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https://www.readbyqxmd.com/read/29341389/detection-of-escherichia-coli-in-ready-to-eat-fresh-vegetables-using-broad-host-range-recombinant-phages
#1
Hoang A Hoang, Nguyen T C Quy, Nguyen V T Chi
AIM: To construct a simple method to detect E. coli in ready-to-eat fresh vegetables using broad-host-range recombinant phages. METHODS AND RESULTS: Firstly, a gene encoding Cytochrome c Peroxidase (CCP) chromogenic enzyme was inserted into genomes of wild-type phages IP008 and IP052 to produce recombinant phages IP008BK and IP052BK. They were then used in the production of the chromogenic enzyme (CCP) through infection into E. coli. The method was then examined in the colorimetric detection of E...
January 16, 2018: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29340239/fastviromeexplorer-a-pipeline-for-virus-and-phage-identification-and-abundance-profiling-in-metagenomics-data
#2
Saima Sultana Tithi, Frank O Aylward, Roderick V Jensen, Liqing Zhang
With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets...
2018: PeerJ
https://www.readbyqxmd.com/read/29339825/corallivory-and-the-microbial-debacle-in-two-branching-scleractinians
#3
Yvan Bettarel, Sébastien Halary, Jean-Christophe Auguet, Thanh Chi Mai, Ngoc Van Bui, Thierry Bouvier, Patrice Got, Corinne Bouvier, Sonia Monteil-Bouchard, Desnues Christelle
The grazing activity by specific marine organisms represents a growing threat to the survival of many scleractinian species. For example, the recent proliferation of the corallivorous gastropod Drupella now constitutes a critical case in all South-East Asian waters. If the damaging effects caused by this marine snail on coral polyps are relatively well known, the indirect incidence of predation on coral microbial associates is still obscure and might also potentially impair coral health. In this study, we compared the main ecological traits of coral-associated bacterial and viral communities living in the mucus layer of Acropora formosa and Acropora millepora, of healthy and predated individuals (i...
January 16, 2018: ISME Journal
https://www.readbyqxmd.com/read/29339418/an-evolutionary-biochemical-connection-between-promoter-and-primer-dependent-polymerases-revealed-by-selective-evolution-of-ligands-by-exponential-enrichment-selex
#4
Katherine J Fenstermacher, Vasudevan Achuthan, Thomas D Schneider, Jeffrey J DeStefano
DNA polymerases (DNAPs) recognize 3' recessed termini on duplex DNA and carry out nucleotide catalysis. Unlike promoter-specific RNA polymerases (RNAPs), no sequence specificity is required for binding or initiation of catalysis. Despite this, previous results indicate that viral reverse transcriptases bind much more tightly to DNA primers that mimic the polypurine tract. In the current report, primer sequences that bind with high affinity to Taq and Klenow polymerases were identified using a modified Selective Evolution of Ligands by Exponential Enrichment (SELEX) approach...
January 16, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29338017/comparative-genomics-identifies-distinct-lineages-of-s-enteritidis-from-queensland-australia
#5
Rikki M A Graham, Lester Hiley, Irani U Rathnayake, Amy V Jennison
Salmonella enterica is a major cause of gastroenteritis and foodborne illness in Australia where notification rates in the state of Queensland are the highest in the country. S. Enteritidis is among the five most common serotypes reported in Queensland and it is a priority for epidemiological surveillance due to concerns regarding its emergence in Australia. Using whole genome sequencing, we have analysed the genomic epidemiology of 217 S. Enteritidis isolates from Queensland, and observed that they fall into three distinct clades, which we have differentiated as Clades A, B and C...
2018: PloS One
https://www.readbyqxmd.com/read/29337868/bacteriophage-gc1-a-novel-tectivirus-infecting-gluconobacter-cerinus-an-acetic-acid-bacterium-associated-with-wine-making
#6
Cécile Philippe, Mart Krupovic, Fety Jaomanjaka, Olivier Claisse, Melina Petrel, Claire le Marrec
The Gluconobacter phage GC1 is a novel member of the Tectiviridae family isolated from a juice sample collected during dry white wine making. The bacteriophage infects Gluconobacter cerinus, an acetic acid bacterium which represents a spoilage microorganism during wine making, mainly because it is able to produce ethyl alcohol and transform it into acetic acid. Transmission electron microscopy revealed tail-less icosahedral particles with a diameter of ~78 nm. The linear double-stranded DNA genome of GC1 (16,523 base pairs) contains terminal inverted repeats and carries 36 open reading frames, only a handful of which could be functionally annotated...
January 16, 2018: Viruses
https://www.readbyqxmd.com/read/29335804/identification-of-a-functional-toxin-antitoxin-system-located-in-the-genomic-island-pyg1-of-piezophilic-hyperthermophilic-archaeon-pyrococcus-yayanosii
#7
Zhen Li, Qinghao Song, Yinzhao Wang, Xiang Xiao, Jun Xu
Toxin-antitoxin (TA) system is bacterial or archaeal genetic module consisting of toxin and antitoxin gene that be organized as a bicistronic operon. TA system could elicit programmed cell death, which is supposed to play important roles for the survival of prokaryotic population under various physiological stress conditions. The phage abortive infection system (AbiE family) belongs to bacterial type IV TA system. However, no archaeal AbiE family TA system has been reported so far. In this study, a putative AbiE TA system (PygAT), which is located in a genomic island PYG1 in the chromosome of Pyrococcus yayanosii CH1, was identified and characterized...
January 15, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29334364/compactness-of-viral-genomes-effect-of-disperse-and-localized-random-mutations
#8
Anže Lošdorfer Božič, Cristian Micheletti, Rudolf Podgornik, Luca Tubiana
Genomes of single-stranded RNA viruses have evolved to optimize several concurrent properties. One of them is the architecture of their genomic folds, which must not only feature precise structural elements at specific positions, but also allow for overall spatial compactness. The latter was shown to be disrupted by random synonymous mutations, a disruption which can consequently negatively affect genome encapsidation. In this study, we use three mutation schemes with different degrees of locality to mutate the genomes of phage MS2 and Brome Mosaic Virus in order to understand the observed sensitivity of the global compactness of their folds...
January 15, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29331148/isolation-of-anti-extra-cellular-vesicle-single-domain-antibodies-by-direct-panning-on-vesicle-enriched-fractions
#9
Milica Popovic, Elisa Mazzega, Barbara Toffoletto, Ario de Marco
BACKGROUND: The thorough understanding of the physiological and pathological processes mediated by extracellular vesicles (EVs) is challenged by purification methods which are cumbersome, not reproducible, or insufficient to yield homogeneous material. Chromatography based on both ion-exchange and immune-capture can represent an effective method to improve EV purification and successive analysis. METHODS: Cell culture supernatant was used as a model sample for assessing the capacity of anion-exchange chromatography to separate distinct EV fractions and to isolate nanobodies by direct panning on whole EVs to recover binders specific for the native conformation of EV-surface epitopes and suitable to develop EV immune-capture reagents...
January 13, 2018: Microbial Cell Factories
https://www.readbyqxmd.com/read/29330770/decoding-selection-bias-imparted-by-unpaired-cysteines-a-tug-of-war-between-expression-and-affinity
#10
B Vijayalakshmi Ayyar, Stephen Hearty, Richard O'Kennedy
In a recombinant antibody scFv format, the presence of an unpaired cysteine (Cys) is implicated in reduced soluble expression and inefficient presentation in phage display. Compared to other species, antibodies derived from rabbits are more likely to contain this unpaired Cys residue at position 80 (Cys80), when generated in a scFv format. In a screening campaign to isolate rabbit scFv against cardiac troponin I (cTnI), it was found that, a large proportion of isolated cTnI-specific clones contained unpaired Cys80...
January 12, 2018: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/29330592/genomic-characterization-of-key-bacteriophages-to-formulate-the-potential-biocontrol-agent-to-combat-enteric-pathogenic-bacteria
#11
Krupa M Parmar, Nishant A Dafale, Hitesh Tikariha, Hemant J Purohit
Combating bacterial pathogens has become a global concern especially when the antibiotics and chemical agents are failing to control the spread due to its resistance. Bacteriophages act as a safe biocontrol agent by selectively lysing the bacterial pathogens without affecting the natural beneficial microflora. The present study describes the screening of prominent enteric pathogens NDK1, NDK2, NDK3, and NDK4 (Escherichia, Klebsiella, Enterobacter, and Serratia) mostly observed in domestic wastewater; against which KNP1, KNP2, KNP3, and KNP4 phages were isolated...
January 12, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29330364/polypharmacy-through-phage-display-selection-of-glucagon-and-glp-1-receptor-co-agonists-from-a-phage-displayed-peptide-library
#12
Anna Demartis, Armin Lahm, Licia Tomei, Elisa Beghetto, Valentina Di Biasio, Federica Orvieto, Francesco Frattolillo, Paul E Carrington, Sheena Mumick, Brian Hawes, Elisabetta Bianchi, Anandan Palani, Antonello Pessi
A promising emerging area for the treatment of obesity and diabetes is combinatorial hormone therapy, where single-molecule peptides are rationally designed to integrate the complementary actions of multiple endogenous metabolically-related hormones. We describe here a proof-of-concept study on developing unimolecular polypharmacy agents through the use of selection methods based on phage-displayed peptide libraries (PDL). Co-agonists of the glucagon (GCG) and GLP-1 receptors were identified from a PDL sequentially selected on GCGR- and GLP1R-overexpressing cells...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330023/unraveling-the-differential-structural-stability-and-dynamics-features-of-t7-endolysin-partially-folded-conformations
#13
Meenakshi Sharma, Dinesh Kumar, Krishna Mohan Poluri
BACKGROUND: Characterization of partially collapsed protein conformations at atomic level is a daunting task due to their inherent flexibility and conformational heterogeneity. T7 bacteriophage endolysin (T7L) is a single-domain amidase that facilitates the lysis of Gram-negative bacteria. T7L exhibits a pH-dependent structural transition from native state to partially folded (PF) conformation. In the pH range 5-3, T7L PF states display differential ANS binding characteristics. METHODS: CD, fluorescence, NMR spectroscopy and lysis assays were used to investigate the structure-stability- dynamics relationships of T7L PF conformations...
January 9, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29329326/utilization-of-peptide-phage-display-to-investigate-hotspots-on-il-17a-and-what-it-means-for-drug-discovery
#14
Joey P Ting, Frances Tung, Stephen Antonysamy, Stephen Wasserman, Spencer B Jones, Feiyu F Zhang, Alfonso Espada, Howard Broughton, Michael J Chalmers, Michael E Woodman, Holly A Bina, Jeffrey A Dodge, Jordi Benach, Aiping Zhang, Christopher Groshong, Danalyn Manglicmot, Marijane Russell, Sepideh Afshar
To date, IL-17A antibodies remain the only therapeutic approach to correct the abnormal activation of the IL-17A/IL-17R signaling complex. Why is it that despite the remarkable success of IL-17 antibodies, there is no small molecule antagonist of IL-17A in the clinic? Here we offer a unique approach to address this question. In order to understand the interaction of IL-17A with its receptor, we combined peptide discovery using phage display with HDX, crystallography, and functional assays to map and characterize hot regions that contribute to most of the energetics of the IL-17A/IL-17R interaction...
2018: PloS One
https://www.readbyqxmd.com/read/29328063/immune-loss-as-a-driver-of-coexistence-during-host-phage-coevolution
#15
Jake L Weissman, Rayshawn Holmes, Rodolphe Barrangou, Sylvain Moineau, William F Fagan, Bruce Levin, Philip L F Johnson
Bacteria and their viral pathogens face constant pressure for augmented immune and infective capabilities, respectively. Under this reciprocally imposed selective regime, we expect to see a runaway evolutionary arms race, ultimately leading to the extinction of one species. Despite this prediction, in many systems host and pathogen coexist with minimal coevolution even when well-mixed. Previous work explained this puzzling phenomenon by invoking fitness tradeoffs, which can diminish an arms race dynamic. Here we propose that the regular loss of immunity by the bacterial host can also produce host-phage coexistence...
January 12, 2018: ISME Journal
https://www.readbyqxmd.com/read/29327434/a-fast-and-reliable-method-for-monitoring-of-prophage-activating-chemicals
#16
Juan Xu, Bärbel Kiesel, René Kallies, Feng-Lei Jiang, Yi Liu, Thomas Maskow
Bacteriophages, that is viruses that infect bacteria, either lyse bacteria directly or integrate their genome into the bacterial genome as so-called prophages, where they remain at a silent state. Both phages and bacteria are able to survive in this state. However, prophages can be reactivated with the introduction of chemicals, followed by the release of a high number of phage particles, which could infect other bacteria, thus harming ecosystems by a viral bloom. The basics for a fast, automatable analytical method for the detection of prophage-activating chemicals are developed and successfully tested here...
January 12, 2018: Microbial Biotechnology
https://www.readbyqxmd.com/read/29327235/complete-genome-sequence-of-a-phage-hyperparasite-of-candidatus-xenohaliotis-californiensis-rickettsiales-a-pathogen-of-haliotis-spp-gasteropoda
#17
Roberto Flores, Jorge Cáceres-Martínez, Miguel Ángel Del Río-Portilla, Alexei F Licea-Navarro, Ricardo Gonzales-Sánchez, Abraham Guerrero
Bacteriophages are recognized as major mortality agents of microbes, among them intracellular marine rickettsiales-like bacteria. Recently, a phage hyperparasite of Candidatus Xenohaliotis californiensis (CXc) has been described. This bacterium is considered the causal agent of Withering Syndrome (WS) which is a chronic and potentially lethal disease of abalone species from California, USA and the peninsula of Baja California, Mexico. This hyperparasite which infects CXc could be used as a biocontrol agent for WS...
January 11, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29326975/identifying-the-substrate-proteins-of-u-box-e3s-e4b-and-chip-by-orthogonal-ubiquitin-transfer
#18
Karan Bhuripanyo, Yiyang Wang, Xianpeng Liu, Li Zhou, Ruochuan Liu, Duc Duong, Bo Zhao, Yingtao Bi, Han Zhou, Geng Chen, Nicholas T Seyfried, Walter J Chazin, Hiroaki Kiyokawa, Jun Yin
E3 ubiquitin (UB) ligases E4B and carboxyl terminus of Hsc70-interacting protein (CHIP) use a common U-box motif to transfer UB from E1 and E2 enzymes to their substrate proteins and regulate diverse cellular processes. To profile their ubiquitination targets in the cell, we used phage display to engineer E2-E4B and E2-CHIP pairs that were free of cross-reactivity with the native UB transfer cascades. We then used the engineered E2-E3 pairs to construct "orthogonal UB transfer (OUT)" cascades so that a mutant UB (xUB) could be exclusively used by the engineered E4B or CHIP to label their substrate proteins...
January 2018: Science Advances
https://www.readbyqxmd.com/read/29326209/complete-genome-sequence-of-escherichia-coli-strain-wg5
#19
Lejla Imamovic, Maria-Anna Misiakou, Eric van der Helm, Gianni Panagiotou, Maite Muniesa, Morten Otto Alexander Sommer
Escherichia coli strain WG5 is a widely used host for phage detection, including somatic coliphages employed as standard ISO method 10705-1 (2000). Here, we present the complete genome sequence of a commercial E. coli WG5 strain.
January 11, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29326207/complete-genome-sequence-of-bacteriophage-st11ph5-which-infects-uropathogenic-escherichia-coli-strain-up11
#20
Alla K Golomidova, Eugene E Kulikov, Vladislav V Babenko, Elena S Kostryukova, Andrey V Letarov
Bacteriophage St11Ph5 was isolated from a sewage sample on a particularly phage-resistant uropathogenic Escherichia coli (UPEC) up11 host strain. It appeared to be closely related to bacteriophage G7C, isolated from horse feces; however, it carries a highly divergent host recognition module.
January 11, 2018: Genome Announcements
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