DOCSLIB.ORG

University of Warwick Institutional Repository

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
University of Warwick Institutional Repository University of Warwick institutional repository: http://go.warwick.ac.uk/wrap A Thesis Submitted for the Degree of PhD at the University of Warwick http://go.warwick.ac.uk/wrap/57059 This thesis is made available online and is protected by original copyright. Please scroll down to view the document itself. Please refer to the repository record for this item for information to help you to cite it. Our policy information is available from the repository home page. Detection of Microbial Taxa in Complex Communities: impacts of relative abundance, gene transfer and persistence of target DNA David William Cleary BSc A Thesis submitted for the Degree of Doctor of Philosophy University of Warwick, the School of Life Sciences April 2012 Table of Contents Table of Contents .................................................................................................. i List of Figures ..................................................................................................... vii List of Tables .................................................................................................... xxii Acknowledgements .......................................................................................... xxvi Declaration ...................................................................................................... xxvii Summary ........................................................................................................xxviii List of Abbreviations ...................................................................................... xxix Introduction .......................................................................................................... 1 1.1 Introduction ...................................................................................................... 2 1.2 The Burkholderiaceae ...................................................................................... 3 1.2.1 Burkholderia pseudomallei, B. mallei and B. thailandensis ......................... 4 1.2.2 Burkholderia cepacia Complex .................................................................. 10 1.3 Natural Genetic Transformation of Burkholderia sp. .................................... 14 1.4 DNA Persistence ............................................................................................ 16 1.5 Metagenomics ................................................................................................ 17 1.5.1 Pyrosequencing ........................................................................................... 20 1.5.2 Phylogenetic Markers and Application of High-throughput Sequencing for Analyses of Microbial Community Structure ...................................................... 21 1.5.3 Application of Whole Genome Sequencing to Pathogen Detection ........... 25 1.5.4 Emerging Approaches for Metagenomic Studies - Metatranscriptomics ... 26 1.6 Project Aims ................................................................................................... 29 Materials and Methods ...................................................................................... 30 2.1 Clay Minerals ................................................................................................. 31 2.1.1 Generating Homo-ionic Minerals ............................................................... 31 2.1.2 DNA Adsorption to Homo-ionic Minerals ................................................. 31 2.2 Media and Reagents ....................................................................................... 32 2.2.1 Microbiological Media ................................................................................ 32 2.2.2 Antibiotics ................................................................................................... 33 2.2.3 Buffers and Solutions .................................................................................. 34 2.3 Bacterial Strains ............................................................................................. 34 2.3.1 Bacillus anthracis Ames Spores ................................................................. 34 2.3.2 Bacillus globigii NCTC 10073 ................................................................... 35 2.3.3 Burkholderia cepacia Complex .................................................................. 35 2.3.4 Burkholderia pseudomallei K96243 ........................................................... 36 2.3.5 Determination of Antibiotic Minimum Inhibitory Concentration .............. 37 i 2.3.6 Storage of Strains ........................................................................................ 37 2.4 Nucleic Acid Extractions and Manipulations ................................................ 38 2.4.1 Genomic DNA Extraction ........................................................................... 38 2.4.2 DNA Extraction from Soil .......................................................................... 38 2.4.2.1 MoBio UltraClean® Soil DNA Isolation Kit ............................. 38 2.4.2.2 MoBio PowerSoil® Soil DNA Isolation Kit .............................. 39 2.4.2.3 Modified UltraClean® Soil DNA Isolation Kit (Andrews et al., 2004) 40 2.4.2.4 Phenol / Chloroform (Krsek and Wellington, 1999) .................. 40 2.4.2.5 Epicentre SoilMaster™ DNA Extraction Kit ............................. 41 2.4.2.6 Phenol / Chloroform-based Extraction (Yeates et al., 1998) ..... 42 2.4.2.7 MoBio PowerMax® Soil DNA Isolation Kit ............................. 42 2.4.3 DNA Extraction from Collected-Aerosol Samples ..................................... 43 2.4.4 Plasmid DNA Extraction............................................................................. 44 2.4.5 Agarose Gel Electrophoresis ....................................................................... 44 2.4.6 Nucleic Acid Extraction from Agarose Gels .............................................. 45 2.4.7 Microcon® Purification .............................................................................. 45 2.4.8 Ethanol Precipitation ................................................................................... 45 2.4.9 Quantification of Nucleic Acids.................................................................. 46 2.4.9.1 UV Densitometry ....................................................................... 46 2.4.9.2 Picogreen/Ribogreen Quantification of DNA ............................ 46 2.4.9.3 Agilent 2100 Bioanalyser DNA Analysis .................................. 46 2.4.10 Whole Genome Amplification .................................................................. 47 2.4.11 Removal of Multiple Displacement Amplification-generated, Hyperbranched DNA Structures .......................................................................... 47 2.4.12 Nucleic Acid Manipulations ..................................................................... 47 2.4.12.1 Restriction Endonuclease Digestion of DNA ............................. 47 2.4.12.2 Klenow Treatment ...................................................................... 48 2.4.12.3 Alkaline Phosphatase Treatment ................................................ 48 2.4.13 Plasmids .................................................................................................... 48 2.4.14 Ligations with T4 DNA Ligase ................................................................. 49 2.4.15 Transformation of Competent HB101 E. coli (Promega Ltd, USA)........ 49 2.4.16 One Shot® TOP10 E. coli ......................................................................... 50 2.4.17 Filter Transformations ............................................................................... 50 ii 2.4.18 Polymerase Chain Reaction (PCR) ........................................................... 50 2.4.19 PCR Optimisation ..................................................................................... 51 2.4.19.1 Primers ........................................................................................ 51 2.4.19.2 Magnesium and dNTP Concentration ........................................ 52 2.4.19.3 TaqMan® Real-time PCR Probe ................................................ 52 2.4.19.4 Taq DNA Polymerase ................................................................ 53 2.5 454™ Sequencing .......................................................................................... 57 DNA Persistence in Soil ..................................................................................... 59 3.1 Introduction .................................................................................................... 60 3.1.1 Release and Persistence of Bacterium-derived DNA.................................. 62 3.1.2 Extraction of DNA from Soil ...................................................................... 65 3.2 Aims ............................................................................................................... 67 3.3 Impact of Mineral Concentration on Adsorption of DNA ............................. 68 3.3.1 Comparison of Minerals .............................................................................. 68 3.3.2 Effect of Cation on DNA Adsorption ......................................................... 71 3.3.3 Effect of pH on DNA Adsorption ............................................................... 73 3.3.4 Release of Adsorbed DNA .......................................................................... 74 3.3.5 Protection of Mineral-adsorbed DNA from DNaseI Mediated Degradation
Load more

Recommended publications
  • Reporting of Diseases and Conditions Regulation, Amendment, M.R. 289/2014
    THE PUBLIC HEALTH ACT LOI SUR LA SANTÉ PUBLIQUE (C.C.S.M. c. P210) (c. P210 de la C.P.L.M.) Reporting of Diseases and Conditions Règlement modifiant le Règlement sur la Regulation, amendment déclaration de maladies et d'affections Regulation 289/2014 Règlement 289/2014 Registered December 23, 2014 Date d'enregistrement : le 23 décembre 2014 Manitoba Regulation 37/2009 amended Modification du R.M. 37/2009 1 The Reporting of Diseases and 1 Le présent règlement modifie le Conditions Regulation , Manitoba Règlement sur la déclaration de maladies et Regulation 37/2009, is amended by this d'affections , R.M. 37/2009. regulation. 2 Schedules A and B are replaced with 2 Les annexes A et B sont remplacées Schedules A and B to this regulation. par les annexes A et B du présent règlement. Coming into force Entrée en vigueur 3 This regulation comes into force on 3 Le présent règlement entre en vigueur January 1, 2015, or on the day it is registered le 1 er janvier 2015 ou à la date de son under The Statutes and Regulations Act , enregistrement en vertu de Loi sur les textes whichever is later. législatifs et réglementaires , si cette date est postérieure. December 19, 2014 Minister of Health/La ministre de la Santé, 19 décembre 2014 Sharon Blady 1 SCHEDULE A (Section 1) 1 The following diseases are diseases requiring contact notification in accordance with the disease-specific protocol. Common name Scientific or technical name of disease or its infectious agent Chancroid Haemophilus ducreyi Chlamydia Chlamydia trachomatis (including Lymphogranuloma venereum (LGV) serovars) Gonorrhea Neisseria gonorrhoeae HIV Human immunodeficiency virus Syphilis Treponema pallidum subspecies pallidum Tuberculosis Mycobacterium tuberculosis Mycobacterium africanum Mycobacterium canetti Mycobacterium caprae Mycobacterium microti Mycobacterium pinnipedii Mycobacterium bovis (excluding M.
    [Show full text]
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • Evolution Toward Maximum Transport Capacity of the Ttg2 ABC System In
    bioRxiv preprint doi: https://doi.org/10.1101/834812; this version posted November 8, 2019. 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 Evolution toward maximum transport capacity of the Ttg2 ABC system in 2 Pseudomonas aeruginosa 3 4 Daniel Yero,1,2 Lionel Costenaro,1# Oscar Conchillo-Solé,1 Mireia Díaz-Lobo,3 Adrià 5 Mayo,1 Mario Ferrer-Navarro,1# Marta Vilaseca,3 Isidre Gibert,1,2* Xavier Daura1,4* 6 7 1Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona 8 (UAB), Barcelona, Spain; 9 2Departament de Genètica i de Microbiologia, UAB, Barcelona, Spain; 10 3Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of 11 Science and Technology, Barcelona, Spain; 12 4Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain. 13 14 *Corresponding Authors: Xavier Daura, Tel: (+34)935868940 Email: 15 [email protected]. Isidre Gibert, Tel: (+34)935862050 Email: 16 [email protected]. 17 18 #Present address: Lionel Costenaro, Institut de Biologia Molecular de Barcelona 19 (CSIC), Barcelona, Spain. Mario Ferrer-Navarro, Teknokroma Analítica SA, 20 Barcelona, Spain. 21 1 bioRxiv preprint doi: https://doi.org/10.1101/834812; this version posted November 8, 2019. 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. 22 Abstract 23 In Pseudomonas aeruginosa, Ttg2D is the soluble periplasmic phospholipid-binding 24 component of an ABC transport system thought to be involved in maintaining the 25 asymmetry of the outer membrane.
    [Show full text]
  • Identification of Genes Responsible for Ochratoxin-A Biodegradation By
    Szent István University PhD School of Environmental Sciences Identification of genes responsible for ochratoxin-A biodegradation by Cupriavidus basilensis ŐR16 and valuation of Cupriavidus genus for mycotoxins biodegradation potential Thesis of Doctoral Dissertation (PhD) Mohammed Talib Jasim AL-Nussairawi Gödöllő, Hungary 2020 I. DECLARATION I declare that this thesis is a record of original work and contains no material that has been accepted for the award of any other degree or diploma in any university. To the best of my knowledge and belief, this thesis contains no material previously published or written by another person, except where due reference is made in the text. Name: Ph.D. School of Environmental Sciences Discipline: Environmental Sciences / Biotechnology Leader of Doctoral School: Csákiné Dr. Erika Michéli, Ph.D. professor, head of department Department of Soil science and Agrochemistry Faculty of Agricultural and Environmental Sciences Institute of Environmental Sciences Szent István University Supervisor: Matyas Cserhati, Ph.D. associate professor Department of Environmental Protection and Ecotoxicology Faculty of Agricultural and Environmental Sciences Institute of Aquaculture and Environmental Protection Szent István University ........................................................... ................................................... Approval of School Leader Approval of Supervisor 2 Table of Contents I. DECLARATION ...................................................................................................................
    [Show full text]
  • University of Cincinnati
    UNIVERSITY OF CINCINNATI Date: February 22, 2007 I, _ Samuel Lee Hayes________________________________________, hereby submit this work as part of the requirements for the degree of: Doctor of Philosophy in: Biological Sciences It is entitled: Response of Mammalian Models to Exposure of Bacteria from the Genus Aeromonas Evaluated using Transcriptional Analysis and Conjectures on Disease Mechanisms This work and its defense approved by: Chair: _Brian K. Kinkle _Dennis W. Grogan _Richard D. Karp _Mario Medvedovic _Stephen J. Vesper Response of Mammalian Models to Exposure of Bacteria from the Genus Aeromonas Evaluated using Transcriptional Analysis and Conjectures on Disease Mechanisms A dissertation submitted to the Division of Graduate Studies and Research of the University of Cincinnati in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in the Department of Biological Sciences of the College of Arts and Sciences 2007 by Samuel Lee Hayes B.S. Ohio University, 1978 M.S. University of Cincinnati, 1986 Committee Chair: Dr. Brian K. Kinkle Abstract The genus Aeromonas contains virulent bacteria implicated in waterborne disease, as well as avirulent strains. One of my research objectives was to identify and characterize host- pathogen relationships specific to Aeromonas spp. Aeromonas virulence was assessed using changes in host mRNA expression after infecting cell cultures and live animals. Messenger RNA extracts were hybridized to murine genomic microarrays. Initially, these model systems were infected with two virulent A. hydrophila strains, causing up-regulation of over 200 and 50 genes in animal and cell culture tissues, respectively. Twenty-six genes were common between the two model systems. The live animal model was used to define virulence for many Aeromonas spp.
    [Show full text]
  • Abstract Betaproteobacteria Alphaproteobacteria
    Abstract N-210 Contact Information The majority of the soil’s biosphere containins biodiveristy that remains yet to be discovered. The occurrence of novel bacterial phyla in soil, as well as the phylogenetic diversity within bacterial phyla with few cultured representatives (e.g. Acidobacteria, Anne Spain Dr. Mostafa S.Elshahed Verrucomicrobia, and Gemmatimonadetes) have been previously well documented. However, few studies have focused on the Composition, Diversity, and Novelty within Soil Proteobacteria Department of Botany and Microbiology Department of Microbiology and Molecular Genetics novel phylogenetic diversity within phyla containing numerous cultured representatives. Here, we present a detailed University of Oklahoma Oklahoma State University phylogenetic analysis of the Proteobacteria-affiliated clones identified in a 13,001 nearly full-length 16S rRNA gene clones 770 Van Vleet Oval 307 LSE derived from Oklahoma tall grass prairie soil. Proteobacteria was the most abundant phylum in the community, and comprised Norman, OK 73019 Stillwater, OK 74078 25% of total clones. The most abundant and diverse class within the Proteobacteria was Alphaproteobacteria, which comprised 405 325 5255 405 744 6790 39% of Proteobacteria clones, followed by the Deltaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, which made Anne M. Spain (1), Lee R. Krumholz (1), Mostafa S. Elshahed (2) up 37, 16, and 8% of Proteobacteria clones, respectively. Members of the Epsilonproteobacteria were not detected in the dataset. [email protected] [email protected] Detailed phylogenetic analysis indicated that 14% of the Proteobacteria clones belonged to 15 novel orders and 50% belonged (1) Dept. of Botany and Microbiology, University of Oklahoma, Norman, OK to orders with no described cultivated representatives or were unclassified.
    [Show full text]
  • 國立高雄海洋科技大學 National Kaohsiung Marine University
    國立高雄海洋科技大學 NATIONAL KAOHSIUNG MARINE UNIVERSITY 專任教師著作目錄 2005~2008 序 本校創立於民國 35 年，歷經水產職業學校、海事專科學校、 海洋技術學院等學制的變革，至民國 93 年，始改名為國立高雄海 洋科技大學，成為一所以發展海洋科技教育為主軸的高等科技學 府。回顧這 62 年來，本校一直肩負著為國家培育海洋專業人才， 發展海洋應用科技的重責大任，也見證臺灣在這段期間，於教育、 經濟等方面發展成長的軌跡。 截至 97 學年度第 1 學期為止，本校專任教師（含校長）計 231 名，分屬於海事學院、管理學院、海洋工程學院與水圈學院等四 個學院，以及教導全校學生基礎教育、通識教育的共同教育委員 會。全體教師彼此尊重，各司其職，各盡其分的承擔研究、教學 及服務等工作，推動校務不斷的向上發展。 自 94 學年度起，為彰顯改名科技大學後的績效，鼓勵專任教 師將其研究成果由本校研發處開始逐年編印《專任教師著作目 錄》，用以彙整教師在論文、專利、技術報告及專著等方面的成果。 期待本目錄的編印可以達到下列的效益：一、呈現本校教師辛苦 耕耘的果實及本校研究發展的特色；二、提供海洋科技領域相關 人員最新的資訊；三、帶動本校教師相互切磋琢磨的研究風氣。 自本目錄發行以來，本校的研究風氣已明顯增長，研究的能 量正不斷的累積。從前三年出版的目錄看出，除創刊初期，以海 洋教育為主軸的學科仍維持優異的研究成果之外，隨著海洋相關 系科的增設，研究所的陸續成立，近年來，本校在管理、工程、 電子、生物科技及共同教育等各領域的研究，與產學合作的推動， 成果也相當豐碩。 學術研究的精神是創新，學術研究的核心價值是不斷進步，學 術研究風氣的形成則有賴全體教師共同的經營。在 97 學年度《專任 教師著作目錄》出版前夕，本人衷心期盼全體教師，為了提升教學 品質，促進產學合作，不分專業教師或共同教育的教師，大家都 能在教學、服務之餘，竭盡所能的從事學術研究。因為研究是教 學的基礎，也是促進產學合作的活水源頭。 本目錄資料的編纂力求確實，雖經研發處同仁校對再三，惟 恐仍有疏漏誤植的現象，請不吝賜教指正，不勝感激。是為序。 校長 2008 年 12 月 5 日於國立高雄海洋科技大學 97 專任教師名冊 國立高雄海洋科技大學專任教師名冊(97.11.25) 科 系 職 稱 姓 名 科 系 職 稱 姓 名 校長 校長 周照仁 輪機工程系 副教授 蘇俊連 航運技術系 副教授 廖宗 輪機工程系 助理教授 黃耀新 航運技術系 副教授 林富振 輪機工程系 助理教授 楊政達 航運技術系 副教授 郭福村 輪機工程系 助理教授 蕭海明 航運技術系 副教授 陳希敬 輪機工程系 助理教授 吳俊文 航運技術系 副教授 王一三 輪機工程系 講師 郭振亞 航運技術系 副教授 周建張 輪機工程系 講師 楊子傑 航運技術系 副教授 胡家聲 輪機工程系 講師 鍾振弘 航運技術系 副教授 陳彥宏 輪機工程系 講師 邱時甫 航運技術系 助理教授 蘇東濤 輪機工程系 助教 王水音 航運技術系 助理教授 黃振邦 航運管理系 副教授 戴輝煌 航運技術系 講師 苟榮華 航運管理系 副教授 許文楷 航運技術系 講師 俞惠麟 航運管理系 副教授 于惠蓉 航運技術系 講師 洪秋明 航運管理系 副教授 楊鈺池 航運技術系 講師 陳崑旭 航運管理系 副教授 孫智嫻 航運技術系 講師 謝坤山 航運管理系 副教授 曾文瑞 航運技術系 講師 劉安白 航運管理系 助理教授 趙清成 航運技術系 講師 文展權 航運管理系 講師 連淑君 航運技術系 講師級專業技術人員 蔣克雄 航運管理系 講師 蔣文玉 輪機工程系 教授 張始偉
    [Show full text]
  • Rickettsia Prowazekii Common Human Exposure Routes
    APPENDIX 2 Rickettsia prowazekii Common Human Exposure Routes: Disease Agent: • Exposure to the feces of infected body lice. The lice are infected by a human blood meal. The rickettsiae • Rickettsia prowazekii reproduce in the louse gut epithelium. Infection occurs when louse feces are scratched into the skin, Disease Agent Characteristics: inoculated onto mucous membrane or inhaled. • As a bioweapon, the agent can be aerosolized, with • Rickettsiae are obligate intracellular Gram-negative intent of infection through inhalation. bacteria. • Sporadic cases occur after exposure to flying squir- • Order: Rickettsiales; Family: Rickettsiaceae rels, most likely as a result of exposure to squirrel flea • Size: 0.3 ¥ 1.0 mm intracellular bacteria that take up feces. The organism has also been identified in ticks Gram stain poorly feeding on livestock in Africa. • Nucleic acid: Rickettsial genomes are among the Likelihood of Secondary Transmission: smallest of bacteria at 1000-1600 kb. The R. prowazekii genome is 1100 kb. • No evidence of direct person-to-person transmission • Physicochemical properties: Susceptible to 1% • Under crowded conditions, where bathing and sodium hypochlorite, 70% ethanol, glutaraldehyde, washing clothes are difficult, and where lice are formaldehyde and quaternary ammonium disinfec- present, typhus can spread explosively. tants. Sensitive to moist heat (121°C for at least • Recent outbreaks have occurred in a number of areas 15 min) and dry heat (160-170°C for at least 1 hour). in the world under conditions of war and population The organism is stable in tick tissues or blood under displacement. ambient environmental conditions, surviving up to 1 year; sensitive to drying (feces of infected ticks At-Risk Populations: quickly lose their infectivity on drying).
    [Show full text]
  • Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism
    fmicb-10-02556 November 4, 2019 Time: 15:40 # 1 ORIGINAL RESEARCH published: 06 November 2019 doi: 10.3389/fmicb.2019.02556 Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism Charlotte Peeters1, Evelien De Canck1, Margo Cnockaert1, Evie De Brandt1, Cindy Snauwaert2, Bart Verheyde1, Eliza Depoorter1, Theodore Spilker3, John J. LiPuma3 and Peter Vandamme1,2* 1 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium, 2 BCCM/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent Edited by: University, Ghent, Belgium, 3 Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, United States Iain Sutcliffe, Northumbria University, United Kingdom Comparative analysis of partial gyrB, recA, and gltB gene sequences of 84 Pandoraea Reviewed by: reference strains and field isolates revealed several clusters that included no taxonomic Martin W. Hahn, reference strains. The gyrB, recA, and gltB phylogenetic trees were used to select 27 University of Innsbruck, Austria Stephanus Nicolaas Venter, strains for whole-genome sequence analysis and for a comparative genomics study that University of Pretoria, South Africa also included 41 publicly available Pandoraea genome sequences. The phylogenomic Aharon Oren, The Hebrew University of Jerusalem, analyses included a Genome BLAST Distance Phylogeny approach to calculate pairwise Israel digital DNA–DNA hybridization values and their
    [Show full text]
  • Cryptic Inoviruses Revealed As Pervasive in Bacteria and Archaea Across Earth’S Biomes
    ARTICLES https://doi.org/10.1038/s41564-019-0510-x Corrected: Author Correction Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes Simon Roux 1*, Mart Krupovic 2, Rebecca A. Daly3, Adair L. Borges4, Stephen Nayfach1, Frederik Schulz 1, Allison Sharrar5, Paula B. Matheus Carnevali 5, Jan-Fang Cheng1, Natalia N. Ivanova 1, Joseph Bondy-Denomy4,6, Kelly C. Wrighton3, Tanja Woyke 1, Axel Visel 1, Nikos C. Kyrpides1 and Emiley A. Eloe-Fadrosh 1* Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach lever- aging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem.
    [Show full text]
  • Reportable Disease Surveillance in Virginia, 2013
    Reportable Disease Surveillance in Virginia, 2013 Marissa J. Levine, MD, MPH State Health Commissioner Report Production Team: Division of Surveillance and Investigation, Division of Disease Prevention, Division of Environmental Epidemiology, and Division of Immunization Virginia Department of Health Post Office Box 2448 Richmond, Virginia 23218 www.vdh.virginia.gov ACKNOWLEDGEMENT In addition to the employees of the work units listed below, the Office of Epidemiology would like to acknowledge the contributions of all those engaged in disease surveillance and control activities across the state throughout the year. We appreciate the commitment to public health of all epidemiology staff in local and district health departments and the Regional and Central Offices, as well as the conscientious work of nurses, environmental health specialists, infection preventionists, physicians, laboratory staff, and administrators. These persons report or manage disease surveillance data on an ongoing basis and diligently strive to control morbidity in Virginia. This report would not be possible without the efforts of all those who collect and follow up on morbidity reports. Divisions in the Virginia Department of Health Office of Epidemiology Disease Prevention Telephone: 804-864-7964 Environmental Epidemiology Telephone: 804-864-8182 Immunization Telephone: 804-864-8055 Surveillance and Investigation Telephone: 804-864-8141 TABLE OF CONTENTS INTRODUCTION Introduction ......................................................................................................................................1
    [Show full text]
  • Delineation of Aeromonas Hydrophila Pathotypes by Dectection of Putative Virulence Factors Using Polymerase Chain Reaction and N
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by DigitalCommons@Kennesaw State University Kennesaw State University DigitalCommons@Kennesaw State University Master of Science in Integrative Biology Theses Biology & Physics Summer 7-20-2015 Delineation of Aeromonas hydrophila Pathotypes by Dectection of Putative Virulence Factors using Polymerase Chain Reaction and Nematode Challenge Assay John Metz Kennesaw State University, [email protected] Follow this and additional works at: http://digitalcommons.kennesaw.edu/integrbiol_etd Part of the Integrative Biology Commons Recommended Citation Metz, John, "Delineation of Aeromonas hydrophila Pathotypes by Dectection of Putative Virulence Factors using Polymerase Chain Reaction and Nematode Challenge Assay" (2015). Master of Science in Integrative Biology Theses. Paper 7. This Thesis is brought to you for free and open access by the Biology & Physics at DigitalCommons@Kennesaw State University. It has been accepted for inclusion in Master of Science in Integrative Biology Theses by an authorized administrator of DigitalCommons@Kennesaw State University. For more information, please contact [email protected]. Delineation of Aeromonas hydrophila Pathotypes by Detection of Putative Virulence Factors using Polymerase Chain Reaction and Nematode Challenge Assay John Michael Metz Submitted in partial fulfillment of the requirements for the Master of Science Degree in Integrative Biology Thesis Advisor: Donald J. McGarey, Ph.D Department of Molecular and Cellular Biology Kennesaw State University ABSTRACT Aeromonas hydrophila is a Gram-negative, bacterial pathogen of humans and other vertebrates. Human diseases caused by A. hydrophila range from mild gastroenteritis to soft tissue infections including cellulitis and acute necrotizing fasciitis. When seen in fish it causes dermal ulcers and fatal septicemia, which are detrimental to aquaculture stocks and has major economic impact to the industry.
    [Show full text]