Geographic Differences in Sexual Reassortment in Rna Phage
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Entry of the Membrane-Containing Bacteriophages Into Their Hosts
Entry of the membrane-containing bacteriophages into their hosts - Institute of Biotechnology and Department of Biosciences Division of General Microbiology Faculty of Biosciences and Viikki Graduate School in Molecular Biosciences University of Helsinki ACADEMIC DISSERTATION To be presented for public examination with the permission of the Faculty of Biosciences, University of Helsinki, in the auditorium 3 of Info center Korona, Viikinkaari 11, Helsinki, on June 18th, at 8 a.m. HELSINKI 2010 Supervisor Professor Dennis H. Bamford Department of Biosciences University of Helsinki, Finland Reviewers Professor Martin Romantschuk Department of Ecological and Environmental Sciences University of Helsinki, Finland Professor Mikael Skurnik Department of Bacteriology and Immunology University of Helsinki, Finland Opponent Dr. Alasdair C. Steven Laboratory of Structural Biology Research National Institute of Arthritis and Musculoskeletal and Skin Diseases National Institutes of Health, USA ISBN 978-952-10-6280-3 (paperback) ISBN 978-952-10-6281-0 (PDF) ISSN 1795-7079 Yliopistopaino, Helsinki University Printing House Helsinki 2010 ORIGINAL PUBLICATIONS This thesis is based on the following publications, which are referred to in the text by their roman numerals: I. 6 - Verkhovskaya R, Bamford DH. 2005. Penetration of enveloped double- stranded RNA bacteriophages phi13 and phi6 into Pseudomonas syringae cells. J Virol. 79(8):5017-26. II. Gaidelyt A*, Cvirkait-Krupovi V*, Daugelaviius R, Bamford JK, Bamford DH. 2006. The entry mechanism of membrane-containing phage Bam35 infecting Bacillus thuringiensis. J Bacteriol. 188(16):5925-34. III. Cvirkait-Krupovi V, Krupovi M, Daugelaviius R, Bamford DH. 2010. Calcium ion-dependent entry of the membrane-containing bacteriophage PM2 into Pseudoalteromonas host. -
First Description of a Temperate Bacteriophage (Vb Fhim KIRK) of Francisella Hispaniensis Strain 3523
viruses Article First Description of a Temperate Bacteriophage (vB_FhiM_KIRK) of Francisella hispaniensis Strain 3523 Kristin Köppen 1,†, Grisna I. Prensa 1,†, Kerstin Rydzewski 1, Hana Tlapák 1, Gudrun Holland 2 and Klaus Heuner 1,* 1 Centre for Biological Threats and Special Pathogens, Cellular Interactions of Bacterial Pathogens, ZBS 2, Robert Koch Institute, 13353 Berlin, Germany; [email protected] (K.K.); [email protected] (G.I.P.); [email protected] (K.R.); [email protected] (H.T.) 2 Centre for Biological Threats and Special Pathogens, Advanced Light and Electron Microscopy, ZBS 4, Robert Koch Institute, D-13353 Berlin, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-30-18754-2226 † Both authors contributed equally to this work. Abstract: Here we present the characterization of a Francisella bacteriophage (vB_FhiM_KIRK) includ- ing the morphology, the genome sequence and the induction of the prophage. The prophage sequence (FhaGI-1) has previously been identified in F. hispaniensis strain 3523. UV radiation induced the prophage to assemble phage particles consisting of an icosahedral head (~52 nm in diameter), a tail of up to 97 nm in length and a mean width of 9 nm. The double stranded genome of vB_FhiM_KIRK contains 51 open reading frames and is 34,259 bp in length. The genotypic and phylogenetic analysis indicated that this phage seems to belong to the Myoviridae family of bacteriophages. Under the Citation: Köppen, K.; Prensa, G.I.; conditions tested here, host cell (Francisella hispaniensis 3523) lysis activity of KIRK was very low, and Rydzewski, K.; Tlapák, H.; Holland, the phage particles seem to be defective for infecting new bacterial cells. -
The Diversity of Bacterial Lifestyles Hampers Bacteriophage Tenacity
viruses Review The Diversity of Bacterial Lifestyles Hampers Bacteriophage Tenacity Marta Lourenço 1,2, Luisa De Sordi 1 and Laurent Debarbieux 1,* ID 1 Department of Microbiology, Institut Pasteur, F-75015 Paris, France; [email protected] (M.L.); [email protected] (L.D.S.) 2 Collège Doctoral, Sorbonne Université, F-75005 Paris, France * Correspondence: [email protected] Received: 18 May 2018; Accepted: 11 June 2018; Published: 15 June 2018 Abstract: Phage therapy is based on a simple concept: the use of a virus (bacteriophage) that is capable of killing specific pathogenic bacteria to treat bacterial infections. Since the pioneering work of Félix d’Herelle, bacteriophages (phages) isolated in vitro have been shown to be of therapeutic value. Over decades of study, a large number of rather complex mechanisms that are used by phages to hijack bacterial resources and to produce their progeny have been deciphered. While these mechanisms have been identified and have been studied under optimal conditions in vitro, much less is known about the requirements for successful viral infections in relevant natural conditions. This is particularly true in the context of phage therapy. Here, we highlight the parameters affecting phage replication in both in vitro and in vivo environments, focusing, in particular, on the mammalian digestive tract. We propose avenues for increasing the knowledge-guided implementation of phages as therapeutic tools. Keywords: virus–host interactions; bacteriophage efficacy; gastrointestinal tract; phage therapy 1. Introduction With the alarming worldwide increase in the prevalence of multidrug-resistant bacteria, phage therapy—the use of phages to target pathogenic bacteria [1]—has recently returned to the spotlight in the USA and Europe, although it had never fallen out of favour in countries such as Georgia [2]. -
Exposure Pathways to High-Consequence Pathogens in the Wastewater Collection and Treatment Systems
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/326786071 Exposure Pathways to High-Consequence Pathogens in the Wastewater Collection and Treatment Systems Technical Report · July 2018 DOI: 10.13140/RG.2.2.14738.15043 CITATIONS READS 0 608 2 authors: Sandip Chattopadhyay Sarah Taft United States Environmental Protection Agency United States Environmental Protection Agency 74 PUBLICATIONS 435 CITATIONS 17 PUBLICATIONS 170 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: Exposure Assessment of Livestock Carcass Management Options During Emergencies View project Waste Management - Encapsulation of Contaminated Wastes View project All content following this page was uploaded by Sandip Chattopadhyay on 02 August 2018. The user has requested enhancement of the downloaded file. EPA/600/R-18/221 | July 2018 www.epa.gov/homeland-security-research Exposure Pathways to High-Consequence Pathogens in the Wastewater Collection and Treatment Systems Office of Research and Development Homeland Security Research Program EPA/600/R-18/221 July 2018 Exposure Pathways to High-Consequence Pathogens in the Wastewater Collection and Treatment Systems by Sandip Chattopadhyay, Ph.D. Sarah Taft, Ph.D. Threat and Consequence Assessment Division National Homeland Security Research Center Cincinnati, OH 45268 Contract No. EP-C-14-001 to ICF under Work Assignment 40 U.S. Environmental Protection Agency Project Officer Office of Research and Development Homeland Security Research Program Cincinnati, OH 45268 Disclaimer The U.S. Environmental Protection Agency (EPA) through its Office of Research and Development funded and managed the research described here under Contract No. -
Origins and Evolution of the Global RNA Virome
bioRxiv preprint doi: https://doi.org/10.1101/451740; this version posted October 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Origins and Evolution of the Global RNA Virome 2 Yuri I. Wolfa, Darius Kazlauskasb,c, Jaime Iranzoa, Adriana Lucía-Sanza,d, Jens H. 3 Kuhne, Mart Krupovicc, Valerian V. Doljaf,#, Eugene V. Koonina 4 aNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA 5 b Vilniaus universitetas biotechnologijos institutas, Vilnius, Lithuania 6 c Département de Microbiologie, Institut Pasteur, Paris, France 7 dCentro Nacional de Biotecnología, Madrid, Spain 8 eIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious 9 Diseases, National Institutes of Health, Frederick, Maryland, USA 10 fDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA 11 12 #Address correspondence to Valerian V. Dolja, [email protected] 13 14 Running title: Global RNA Virome 15 16 KEYWORDS 17 virus evolution, RNA virome, RNA-dependent RNA polymerase, phylogenomics, horizontal 18 virus transfer, virus classification, virus taxonomy 1 bioRxiv preprint doi: https://doi.org/10.1101/451740; this version posted October 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 ABSTRACT 20 Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in 21 animals and plants. The recent advances of metaviromics prompted us to perform a detailed 22 phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. -
ICTV Code Assigned: 2011.001Ag Officers)
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2011.001aG officers) Short title: Change existing virus species names to non-Latinized binomials (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Van Regenmortel Marc, [email protected] Burke Donald, [email protected] Calisher Charles, [email protected] Dietzgen Ralf, [email protected] Fauquet Claude, [email protected] Ghabrial Said, [email protected] Jahrling Peter, [email protected] Johnson Karl, [email protected] Holbrook Michael, [email protected] Horzinek Marian, [email protected] Keil Guenther, [email protected] Kuhn Jens, [email protected] Mahy Brian, [email protected] Martelli Giovanni, [email protected] Pringle Craig, [email protected] Rybicki Ed, [email protected] Skern Tim, [email protected] Tesh Robert, [email protected] Wahl-Jensen Victoria, [email protected] Walker Peter, [email protected] Weaver Scott, [email protected] List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . -
Unlocking the M13 (F1 and Fd) Virion
Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. Unlocking the M13 (f1 and fd) virion Investigation into the role of the pIII C-domain of F specific filamentous bacteriophage in infection A thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Biochemistry at Massey University, Palmerston North, New Zealand. Nicholas James Bennett 2009 Abstract Ff filamentous bacteriophage infect male (F+) strains of Escherichia coli and are assembled at the cell membranes, by a secretion-like, non-lethal process. The pIII protein, located at one end of the virion-filament, is required at both the beginning and the end of the phage life cycle. During infection, the N-terminal domains of pIII, N2 and N1, bind to the primary and secondary host receptors, F pilus and TolA protein, respectively. At the end of the life cycle, the pIII C-domain mediates the termination and release of virions. Thus, both entry and release involve structural transitions of the virus coupled to membrane transactions of the virion proteins. "Unlocking” of the highly stable virion presumably results in membrane integration during entry, whereas a reverse event, “locking” of the virion, occurs upon detachment from the membrane at termination step of assembly/secretion. Recently, it was shown that the pIII C-domain plays an active role at the step of entry. This finding implicates the C-domain of pIII in “unlocking” of the virion, presumably resulting in the exposure of the membrane anchor at the very C-terminus of pIII (Bennett & Rakonjac, 2006). -
Insights Into the Dynamics Between Viruses and Their Hosts in a Hot Spring Microbial Mat
The ISME Journal (2020) 14:2527–2541 https://doi.org/10.1038/s41396-020-0705-4 ARTICLE Insights into the dynamics between viruses and their hosts in a hot spring microbial mat 1,2,11 1,2 1,2 1,2 1,2 Jessica K. Jarett ● Mária Džunková ● Frederik Schulz ● Simon Roux ● David Paez-Espino ● 1,2 1,2 1,2 3 4 Emiley Eloe-Fadrosh ● Sean P. Jungbluth ● Natalia Ivanova ● John R. Spear ● Stephanie A. Carr ● 5 6 7 8,9 1,2 Christopher B. Trivedi ● Frank A. Corsetti ● Hope A. Johnson ● Eric Becraft ● Nikos Kyrpides ● 9 1,2,10 Ramunas Stepanauskas ● Tanja Woyke Received: 13 January 2020 / Revised: 3 June 2020 / Accepted: 11 June 2020 / Published online: 13 July 2020 © The Author(s) 2020. This article is published with open access Abstract Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics – 1234567890();,: 1234567890();,: applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. -
Detection of Bacteriophage Infection Using Absorbance
DETECTION OF BACTERIOPHAGE INFECTION USING ABSORBANCE, BIOLUMINESCENCE, AND FLUORESCENCE TESTS Thesis Submitted to The School of Engineering of the UNIVERSITY OF DAYTON In Partial Fulfillment of the Requirements for The Degree Master of Science in Civil Engineering By Lindsey Marie Staley UNIVERSITY OF DAYTON Dayton, Ohio May, 2011 DETECTION OF BACTERIOPHAGE INFECTION USING ABSORBANCE, BIOLUMINESCENCE, AND FLUORESCENCE TESTS Name: Staley, Lindsey Marie APPROVED BY: ___________________________ __________________________ Denise Taylor, Ph. D., P.E. Kenya Crosson, Ph.D. Advisory Committee Chairman Committee Member Assistant Professor Assistant Professor Department of Civil and Department of Civil and Environmental Engineering and Environmental Engineering and Engineering Mechanics Engineering Mechanics ____________________________ Deogratias Eustace, Ph.D. Committee Member Assistant Professor Department of Civil and Environmental Engineering and Engineering Mechanics ___________________________ __________________________ John G. Weber, Ph.D. Tony E. Saliba, Ph.D. Associate Dean Wilke Distinguished Professor & School of Engineering Dean School of Engineering ii ABSTRACT DETECTION OF BACTERIOPHAGE INFECTION USING ABSORBANCE, BIOLUMINESCENCE, AND FLUORESCENCE TESTS Name: Staley, Lindsey Marie University of Dayton Advisor: Dr. Denise Taylor The activated sludge treatment process is a common method employed to treat wastewater. Normal operation of this process results in a floc-forming bacterial mixture, which settles rapidly. However, filamentous bacteria can cause sludge bulking, which interferes with the compaction and settling of flocs. A common method to control sludge bulking is adding a chemical such as chlorine to the activated sludge basin, which kills not only the problematic bacteria, but also the essential floc-forming bacteria. Bacteriophages (phages) are viruses that only infect bacteria. It is hypothesized that phages of filamentous bacteria can be added to the activated sludge basin to control sludge bulking, rather than a chemical. -
Rapid Detection of Enterohaemorrhagic E.Coli Using
Review Article Clinician’s corner Images in Medicine Experimental Research Case Report Miscellaneous Letter to Editor DOI: 10.7860/JCDR/2018/36748.12251 Original Article Postgraduate Education Rapid Detection of Enterohaemorrhagic E.coli Case Series Using Phage-Based Bioluminescent Assay Microbiology Section Microbiology Short Communication SABAH AA JASSIM1, RAND R HAFIDH2, ZAHRAA Q ALI3, AHMED S ABDULAMIR4 ABSTRACT Results: AKBA showed positive detection of E.coli bacteria Introduction: There is a need for a reliable, time-saving, and at 103 CFU in just 20 minutes. The phage-based detection specific detection assay for coliforms, environmental E. coli, was highly specific at strain level of E.coli. The sensitivity and and Enterobacteriaceae worldwide. specificity of AKBA was 74% and 78%, respectively. Aim: To innovate a new principle of phage-based rapid diagnostic Conclusion: A rapid and strain-specific diagnostic test was test for detecting E. coli bacteria in short time and low titer. prepared for E.coli by using coliphages. The significance and impact of the study shows that it might be feasible to formulate Materials and Methods: A phage mixture of 200 E. coli specific a phage-based assay against any Gram negative or positive phages, including 22 specific for Enterohaemorrhagic E.coli bacteria using the same approaches of the current AKBA assay (EHEC), were used in a new detection platform, a phage-based with slight modifications. Adenylate Kinase Bioluminescence Assay (AKBA). Ten EHEC E. coli and 30 universal E.coli isolates were used for AKBA assay. Keywords: Adenylate kinase, Bacteriophage, Bioluminescence, Rapid diagnostic tests INTRODUCTION Media E. coli detection is considered more specific than the detection of Bacterial dilutions from 18 hour Luria Broth (LB) cultures grown at fecal coliforms in water quality testing [1]. -
Bacteriophages: Ecological Role in the Marine Environment and Potential Applications
Egyptian Journal of Aquatic Biology & Fisheries Zoology Department, Faculty of Science, Ain Shams University, Cairo, Egypt. ISSN 1110 – 6131 Vol. 24(7): 93 – 117 (2020) www.ejabf.journals.ekb.eg Bacteriophages: Ecological role in the marine environment and potential applications Sahar W. M. Hassan, Hanan Abd-ElNaby, Gehan M. Abou-Elela, Ahmed E. Abouelwafa , Nermeen A. El-Sersy * Marine Microbiology Lab., Environmental Division, National Institute of Oceanography and Fisheries (NIOF), Egypt. *Corresponding author: nermeen_ok @yahoo.co.uk ARTICLE INFO ABSTRACT Article History: Bacteriophages are the most plentiful organisms on the earth and they are Received: Sept. 3, 2020 a ubiquitous trait of prokaryotic existence. They exist in all environments Accepted: Oct. 7, 2020 as a part of a complex microbial ecosystem. A phage is a virus that can Online: Oct. 17, 2020 infect bacteria where the distribution and abundance are based on the host _______________ organisms. Bacteriophages can impact their host populations in different ways and also have impacts on the microbial ecology and geochemical Keywords: cycles. The concept of phage therapy as a fundamental application of Bacteriophages, Ecological role, bacteriophages is deeply relying on the facts of their host specificity, Applications, abundance in the environment with limited ecological impact. This review Phage therapy. focuses on the ecological role of bacteriophages in the marine environment and some applications. INTRODUCTION Bacteriophages (phages) are bacteria-specific viruses. They are the most abundant biological entities on earth (Katsamba and Lauga, 2019). They exist in all ecosystems. The microbiota of healthy humans also contains a large number of bacterial viruses (Van Belleghem et al., 2019). -
Ecology of Inorganic Sulfur Auxiliary Metabolism in Widespread Bacteriophages 2 3 4 Kristopher Kieft1#, Zhichao Zhou1#, Rika E
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.24.253096; this version posted August 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Ecology of inorganic sulfur auxiliary metabolism in widespread bacteriophages 2 3 4 Kristopher Kieft1#, Zhichao Zhou1#, Rika E. Anderson2, Alison Buchan3, Barbara J. Campbell4, Steven J. 5 Hallam5,6,7,8,9, Matthias Hess10, Matthew B. Sullivan11, David A. Walsh12, Simon Roux13, Karthik 6 Anantharaman1* 7 8 Affiliations: 9 1 Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, 53706, USA 10 2 Biology Department, Carleton College, Northfield, Minnesota, USA 11 3 Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA 12 4 Department of Biological Sciences, Life Science Facility, Clemson University, Clemson, SC, 29634, USA 13 5 Department of Microbiology & Immunology, University of British Columbia, Vancouver, British 14 Columbia V6T 1Z3, Canada 15 6 Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, 16 Vancouver, British Columbia V5Z 4S6, Canada 17 7 Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 18 1Z4, Canada 19 8 Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada 20 9 ECOSCOPE Training Program, University of British Columbia, Vancouver,