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Bacteriophages

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https://www.readbyqxmd.com/read/28102347/low-level-predation-by-lytic-phage-phiipla-rodi-promotes-biofilm-formation-and-triggers-the-stringent-response-in-staphylococcus-aureus
#1
Lucía Fernández, Silvia González, Ana Belén Campelo, Beatriz Martínez, Ana Rodríguez, Pilar García
An important lesson from the war on pathogenic bacteria has been the need to understand the physiological responses and evolution of natural microbial communities. Bacterial populations in the environment are generally forming biofilms subject to some level of phage predation. These multicellular communities are notoriously resistant to antimicrobials and, consequently, very difficult to eradicate. This has sparked the search for new therapeutic alternatives, including phage therapy. This study demonstrates that S...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28100693/viral-genome-packaging-terminase-cleaves-dna-using-the-canonical-ruvc-like-two-metal-catalysis-mechanism
#2
Rui-Gang Xu, Huw T Jenkins, Maria Chechik, Elena V Blagova, Anna Lopatina, Evgeny Klimuk, Leonid Minakhin, Konstantin Severinov, Sandra J Greive, Alfred A Antson
Bacteriophages and large dsDNA viruses encode sophisticated machinery to translocate their DNA into a preformed empty capsid. An essential part of this machine, the large terminase protein, processes viral DNA into constituent units utilizing its nuclease activity. Crystal structures of the large terminase nuclease from the thermophilic bacteriophage G20c show that it is most similar to the RuvC family of the RNase H-like endonucleases. Like RuvC proteins, the nuclease requires either Mn(2+), Mg(2+) or Co(2+) ions for activity, but is inactive with Zn(2+) and Ca(2+) High resolution crystal structures of complexes with different metals reveal that in the absence of DNA, only one catalytic metal ion is accommodated in the active site...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28100665/co-option-of-bacteriophage-lysozyme-genes-by-bivalve-genomes
#3
Qian Ren, Chunyang Wang, Min Jin, Jiangfeng Lan, Ting Ye, Kaimin Hui, Jingmin Tan, Zheng Wang, Gerald J Wyckoff, Wen Wang, Guan-Zhu Han
Eukaryotes have occasionally acquired genetic material through horizontal gene transfer (HGT). However, little is known about the evolutionary and functional significance of such acquisitions. Lysozymes are ubiquitous enzymes that degrade bacterial cell walls. Here, we provide evidence that two subclasses of bivalves (Heterodonta and Palaeoheterodonta) acquired a lysozyme gene via HGT, building on earlier findings. Phylogenetic analyses place the bivalve lysozyme genes within the clade of bacteriophage lysozyme genes, indicating that the bivalves acquired the phage-type lysozyme genes from bacteriophages, either directly or through intermediate hosts...
January 2017: Open Biology
https://www.readbyqxmd.com/read/28098963/scaffolding-of-enzymes-on-virus-nanoarrays-effects-of-confinement-and-virus-organization-on-biocatalysis
#4
Anisha N Patel, Agnès Anne, Arnaud Chovin, Christophe Demaille, Eric Grelet, Thierry Michon, Cécilia Taofifenua
Organizing active enzyme molecules on nanometer-sized scaffolds is a promising strategy for designing highly efficient supported catalytic systems for biosynthetic and sensing applications. This is achieved by designing model nanoscale enzymatic platforms followed by thorough analysis of the catalytic activity. Herein, the virus fd bacteriophage is considered as an enzyme nanocarrier to study the scaffolding effects on enzymatic activity. Nanoarrays of randomly oriented, or directionally patterned, fd bacteriophage virus are functionalized with the enzyme glucose oxidase (GOx), using an immunological assembly strategy, directly on a gold electrode support...
January 18, 2017: Small
https://www.readbyqxmd.com/read/28098241/characterization-of-a-p1-like-bacteriophage-carrying-ctx-m-27-in-salmonella-spp-resistant-to-third-generation-cephalosporins-isolated-from-pork-in-china
#5
Ling Yang, Wan Li, Gui-Ze Jiang, Wen-Hui Zhang, Huan-Zhong Ding, Ya-Hong Liu, Zhen-Ling Zeng, Hong-Xia Jiang
The aim of this study was to elucidate the epidemiology of third generation cephalosporin resistant Samonella isolates from pork of a slaughterhouse in China and the features of transferable elements carrying blaCTX-M genes. One hundred and twenty-six (7.3%) Salmonella isolates were identified; S. Derby and S. Rissen were the most two prevalent serotypes. Among these isolates 20 (15.8%) were resistant to third generation cephalosporins and nine of them carried blaCTX-M-27. S1-PFGE and replicon typing of blaCTX-M-27-carrying plasmids showed that seven were untypeable plasmids of about 104 Kb and two were IncP plasmids of about 300 Kb...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096488/novel-superspreader-bacteriophages-promote-horizontal-gene-transfer-by-transformation
#6
Eric C Keen, Valery V Bliskovsky, Francisco Malagon, James D Baker, Jeffrey S Prince, James S Klaus, Sankar L Adhya
: Bacteriophages infect an estimated 10(23) to 10(25) bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub "superspreaders," releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096443/stem-loop-rna-labeling-can-affect-nuclear-and-cytoplasmic-mrna-processing
#7
Stephanie Heinrich, Corinne L Sidler, Claus M Azzalin, Karsten Weis
The binding of sequence-specific RNA-interacting proteins, such as the bacteriophage MS2 or PP7 coat proteins, to their corresponding target sequences has been extremely useful and widely used to visualize single mRNAs in vivo. However, introduction of MS2 stem-loops into yeast mRNAs has recently been shown to lead to the accumulation of RNA fragments, suggesting that the loops impair mRNA decay. This result was questioned, because fragment occurrence was mainly assessed using ensemble methods, and their cellular localization and its implications had not been addressed on a single transcript level...
February 2017: RNA
https://www.readbyqxmd.com/read/28094048/optimization-of-the-skimmed-milk-flocculation-method-for-recovery-of-adenovirus-from-sludge
#8
Andrêssa S F Assis, Marcelo Henrique Otenio, Betânia P Drumond, Tulio M Fumian, Marize P Miagostovich, Maria Luzia da Rosa E Silva
Return of treated sludge to the environment poses concerns and has stimulated the development of studies on viral monitoring in this matrix, in order to assess its potential risks for public health. Human adenovirus (HAdV) has been identified as a putative viral marker of faecal contamination due to its stability and resistance to the sewage treatment process. The aim of this study was to optimize the organic flocculation procedure in order to establish an appropriate methodology for HAdV recovery from sewage sludge samples...
January 13, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28093213/characterization-of-the-efficiency-and-uncertainty-of-skimmed-milk-flocculation-for-the-simultaneous-concentration-and-quantification-of-water-borne-viruses-bacteria-and-protozoa
#9
Eloy Gonzales-Gustavson, Yexenia Cardenas-Youngs, Miquel Calvo, Marcelle Figueira Marques da Silva, Ayalkibet Hundesa, Inmaculada Amorós, Yolanda Moreno, Laura Moreno-Mesonero, Rosa Rosell, Lliliane Ganges, Rosa Araujo, Rosina Girones
In this study, the use of skimmed milk flocculation (SMF) to simultaneously concentrate viruses, bacteria and protozoa was evaluated. We selected strains of faecal indicator bacteria and pathogens, such as Escherichia coli and Helicobacter pylori. The viruses selected were adenovirus (HAdV 35), rotavirus (RoV SA-11), the bacteriophage MS2 and bovine viral diarrhoea virus (BVDV). The protozoa tested were Acanthamoeba, Giardia and Cryptosporidium. The mean recoveries with q(RT)PCR were 66% (HAdV 35), 24% (MS2), 28% (RoV SA-11), 15% (BVDV), 60% (E...
January 13, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28093096/structural-biology-of-supramolecular-assemblies-by-magic-angle-spinning-nmr-spectroscopy
#10
Caitlin M Quinn, Tatyana Polenova
In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/28091598/characterization-of-two-polyvalent-phages-infecting-enterobacteriaceae
#11
Sana Hamdi, Geneviève M Rousseau, Simon J Labrie, Denise M Tremblay, Rim Saïed Kourda, Karim Ben Slama, Sylvain Moineau
Bacteriophages display remarkable genetic diversity and host specificity. In this study, we explore phages infecting bacterial strains of the Enterobacteriaceae family because of their ability to infect related but distinct hosts. We isolated and characterized two novel virulent phages, SH6 and SH7, using a strain of Shigella flexneri as host bacterium. Morphological and genomic analyses revealed that phage SH6 belongs to the T1virus genus of the Siphoviridae family. Conversely, phage SH7 was classified in the T4virus genus of the Myoviridae family...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28089070/steric-exclusion-chromatography-for-purification-of-cell-culture-derived-influenza-a-virus-using-regenerated-cellulose-membranes-and-polyethylene-glycol
#12
Pavel Marichal-Gallardo, Michael M Pieler, Michael W Wolff, Udo Reichl
Steric exclusion chromatography has been used for the purification of proteins and bacteriophages using monoliths. The operation is carried out by mixing a crude sample containing the target species with a predetermined concentration and molecular weight of polyethylene glycol (PEG) and loading it onto a non-reactive hydrophilic surface. Product capture occurs by the mutual steric exclusion of PEG between the product and the matrix. Selectivity is significantly influenced by target product size. Product elution is achieved by decreasing the PEG concentration...
December 29, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28088766/staphylococcus-aureus-cc395-harbours-a-novel-composite-staphylococcal-cassette-chromosome-mec-element
#13
Jesper Larsen, Paal S Andersen, Volker Winstel, Andreas Peschel
BACKGROUND: CoNS species are likely reservoirs of the staphylococcal cassette chromosome mec (SCCmec) in Staphylococcus aureus S aureus CC395 is unique as it is capable of exchanging DNA with CoNS via bacteriophages, which are also known to mediate transfer of SCCmec OBJECTIVES: To analyse the structure and putative origin of the SCCmec element in S aureus CC395. METHODS: The only MRSA CC395 strain described in the literature, JS395, was subjected to WGS, and its SCCmec element was compared with those found in CoNS species and other S...
January 14, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28077763/a-simplified-mathematical-model-of-directional-dna-site-specific-recombination-by-serine-integrases
#14
Alexandra Pokhilko, Jia Zhao, W Marshall Stark, Sean D Colloms, Oliver Ebenhöh
Serine integrases catalyse site-specific recombination to integrate and excise bacteriophage genomes into and out of their host's genome. These enzymes exhibit remarkable directionality; in the presence of the integrase alone, recombination between attP and attB DNA sites is efficient and irreversible, giving attL and attR products which do not recombine further. However, in the presence of the bacteriophage-encoded recombination directionality factor (RDF), integrase efficiently promotes recombination between attL and attR to re-form attP and attB The DNA substrates and products of both reactions are approximately isoenergetic, and no cofactors (such as adenosine triphosphate) are required for recombination...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28077636/klebsiella-phage-%C3%AE-k64-1-encodes-multiple-depolymerases-for-multiple-host-capsular-types
#15
Yi-Jiun Pan, Tzu-Lung Lin, Ching-Ching Chen, Yun-Ting Tsai, Yi-Hsiang Cheng, Yi-Yin Chen, Pei-Fang Hsieh, Yi-Tsung Lin, Jin-Town Wang
: The genome of the multi-host bacteriophage ΦK64-1, capable of infecting Klebsiella capsular types K1, K11, K21, K25, K30, K35, K64, and K69, as well as new capsular types KN4 and KN5 was analyzed and revealed that 11 genes (S1-1, S1-2, S1-3, S2-1, S2-2, S2-3, S2-4, S2-5, S2-6, S2-7, and S2-8) encode proteins with amino acid sequence similarity to tail fibers/spikes or lyases. S2-5 previously was shown to encode a K64 capsule depolymerase (K64dep). Specific capsule-degrading activities of an additional 8 putative capsule depolymerases (S2-4 against K1; S1-1 against K11; S1-3 against K21; S2-2 against K25; S2-6 against K30/K69; S2-3 against K35; S1-2 against KN4; S2-1 against KN5) was demonstrated by expression and purification of the recombinant proteins...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28076361/synergy-and-order-effects-of-antibiotics-and-phages-in-killing-pseudomonas-aeruginosa-biofilms
#16
Waqas Nasir Chaudhry, Jeniffer Concepción-Acevedo, Taehyun Park, Saadia Andleeb, James J Bull, Bruce R Levin
In contrast to planktonic cells, bacteria imbedded biofilms are notoriously refractory to treatment by antibiotics or bacteriophage (phage) used alone. Given that the mechanisms of killing differ profoundly between drugs and phages, an obvious question is whether killing is improved by combining antibiotic and phage therapy. However, this question has only recently begun to be explored. Here, in vitro biofilm populations of Pseudomonas aeruginosa PA14 were treated singly and with combinations of two phages and bactericidal antibiotics of five classes...
2017: PloS One
https://www.readbyqxmd.com/read/28074119/complete-genome-sequence-of-the-salmonella-enterica-serovar-enteritidis-bacteriophages-fse1c-and-fse4c-isolated-from-food-matrices
#17
Javier Santander, Jose I Vasquez, Cristopher Segovia, Leonardo Santos, Gabriel Turra, Karen Huber, James Robeson
Salmonella enterica serovar Enteritidis is one of the most common causes of Salmonellosis worldwide. Utilization of bacteriophages as prophylactic agents is a practical solution to prevent Salmonellosis in ready-to-eat products. Shelf stability is one of the desirable properties for prophylactic bacteriophages. Here, we describe the phenotype, genome, and phylogeny of fSE1C and fSE4S Salmonella bacteriophages. fSE1C and fSE4S were previously isolated from pickle sauce and ground beef respectively and selected for their significant shelf stability...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28071145/bacteriophages-and-their-derivatives-for-the-treatment-and-control-of-food-producing-animal-infections
#18
Carla Carvalho, Ana Rita Costa, Filipe Silva, Ana Oliveira
Nowadays, the world is facing an increasing emergence of antibiotic resistant bacteria. Simultaneously, the banning of some existing antibiotics and the lack of development of new antimicrobials have created an urgent need to find new alternatives against animal infections. Bacteriophages (phages) are naturally occurring predators of bacteria, ubiquitous in the environment, with high host specificity and harmless to animals. For these reasons, phages and their derivatives are being considered valuable antimicrobial alternatives and an opportunity to reduce the current use of antibiotics in agri-food production, increasing animal productivity and providing environmental protection...
January 10, 2017: Critical Reviews in Microbiology
https://www.readbyqxmd.com/read/28070487/unraveling-the-microbial-and-functional-diversity-of-coamo-thermal-spring-in-puerto-rico-using-metagenomic-library-generation-and-shotgun-sequencing
#19
Ricky Padilla-Del Valle, Luis R Morales-Vale, Carlos Ríos-Velázquez
In Puerto Rico, the microbial diversity of the thermal spring (ThS) in Coamo has never been studied using metagenomics. The focus of our research was to generate a metagenomic library from the ThS of Coamo, Puerto Rico and explore the microbial and functional diversity. The metagenomic library from the ThS waters was generated using direct DNA isolation. High molecular weight (40 kbp) DNA was end-repaired, electro eluted and ligated into a fosmid vector (pCCFOS1); then transduced into Escherichia coli EPI300-T1R using T1 bacteriophages...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28069947/first-passage-time-approach-to-controlling-noise-in-the-timing-of-intracellular-events
#20
Khem Raj Ghusinga, John J Dennehy, Abhyudai Singh
In the noisy cellular environment, gene products are subject to inherent random fluctuations in copy numbers over time. How cells ensure precision in the timing of key intracellular events despite such stochasticity is an intriguing fundamental problem. We formulate event timing as a first-passage time problem, where an event is triggered when the level of a protein crosses a critical threshold for the first time. Analytical calculations are performed for the first-passage time distribution in stochastic models of gene expression...
January 9, 2017: Proceedings of the National Academy of Sciences of the United States of America
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