A Virus of Hyperthermophilic Archaea with a Unique Architecture Among DNA Viruses
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Bacteriophage of Enterococcus Species for Microbial Source Tracking
Bacteriophage of Enterococcus species for microbial source tracking Sarah Elizabeth Purnell A thesis submitted in partial fulfilment of the requirements of the University of Brighton for the degree of Doctor of Philosophy 2012 School of Environment and Technology University of Brighton United Kingdom Abstract Contamination of surface waters with faeces may lead to increased public risk of human exposure to pathogens through drinking water supply, aquaculture, and recreational activities. Determining the source(s) of contamination is important for assessing the degree of risk to public health, and for selecting appropriate mitigation measures. Phage-based microbial source tracking (MST) techniques have been promoted as effective, simple and low-cost. The intestinal enterococci are a faecal “indicator of choice” in many parts of the world for determining water quality, and recently, phages capable of infecting Enterococcus faecalis have been proposed as a potential alternative indicator of human faecal contamination. The primary aim of this study was to evaluate critically the suitability and efficacy of phages infecting host strains of Enterococcus species as a low-cost tool for MST. In total, 390 potential Enterococcus hosts were screened for their ability to detect phage in reference faecal samples. Development and implementation of a tiered screening approach allowed the initial large number of enterococcal hosts to be reduced rapidly to a smaller subgroup suitable for phage enumeration and MST. Twenty-nine hosts were further tested using additional faecal samples of human and non-human origin. Their specificity and sensitivity were found to vary, ranging from 44 to 100% and from 17 to 83%, respectively. Most notably, seven strains exhibited 100% specificity to cattle, human, or pig samples. -
The Common Ancestor of Archaea and Eukarya Was Not an Archaeon
Hindawi Publishing Corporation Archaea Volume 2013, Article ID 372396, 18 pages http://dx.doi.org/10.1155/2013/372396 Review Article The Common Ancestor of Archaea and Eukarya Was Not an Archaeon Patrick Forterre1,2 1 Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France 2 Universite´ Paris-Sud, Institut de Gen´ etique´ et Microbiologie, CNRS UMR 8621, 91405 Orsay Cedex, France Correspondence should be addressed to Patrick Forterre; [email protected] Received 22 July 2013; Accepted 24 September 2013 Academic Editor: Gustavo Caetano-Anolles´ Copyright © 2013 Patrick Forterre. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. -
WO 2018/107129 Al O
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/107129 Al 14 June 2018 (14.06.2018) W !P O PCT (51) International Patent Classification: VARD COLLEGE [US/US]; 17 Quincy Street, Cam- C12N 15/09 (2006.01) C12N 15/11 (2006.01) bridge, MA 02138 (US). C12N 15/10 (2006.01) C12Q 1/68 (2006 .01) (72) Inventors: ABUDAYYEH, Omar; 77 Massachusetts Av (21) International Application Number: enue, Cambridge, MA 02139 (US). COLLINS, James PCT/US20 17/065477 Joseph; 77 Massachusetts Avenue, Cambridge, MA 02 139 (US). GOOTENBERG, Jonathan; 17 Quincy Street, (22) International Filing Date: Cambridge, MA 02138 (US). ZHANG, Feng; 415 Main 08 December 2017 (08.12.2017) Street, Cambridge, MA 02142 (US). LANDER, Eric, S.; (25) Filing Language: English 415 Main Street, Cambridge, MA 02142 (US). (26) Publication Language: English (74) Agent: NLX, F., Brent; Johnson, Marcou & Isaacs, LLC, 27 City Square, Suite 1, Hoschton, GA 30548 (US). (30) Priority Data: 62/432,553 09 December 20 16 (09. 12.20 16) US (81) Designated States (unless otherwise indicated, for every 62/456,645 08 February 2017 (08.02.2017) US kind of national protection available): AE, AG, AL, AM, 62/471,930 15 March 2017 (15.03.2017) US AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, 62/484,869 12 April 2017 (12.04.2017) US CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, 62/568,268 04 October 2017 (04.10.2017) US DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, (71) Applicants: THE BROAD INSTITUTE, INC. -
Ep 1734129 B1
(19) TZZ_¥_ _T (11) EP 1 734 129 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12P 7/24 (2006.01) C12P 17/06 (2006.01) 24.02.2016 Bulletin 2016/08 (86) International application number: (21) Application number: 05727417.7 PCT/JP2005/005719 (22) Date of filing: 28.03.2005 (87) International publication number: WO 2005/098012 (20.10.2005 Gazette 2005/42) (54) PROCESS FOR PRODUCTION OF CHIRAL HYDROXYALDEHYDES VERFAHREN ZUR HERSTELLUNG CHIRALER HYDROXYALDEHYDE PROCÉDÉ DE FABRICATION D’HYDROXYALDÉHYDES CHIRALES (84) Designated Contracting States: (56) References cited: AT BE BG CH CY CZ DE DK EE ES FI FR GB GR WO-A2-03/006656 HU IE IS IT LI LT LU MC NL PL PT RO SE SI SK TR • SAKURABA, H. ET AL.: "The First Crystal (30) Priority: 29.03.2004 JP 2004095263 Structure of Archaeal Aldolase. unique tetrameric structure of (43) Date of publication of application: 2-deoxy-D-ribose-5-phosphate aldolase from the 20.12.2006 Bulletin 2006/51 hyperthermophilic Archaea Aeropyrum pernix" JOURNAL OF BIOLOGICAL CHEMISTRY, vol. (73) Proprietor: Mitsui Chemicals, Inc. 278, no. 12, 21 March 2003 (2003-03-21), pages Tokyo 105-7117 (JP) 10799-10806, XP002596667 • SAKURABA, H. ET AL.: "Sequential Aldol (72) Inventors: Condensation Catalyzed by Hyperthermophilic • MATSUMOTO, Kazuya, 2-Deoxy-D-Ribose-5-Phosphate Aldolase" c/o Mitsui Chemicals, Inc. APPLIED AND ENVIRONMENTAL Mobara-shi, Chiba 2970017 (JP) MICROBIOLOGY, vol. 73, no. 22, November 2007 • KAZUNO, Yasushi, (2007-11), pages 7427-7434, XP002596660 c/o Mitsui Chemicals, Inc. -
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. -
Supplementary Text S1
1 Supplementary Text S1 2 Dataset of reference viral genomes Viral genome sequences and taxonomic 3 information of viruses and their hosts are based on the GenomeNet/Virus-Host DB 4 (Mihara, et al., 2016). The Virus-Host DB covers viruses with complete genomes stored 5 in RefSeq/viral and GenBank. The sequence and taxonomic data are downloadable at 6 http://www.genome.jp/virushostdb/. Viral genome sequences and taxonomic 7 information used in ViPTree will be updated every few months following Virus-Host 8 DB updates. 9 Calculation of genomic similarity (SG) and proteomic tree The original Phage 10 Proteomic Tree (Rohwer and Edwards, 2002) tested multiple approaches and 11 parameters to calculate genomic distance for evaluation of compatibility between the 12 Phage Proteomic Tree and taxonomical system of the International Committee on 13 Taxonomy of Viruses. In contrast, ViPTree performs proteomic tree calculation based 14 on tBLASTx as reported previously by other several studies (Bellas, et al., 2015; 15 Bhunchoth, et al., 2016; Mizuno, et al., 2013). Specifically, normalized tBLASTx scores 16 (SG; 0 ≤ SG ≤ 1) between viral genomes are calculated as described (Bhunchoth, et al., 17 2016). For simple calculation of SG of segmented viruses, sequences of each segmented 18 viral genome were concatenated into one sequence by inserting a sequence of 100 19 ambiguous nucleotides (N) at each concatenation site. In addition, genome sequences 20 longer than 100 kb are split into each 100 kb fragment just for faster tBLASTx 21 calculation. Genomic distance is calculated as 1−SG. Proteomic tree generation is 22 performed by BIONJ (Gascuel, 1997) based on the genomic distance, using the R 23 package ‘Ape’. -
On the Biological Success of Viruses
MI67CH25-Turner ARI 19 June 2013 8:14 V I E E W R S Review in Advance first posted online on June 28, 2013. (Changes may still occur before final publication E online and in print.) I N C N A D V A On the Biological Success of Viruses Brian R. Wasik and Paul E. Turner Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520-8106; email: [email protected], [email protected] Annu. Rev. Microbiol. 2013. 67:519–41 Keywords The Annual Review of Microbiology is online at adaptation, biodiversity, environmental change, evolvability, extinction, micro.annualreviews.org robustness This article’s doi: 10.1146/annurev-micro-090110-102833 Abstract Copyright c 2013 by Annual Reviews. Are viruses more biologically successful than cellular life? Here we exam- All rights reserved ine many ways of gauging biological success, including numerical abun- dance, environmental tolerance, type biodiversity, reproductive potential, and widespread impact on other organisms. We especially focus on suc- cessful ability to evolutionarily adapt in the face of environmental change. Viruses are often challenged by dynamic environments, such as host immune function and evolved resistance as well as abiotic fluctuations in temperature, moisture, and other stressors that reduce virion stability. Despite these chal- lenges, our experimental evolution studies show that viruses can often readily adapt, and novel virus emergence in humans and other hosts is increasingly problematic. We additionally consider whether viruses are advantaged in evolvability—the capacity to evolve—and in avoidance of extinction. On the basis of these different ways of gauging biological success, we conclude that viruses are the most successful inhabitants of the biosphere. -
Pyrobaculum Igneiluti Sp. Nov., a Novel Anaerobic Hyperthermophilic Archaeon That Reduces Thiosulfate and Ferric Iron
TAXONOMIC DESCRIPTION Lee et al., Int J Syst Evol Microbiol 2017;67:1714–1719 DOI 10.1099/ijsem.0.001850 Pyrobaculum igneiluti sp. nov., a novel anaerobic hyperthermophilic archaeon that reduces thiosulfate and ferric iron Jerry Y. Lee, Brenda Iglesias, Caleb E. Chu, Daniel J. P. Lawrence and Edward Jerome Crane III* Abstract A novel anaerobic, hyperthermophilic archaeon was isolated from a mud volcano in the Salton Sea geothermal system in southern California, USA. The isolate, named strain 521T, grew optimally at 90 C, at pH 5.5–7.3 and with 0–2.0 % (w/v) NaCl, with a generation time of 10 h under optimal conditions. Cells were rod-shaped and non-motile, ranging from 2 to 7 μm in length. Strain 521T grew only in the presence of thiosulfate and/or Fe(III) (ferrihydrite) as terminal electron acceptors under strictly anaerobic conditions, and preferred protein-rich compounds as energy sources, although the isolate was capable of chemolithoautotrophic growth. 16S rRNA gene sequence analysis places this isolate within the crenarchaeal genus Pyrobaculum. To our knowledge, this is the first Pyrobaculum strain to be isolated from an anaerobic mud volcano and to reduce only either thiosulfate or ferric iron. An in silico genome-to-genome distance calculator reported <25 % DNA–DNA hybridization between strain 521T and eight other Pyrobaculum species. Due to its genotypic and phenotypic differences, we conclude that strain 521T represents a novel species, for which the name Pyrobaculum igneiluti sp. nov. is proposed. The type strain is 521T (=DSM 103086T=ATCC TSD-56T). Anaerobic respiratory processes based on the reduction of recently revealed by the receding of the Salton Sea, ejects sulfur compounds or Fe(III) have been proposed to be fluid of a similar composition at 90–95 C. -
Viruses of Hyperthermophilic Archaea: Entry and Egress from the Host Cell
Viruses of hyperthermophilic archaea : entry and egress from the host cell Emmanuelle Quemin To cite this version: Emmanuelle Quemin. Viruses of hyperthermophilic archaea : entry and egress from the host cell. Microbiology and Parasitology. Université Pierre et Marie Curie - Paris VI, 2015. English. NNT : 2015PA066329. tel-01374196 HAL Id: tel-01374196 https://tel.archives-ouvertes.fr/tel-01374196 Submitted on 30 Sep 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Université Pierre et Marie Curie – Paris VI Unité de Biologie Moléculaire du Gène chez les Extrêmophiles Ecole doctorale Complexité du Vivant ED515 Département de Microbiologie - Institut Pasteur 7, quai Saint-Bernard, case 32 25, rue du Dr. Roux 75252 Paris Cedex 05 75015 Paris THESE DE DOCTORAT DE L’UNIVERSITE PIERRE ET MARIE CURIE Spécialité : Microbiologie Pour obtenir le grade de DOCTEUR DE L’UNIVERSITE PIERRE ET MARIE CURIE VIRUSES OF HYPERTHERMOPHILIC ARCHAEA: ENTRY INTO AND EGRESS FROM THE HOST CELL Présentée par M. Emmanuelle Quemin Soutenue le 28 Septembre 2015 devant le jury composé de : Prof. Guennadi Sezonov Président du jury Prof. Christa Schleper Rapporteur de thèse Dr. Paulo Tavares Rapporteur de thèse Dr. -
Sulfolobus As a Model Organism for the Study of Diverse
SULFOLOBUS AS A MODEL ORGANISM FOR THE STUDY OF DIVERSE BIOLOGICAL INTERESTS; FORAYS INTO THERMAL VIROLOGY AND OXIDATIVE STRESS by Blake Alan Wiedenheft A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Microbiology MONTANA STATE UNIVERSITY Bozeman, Montana November 2006 © COPYRIGHT by Blake Alan Wiedenheft 2006 All Rights Reserved ii APPROVAL of a dissertation submitted by Blake Alan Wiedenheft This dissertation has been read by each member of the dissertation committee and has been found to be satisfactory regarding content, English usage, format, citations, bibliographic style, and consistency, and is ready for submission to the Division of Graduate Education. Dr. Mark Young and Dr. Trevor Douglas Approved for the Department of Microbiology Dr.Tim Ford Approved for the Division of Graduate Education Dr. Carl A. Fox iii STATEMENT OF PERMISSION TO USE In presenting this dissertation in partial fulfillment of the requirements for a doctoral degree at Montana State University – Bozeman, I agree that the Library shall make it available to borrowers under rules of the Library. I further agree that copying of this dissertation is allowable only for scholarly purposes, consistent with “fair use” as prescribed in the U.S. Copyright Law. Requests for extensive copying or reproduction of this dissertation should be referred to ProQuest Information and Learning, 300 North Zeeb Road, Ann Arbor, Michigan 48106, to whom I have granted “the exclusive right to reproduce and distribute my dissertation in and from microfilm along with the non-exclusive right to reproduce and distribute my abstract in any format in whole or in part.” Blake Alan Wiedenheft November, 2006 iv DEDICATION This work was funded in part through grants from the National Aeronautics and Space Administration Program (NAG5-8807) in support of Montana State University’s Center for Life in Extreme Environments (MCB-0132156), and the National Institutes of Health (R01 EB00432 and DK57776). -
Molecular Identification and Characterization of Two Rubber Dandelion
Molecular Identification and Characterization of Two Rubber Dandelion Amalgaviruses Archives of Virology – Annotated Sequence Record Humberto Debat1*, Zinan Luo, Brian J. Iaffaldano, Xiaofeng Zhuang, Katrina Cornish 2 1 Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), 11 de setiembre 4755, Córdoba, Argentina, X5020ICA. 2 Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Williams Hall, 1680 Madison Avenue, Wooster, OH 44691. * Corresponding author: Humberto Debat, [email protected], Tel: +54 9 351 4973636, Fax: +54 9 351 4974330 Abstract The Amalgaviridae family is composed of persistent viruses that share the genome architecture of Totiviridae and gene evolutionary resemblance to Partitiviridae. A single Amalgavirus genus has been assigned to this family, harboring only four recognized species, corresponding to plant infecting viruses with dsRNA monopartite genomes of ca. 3.4 kb. Here, we present the genomic identification and characterization of two novel Amalgavirus detected in Rubber dandelion (Taraxacum kok-saghyz). The sequenced isolates presented a 3,409 and 3,413 nt long genome, harbouring two partially overlapping ORFs encoding a putative coat protein and an RNA-dependent RNA polymerase (RdRP). Multiple independent RNAseq data suggest that the identified viruses have a differential distribution and low relative RNA levels in infected plants. Virus presence was not associated with any apparent symptoms on the plant host. We propose the name rubber dandelion latent virus 1 & 2 to the detected Amalgavirus. Annotated sequence record Natural rubber is an essential material to the manufacture of 50,000 different rubber and latex products.