templates in biomimetic synthesis of gold nanocrystals. However, the role of proteins in mediating the pathways for gold nucleation and growth is not well understood, in part because of the lack of spatial resolution in probing the complicated biomimetic mineralization process. Self-assembled protein cages, with larger size and symmetry, can facilitate in the visualization of both biological and inorganic components. We have utilized bacteriophage P22 protein cages of ~ 60 nm diameter for investigating the nucleation and growth of gold nanocrystals...
May 18, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28513100/function-of-bacteriophage-g7c-esterase-tailspike-in-host-cell-adsorption
#20
Nikolai S Prokhorov, Cristian Riccio, Evelina L Zdorovenko, Mikhail M Shneider, Christopher Browning, Yuriy A Knirel, Petr G Leiman, Andrey V Letarov
Bacteriophages recognize and bind to their hosts with the help of receptor-binding proteins (RBPs) that emanate from the phage particle in the form of fibers or tailspikes. RBPs show a great variability in their shapes, sizes, and location on the particle. Some RBPs are known to depolymerize surface polysaccharides of the host while others show no enzymatic activity. Here we report that both RBPs of podovirus G7C - tailspikes gp63.1 and gp66 - are essential for infection of its natural host bacterium E. coli 4s that populates the equine intestinal tract...
May 17, 2017: Molecular Microbiology
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