Resistance of Aerosolized Bacterial Viruses to Four Germicidal Products
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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. -
The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V
PERSPECTIVES archaea that form several distinct, seemingly unrelated groups16–18. The LUCA and its complex virome In another recent synthesis, we examined the origins of the replication and structural Mart Krupovic , Valerian V. Dolja and Eugene V. Koonin modules of viruses and posited a ‘chimeric’ scenario of virus evolution19. Under this Abstract | The last universal cellular ancestor (LUCA) is the most recent population model, the replication machineries of each of of organisms from which all cellular life on Earth descends. The reconstruction of the four realms derive from the primordial the genome and phenotype of the LUCA is a major challenge in evolutionary pool of genetic elements, whereas the major biology. Given that all life forms are associated with viruses and/or other mobile virion structural proteins were acquired genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by from cellular hosts at different stages of evolution giving rise to bona fide viruses. projecting back in time using the extant distribution of viruses across the two In this Perspective article, we combine primary domains of life, bacteria and archaea, and tracing the evolutionary this recent work with observations on the histories of some key virus genes, we attempt a reconstruction of the LUCA virome. host ranges of viruses in each of the four Even a conservative version of this reconstruction suggests a remarkably complex realms, along with deeper reconstructions virome that already included the main groups of extant viruses of bacteria and of virus evolution, to tentatively infer archaea. We further present evidence of extensive virus evolution antedating the the composition of the virome of the last universal cellular ancestor (LUCA; also LUCA. -
Virus–Host Interactions and Their Roles in Coral Reef Health and Disease
!"#$"%& Virus–host interactions and their roles in coral reef health and disease Rebecca Vega Thurber1, Jérôme P. Payet1,2, Andrew R. Thurber1,2 and Adrienne M. S. Correa3 !"#$%&'$()(*+%&,(%--.#(+''/%!01(1/$%0-1$23++%(#4&,,+5(5&$-%#6('+1#$0$/$-("0+708-%#0$9(&17( 3%+7/'$080$9(4+$#3+$#6(&17(&%-($4%-&$-1-7("9(&1$4%+3+:-10'(70#$/%"&1'-;(<40#(=-80-5(3%+807-#( &1(01$%+7/'$0+1($+('+%&,(%--.(80%+,+:9(&17(->34�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cycling. Last, we outline how marine viruses are an integral part of the reef system and suggest $4&$($4-(01.,/-1'-(+.(80%/#-#(+1(%--.(./1'$0+1(0#(&1(-##-1$0&,('+>3+1-1$(+.($4-#-(:,+"&,,9( 0>3+%$&1$(-180%+1>-1$#; To p - d ow n e f f e c t s Viruses infect all cellular life, including bacteria and evidence that macroorganisms play important parts in The ecological concept that eukaryotes, and contain ~200 megatonnes of carbon the dynamics of viroplankton; for example, sponges can organismal growth and globally1 — thus, they are integral parts of marine eco- filter and consume viruses6,7. -
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. -
Geographic Differences in Sexual Reassortment in Rna Phage
ORIGINAL ARTICLE doi:10.1111/j.1558-5646.2010.01040.x GEOGRAPHIC DIFFERENCES IN SEXUAL REASSORTMENT IN RNA PHAGE Kara J. O’Keefe,1,2 Olin K. Silander,3 Helen McCreery,4 Daniel M. Weinreich,5 Kevin M. Wright,6 Lin Chao,7 Scott V. Edwards,2 Susanna K. Remold,8 and Paul E. Turner1,9 1Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520-8106 2Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138 3Core Program Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland 4Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 5Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912 6Department of Biology, Duke University, Durham, North Carolina 27708 7Section of Ecology, Evolution and Behavior, University of California, San Diego, La Jolla, California 92093 8Department of Biology, University of Louisville, Louisville, Kentucky 40292 9E-mail: [email protected] Received November 5, 2008 Accepted April 20, 2010 The genetic structure of natural bacteriophage populations is poorly understood. Recent metagenomic studies suggest that phage biogeography is characterized by frequent migration. Using virus samples mostly isolated in Southern California, we recently showed that very little population structure exists in segmented RNA phage of the Cystoviridae family due to frequent segment reassortment (sexual genetic mixis) between unrelated virus individuals. Here we use a larger genetic dataset to examine the structure of Cystoviridae phage isolated from three geographic locations in Southern New England. We document extensive natural variation in the physical sizes of RNA genome segments for these viruses. -
Microorganisms
microorganisms Brief Report Temporal Variability of Virioplankton during a Gymnodinium catenatum Algal Bloom Xiao-Peng Du 1, Zhong-Hua Cai 1, Ping Zuo 2 , Fan-Xu Meng 3, Jian-Ming Zhu 1 and Jin Zhou 1,* 1 The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; [email protected] (X.-P.D.); [email protected] (Z.-H.C.); [email protected] (J.-M.Z.) 2 The School of Geography and Ocean Science, Nanjing University, Nanjing 210000, China; [email protected] 3 Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310000, China; [email protected] * Correspondence: [email protected] Received: 13 October 2019; Accepted: 10 January 2020; Published: 12 January 2020 Abstract: Viruses are key biogeochemical engines in the regulation of the dynamics of phytoplankton. However, there has been little research on viral communities in relation to algal blooms. Using the virMine tool, we analyzed viral information from metagenomic data of field dinoflagellate (Gymnodinium catenatum) blooms at different stages. Species identification indicated that phages were the main species. Unifrac analysis showed clear temporal patterns in virioplankton dynamics. The viral community was dominated by Siphoviridae, Podoviridae, and Myoviridae throughout the whole bloom cycle. However, some changes were observed at different phases of the bloom; the relatively abundant Siphoviridae and Myoviridae dominated at pre-bloom and peak bloom stages, while at the post-bloom stage, the members of Phycodnaviridae and Microviridae were more abundant. Temperature and nutrients were the main contributors to the dynamic structure of the viral community. -
Bdellovibrio Bacteriovorus Karie L
JOURNAL OF BACTERIOLOGY, Feb. 2002, p. 1089–1094 Vol. 184, No. 4 0021-9193/02/$04.00ϩ0 DOI: 10.1128/JB.184.4.1089–1094.2002 Copyright © 2002, American Society for Microbiology. All Rights Reserved. Microviridae, a Family Divided: Isolation, Characterization, and Genome Sequence of MH2K, a Bacteriophage of the Obligate Intracellular Parasitic Bacterium Bdellovibrio bacteriovorus Karie L. Brentlinger,1 Susan Hafenstein,1 Christopher R. Novak,1 Bentley A. Fane,1* Robert Borgon,2 Robert McKenna,2 and Mavis Agbandje-McKenna2 Department of Veterinary Sciences and Microbiology, University of Arizona, Tucson, Arizona,1 and Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida2 Received 11 September 2001/Accepted 11 November 2001 Downloaded from A novel single-stranded DNA phage, MH2K, of Bdellovibrio bacteriovorus was isolated, characterized, and sequenced. This phage is a member of the Microviridae, a family typified by bacteriophage X174. Although B. bacteriovorus and Escherichia coli are both classified as proteobacteria, MH2K is only distantly related to X174. Instead, MH2K exhibits an extremely close relationship to the Microviridae of Chlamydia in both genome orga- nization and encoded proteins. Unlike the double-stranded DNA bacteriophages, for which a wide spectrum of diversity has been observed, the single-stranded icosahedral bacteriophages appear to fall into two distinct jb.asm.org subfamilies. These observations suggest that the mechanisms driving single-stranded DNA bacteriophage evolution are inherently different from those driving the evolution of the double-stranded bacteriophages. at UNIVERSITY OF ARIZONA LIBRARY on December 8, 2009 Bacteriophages have been isolated and characterized from a proximately 20% or less (6), a typical value when comparing wide range of microorganisms for more than 80 years. -
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. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
The Virome Hunters Diversity Was—And Still Is to This Day— Mostly Uncharacterized
NEWS FEATURE Virus images: colematt / iStock Getty Images Plus The virome hunters diversity was—and still is to this day— mostly uncharacterized. Scientists have since Ambitious efforts to catalog viruses across the globe may facilitate expanded their analyses into other many environments, as well as animal and human our understanding of viral communities and ecology, boost viromes. Indeed, a pure metagenomic analysis infectious disease diagnostics and surveillance, and spur new of human fecal samples revealed a previously unknown virus that represents a large part therapeutics. Charles Schmidt investigates. of the dark matter—as much as 90%—of the human gut virome. Dubbed the crAssphage by Robert Edwards and collaborators from In July, scientists from UC Davis and Columbia and our questions about the viral world are San Diego State because it was pieced together University announced they had isolated a new profound,” says Edward Holmes, a virologist by tool they invented called cross assembly species of the Ebola virus from bats roosting and professor at the University of Sydney in analysis (although its origin in stool seems to inside houses in Sierra Leone. Dubbed Bombali Australia. Along with new species, investigators have been in the minds of the researchers), it after the district where the bats were captured, are turning up vast stretches of what they call was called “one of the most striking feats of this new species is the first Ebola virus to have dark matter—viral sequences unlike any seen metagenomics at that time” by Eugene Koonin its initial identification in an animal host previously. They’re using sophisticated bioin- at US National Center for Biotechnology rather than from a sick person. -
Rapid Evolution of the Human Gut Virome
Rapid evolution of the human gut virome Samuel Minota, Alexandra Brysona, Christel Chehouda, Gary D. Wub, James D. Lewisb,c, and Frederic D. Bushmana,1 aDepartment of Microbiology, bDivision of Gastroenterology, and cCenter for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104 Edited by Sankar Adhya, National Institutes of Health, National Cancer Institute, Bethesda, MD, and approved May 31, 2013 (received for review January 15, 2013) Humans are colonized by immense populations of viruses, which sequenced independently to allow estimation of within-time point metagenomic analysis shows are mostly unique to each individual. sample variation. Virus-like particles were extracted by sequential To investigate the origin and evolution of the human gut virome, filtration, Centricon ultrafiltration, nuclease treatment, and sol- we analyzed the viral community of one adult individual over 2.5 y vent extraction. Purified viral DNA was subjected to linear am- by extremely deep metagenomic sequencing (56 billion bases of plification using Φ29 DNA polymerase, after which quantitative purified viral sequence from 24 longitudinal fecal samples). After PCR showed that bacterial 16S sequences were reduced to less assembly, 478 well-determined contigs could be identified, which than 10 copies per nanogram of DNA, and human sequences were are inferred to correspond mostly to previously unstudied bacterio- reduced to below 0.1 copies per nanogram, the limit of detection. phage genomes. Fully 80% of these types persisted throughout the Paired-end reads then were acquired using Illumina HiSeq se- duration of the 2.5-y study, indicating long-term global stability. -
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 .