Kilmer Conference Proceedings: Volume 7
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Evolutionary Relationships and Systematics of the Alphaviruses ANN M
JOURNAL OF VIROLOGY, Nov. 2001, p. 10118–10131 Vol. 75, No. 21 0022-538X/01/$04.00ϩ0 DOI: 10.1128/JVI.75.21.10118–10131.2001 Copyright © 2001, American Society for Microbiology. All Rights Reserved. Evolutionary Relationships and Systematics of the Alphaviruses ANN M. POWERS,1,2† AARON C. BRAULT,1† YUKIO SHIRAKO,3‡ ELLEN G. STRAUSS,3 1 3 1 WENLI KANG, JAMES H. STRAUSS, AND SCOTT C. WEAVER * Department of Pathology and Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas 77555-06091; Division of Vector-Borne Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado2; and Division of Biology, California Institute of Technology, Pasadena, California 911253 Received 1 May 2001/Accepted 8 August 2001 Partial E1 envelope glycoprotein gene sequences and complete structural polyprotein sequences were used to compare divergence and construct phylogenetic trees for the genus Alphavirus. Tree topologies indicated that the mosquito-borne alphaviruses could have arisen in either the Old or the New World, with at least two transoceanic introductions to account for their current distribution. The time frame for alphavirus diversifi- cation could not be estimated because maximum-likelihood analyses indicated that the nucleotide substitution rate varies considerably across sites within the genome. While most trees showed evolutionary relationships consistent with current antigenic complexes and species, several changes to the current classification are proposed. The recently identified fish alphaviruses salmon pancreas disease virus and sleeping disease virus appear to be variants or subtypes of a new alphavirus species. Southern elephant seal virus is also a new alphavirus distantly related to all of the others analyzed. -
Characterization of the Interaction Between R. Conorii and Human
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 4-5-2018 Characterization of the Interaction Between R. Conorii and Human Host Vitronectin in Rickettsial Pathogenesis Abigail Inez Fish Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Bacteria Commons, Bacteriology Commons, Biology Commons, Immunology of Infectious Disease Commons, and the Pathogenic Microbiology Commons Recommended Citation Fish, Abigail Inez, "Characterization of the Interaction Between R. Conorii and Human Host Vitronectin in Rickettsial Pathogenesis" (2018). LSU Doctoral Dissertations. 4566. https://digitalcommons.lsu.edu/gradschool_dissertations/4566 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. CHARACTERIZATION OF THE INTERACTION BETWEEN R. CONORII AND HUMAN HOST VITRONECTIN IN RICKETTSIAL PATHOGENESIS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Interdepartmental Program in Biomedical and Veterinary Medical Sciences Through the Department of Pathobiological Sciences by Abigail Inez -
Sanguineus Bacterial Communities Rhipicephalus
Composition and Seasonal Variation of Rhipicephalus turanicus and Rhipicephalus sanguineus Bacterial Communities Itai Lalzar, Shimon Harrus, Kosta Y. Mumcuoglu and Yuval Gottlieb Appl. Environ. Microbiol. 2012, 78(12):4110. DOI: 10.1128/AEM.00323-12. Published Ahead of Print 30 March 2012. Downloaded from Updated information and services can be found at: http://aem.asm.org/content/78/12/4110 These include: SUPPLEMENTAL MATERIAL Supplemental material http://aem.asm.org/ REFERENCES This article cites 44 articles, 17 of which can be accessed free at: http://aem.asm.org/content/78/12/4110#ref-list-1 CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» on June 10, 2013 by guest Information about commercial reprint orders: http://journals.asm.org/site/misc/reprints.xhtml To subscribe to to another ASM Journal go to: http://journals.asm.org/site/subscriptions/ Composition and Seasonal Variation of Rhipicephalus turanicus and Rhipicephalus sanguineus Bacterial Communities Itai Lalzar,a Shimon Harrus,a Kosta Y. Mumcuoglu,b and Yuval Gottlieba Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel,a and Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, Hadassah Medical School, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israelb A 16S rRNA gene approach, including 454 pyrosequencing and quantitative PCR (qPCR), was used to describe the bacterial com- munity in Rhipicephalus turanicus and to evaluate the dynamics of key bacterial tenants of adult ticks during the active questing season. -
Genome Project Reveals a Putative Rickettsial Endosymbiont
GBE Bacterial DNA Sifted from the Trichoplax adhaerens (Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont Timothy Driscoll1,y, Joseph J. Gillespie1,2,*,y, Eric K. Nordberg1,AbduF.Azad2, and Bruno W. Sobral1,3 1Virginia Bioinformatics Institute at Virginia Polytechnic Institute and State University 2Department of Microbiology and Immunology, University of Maryland School of Medicine 3Present address: Nestle´ Institute of Health Sciences SA, Campus EPFL, Quartier de L’innovation, Lausanne, Switzerland *Corresponding author: E-mail: [email protected]. yThese authors contributed equally to this work. Accepted: March 1, 2013 Abstract Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote–microbe interactions. Here, we used the genome of the primitive animal Trichoplax adhaerens (Metazoa: Placozoa), which is known to harbor an uncharacterized Gram-negative endosymbiont, to search for the presence of bacterial DNA sequences. Bioinformatic and phylogenomic analyses of extracted data from the genome assembly (181 bacterial coding sequences [CDS]) and trace read archive (16S rDNA) revealed a dominant proteobacterial profile strongly skewed to Rickettsiales (Alphaproteobacteria) genomes. By way of phylogenetic analysis of 16S rDNA and 113 proteins conserved across proteobacterial genomes, as well as identification of 27 rickettsial signature genes, we propose a Rickettsiales endosymbiont of T. adhaerens (RETA). The majority (93%) of the identified bacterial CDS belongs to small scaffolds containing prokaryotic-like genes; however, 12 CDS were identified on large scaffolds comprised of eukaryotic-like genes, suggesting that T. -
Diapositiva 1
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Diposit Digital de Documents de la UAB Annabel García León, Faculty of Biosciences, Microbiology degree Universitat Autònoma de Barcelona, 2013 EMERGING ARBOVIRAL DISEASES GLOBAL WARMING In the past 50 years, many vector-borne diseases have The accumulation of greenhouse gases (GHG) in the atmosphere by human activity altered emerged. Some of these diseases are produced for exotic the balance of radiation of the atmosphere, altering the TEMPERATURE at the Earth's surface pathogens that have been introduced into new regions and [1]. others are endemic species that have increased in incidence or have started to infect the human populations for first time Growth human Some longwaves ↑ Air Temperature (new pathogens). population Accumulation of radiation from the Near Surface Many of these vector-borne diseases are caused by greenhouse gases sun are absorbed ↑ Specific Humidity arbovirus. Arboviruses are virus transmitted by arthropods in the atmosphere and re-emitted to ↑ Ocean Heat Content vectors, such mosquitoes, ticks or sanflys. The virus is usually (burn fuels in the Earth by GHG ↑ Sea Level electricity generation, transmitted to the vector by a blood meal, after replicates in Increased per molecules ↑ Sea-Surface transport, industry, capita Temperature the vector salivary glands, where it will be transmitted to a agriculture and land consumption other animal upon feeding. Thus, the virus is amplified by use change, use of ↑ Temperature over of resources fluorinated gases in the oceans the vector and without it, the arbovirus can’t spread. (water, energy, industry) ↑ Temperature over In 1991, Robert Shope, presented the hypothesis that material, land, the land global warming might result in a worldwide increase of biodiversity) ↓ Snow Cover zoonotic infectious diseases. -
Characterizing the Fecal Shedding of Swine Infected with Japanese Encephalitis Virus
Characterizing the fecal shedding of swine infected with Japanese encephalitis virus by Konner Cool B.S., Kansas State University, 2017 A REPORT submitted in partial fulfillment of the requirements for the degree MASTER OF SCIENCE Department of Diagnostic Medicine/Pathobiology College of Veterinary Medicine KANSAS STATE UNIVERSITY Manhattan, Kansas 2020 Approved by: Major Professor Dr. Dana Vanlandingham Copyright © Konner Cool 2020. Abstract Japanese encephalitis virus (JEV) is an enveloped, single-stranded, positive sense Flavivirus with five circulating genotypes (GI to GV). JEV has a well described enzootic cycle in endemic regions between swine and avian populations as amplification hosts and Culex species mosquitoes which act as the primary vector. Humans are incidental hosts with no known contributions to sustaining transmission cycles in nature. Vector-free routes of JEV transmission have been described through oronasal shedding of viruses among infected swine. The aim of this study was to characterize the fecal shedding of JEV from intradermally challenged swine. The objective of the study was to advance our understanding of how JEV transmission can be maintained in the absence of arthropod vectors. Our hypothesis is that JEV RNA will be detected in fecal swabs and resemble the shedding profile observed in swine oral fluids, peaking between days three and five. In this study fecal swabs were collected throughout a 28-day JEV challenge experiment in swine and samples were analyzed using reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR). Quantification of viral loads in fecal shedding will provide a more complete understanding of the potential host-host transmission in susceptible swine populations. -
Paradoxical Evolution of Rickettsial Genomes
Ticks and Tick-borne Diseases 10 (2019) 462–469 Contents lists available at ScienceDirect Ticks and Tick-borne Diseases journal homepage: www.elsevier.com/locate/ttbdis Paradoxical evolution of rickettsial genomes T ⁎ Awa Diopa, Didier Raoultb, Pierre-Edouard Fourniera, a UMR VITROME, Aix-Marseille University, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Uuniversitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France b UMR MEPHI, Aix-Marseille University, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Uuniversitaire Méditerranée Infection, Marseille, France ARTICLE INFO ABSTRACT Keywords: Rickettsia species are strictly intracellular bacteria that evolved approximately 150 million years ago from a Rickettsia presumably free-living common ancestor from the order Rickettsiales that followed a transition to an obligate Genomics intracellular lifestyle. Rickettsiae are best known as human pathogens vectored by various arthropods causing a Evolution range of mild to severe human diseases. As part of their obligate intracellular lifestyle, rickettsial genomes have Virulence undergone a convergent evolution that includes a strong genomic reduction resulting from progressive gene Genome rearrangement degradation, genomic rearrangements as well as a paradoxical expansion of various genetic elements, notably Non-coding DNA Gene loss small RNAs and short palindromic elements whose role remains unknown. This reductive evolutionary process is DNA repeats not unique to members of the Rickettsia genus but is common to several human pathogenic bacteria. Gene loss, gene duplication, DNA repeat duplication and horizontal gene transfer all have shaped rickettsial genome evolution. Gene loss mostly involved amino-acid, ATP, LPS and cell wall component biosynthesis and tran- scriptional regulators, but with a high preservation of toxin-antitoxin (TA) modules, recombination and DNA repair proteins. -
Detecting Phylogenetic Signals from Deep Roots of the Tree of Life
UNIVERSITY OF CALIFORNIA,MERCED Detecting Phylogenetic Signals From Deep Roots of the Tree of Life A dissertation submitted in partial fulfillment of the requirements for the degree Doctor of Philosophy in Quantitative and Systems Biology by Katherine Colleen Harris Amrine Committee in charge: Professor Carolin Frank, Chair Professor David Ardell Professor Meng-Lin Tsao Professor Suzanne Sindi August 2013 Copyright Katherine C. Amrine All Rights Reserved UNIVERSITY OF CALIFORNIA,MERCED Graduate Division The Dissertation of Katherine Colleen Harris Amrine is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Faculty Advisor: David H. Ardell Committee Members: Chair: Carolin Frank Meng-Lin Tsao Suzanne Sindi Date iii Contents List of Figures ................................................................. vi List of Tables .................................................................. ix Acknowledgements ............................................................. x Vita ........................................................................... xi Abstract ...................................................................... xii 1 Shifting focus in evolutionary biology – identifying a new signal for phylogenetic tree reconstruction and taxonomic classification 1 1.1 The evolution of bacterial classification and phylogeny . .1 1.2 The historical marker – 16S . .2 1.3 Complications in bacterial classification and phylogeny . .2 1.3.1 Horizontal gene transfer . .2 1.3.2 Does a true tree exist? . .3 1.4 Methods for phylogenetic tree reconstruction . .3 1.4.1 DNA . .3 1.4.2 RNA . .4 1.4.3 Proteins . .4 1.4.4 Data compilation . .5 1.5 Bias in tree-building . .5 1.6 Biological bias in biological data . .6 1.7 The tRNA interaction network . .6 1.8 Information theory . .8 1.9 Machine Learning for bacterial classification . .9 2 tRNA signatures reveal polyphyletic origins of streamlined SAR11 genomes among the Alphaproteobacteria 12 2.1 Abstract . -
Science Article: If the Mercury Soars, So May Health Hazards
If the Mercury Soars, So May Health Hazards Richard Stone Science, New Series, Vol. 267, No. 5200. (Feb. 17, 1995), pp. 957-958. Stable URL: http://links.jstor.org/sici?sici=0036-8075%2819950217%293%3A267%3A5200%3C957%3AITMSSM%3E2.0.CO%3B2-0 Science is currently published by American Association for the Advancement of Science. Your use of the JSTOR archive indicates your acceptance of JSTOR's Terms and Conditions of Use, available at http://www.jstor.org/about/terms.html. JSTOR's Terms and Conditions of Use provides, in part, that unless you have obtained prior permission, you may not download an entire issue of a journal or multiple copies of articles, and you may use content in the JSTOR archive only for your personal, non-commercial use. Please contact the publisher regarding any further use of this work. Publisher contact information may be obtained at http://www.jstor.org/journals/aaas.html. Each copy of any part of a JSTOR transmission must contain the same copyright notice that appears on the screen or printed page of such transmission. The JSTOR Archive is a trusted digital repository providing for long-term preservation and access to leading academic journals and scholarly literature from around the world. The Archive is supported by libraries, scholarly societies, publishers, and foundations. It is an initiative of JSTOR, a not-for-profit organization with a mission to help the scholarly community take advantage of advances in technology. For more information regarding JSTOR, please contact [email protected]. http://www.jstor.org Sun Jul 1 18:16:11 2007 I MALARlA RISK. -
Ribofuranosylselenazole-4-Carboxamide, a New Antiviral Agentt JORMA J
ANTiMICROBIAL AGENTS AND CHEMOTHERAPY, Sept. 1983, P. 353-361 Vol. 24, No. 3 0066-4804/83/090353-09$02.00/0 Copyright 0 1983, American Society for Microbiology Broad-Spectrum Antiviral Activity of 2-p-D- Ribofuranosylselenazole-4-Carboxamide, a New Antiviral Agentt JORMA J. KIRSI,'* JAMES A. NORTH,1 PATRICIA A. McKERNAN,1 BYRON K. MURRAY,2 PETER G. CANONICO,3 JOHN W. HUGGINS,3 PREM C. SRIVASTAVA,4 AND ROLAND K. ROBINS5 Department ofMicrobiology1 and Cancer Research Center, Department of Chemistry,5 Brigham Young University, Provo, Utah 84602; Department ofMicrobiology and Immunology, Virginia Commonwealth University, Richmond, Virginia 232982; Department ofAntiviral Studies, U.S. Army Medical Research Institute ofInfectious Diseases, Fort Detrick, Frederick, Maryland 217103; and Health and Safety Research Division (Nuclear Medicine Technology Group), Oak Ridge National Laboratory, Oak Ridge, Tennessee 378304 Received 7 February 1983/Accepted 13 June 1983 The relative in vitro antiviral activities of three related nucleoside carboxam- ides, ribavirin (1-3-D-ribofuranosyl-1,2,4-triazole-3-carboxamide), tiazofurin (2- 3-D-ribofuranosylthiazole-4-carboxamide), and selenazole (2-p-D-ribofuranosyl- selenazole-4-carboxamide), were studied against selected DNA and RNA viruses. Although the activity of selenazole against different viruses varied, it was significantly more potent than ribavirin and tiazofurin against all tested represen- tatives of the families Paramyxoviridae (parainfluenza virus type 3, mumps virus, measles virus), Reoviridae (reovirus type 3), Poxviridae (vaccinia virus), Herpes- viridae (herpes simplex virus types 1 and 2), Togaviridae (Venezuelan equine encephalomyelitis virus, yellow fever virus, Japanese encephalitis virus), Bunya- viridae (Rift Valley fever virus, sandfly fever virus [strain Sicilian], Korean hemorrhagic fever virus), Arenaviridae (Pichinde virus), Picornaviridae (coxsack- ieviruses B1 and B4, echovirus type 6, encephalomyocarditis virus), Adenoviri- dae (adenovirus type 2), and Rhabdoviridae (vesicular stomatitis virus). -
A Deadly Virus Escapes
EBSCOhost http://web3.epnet.com/delivery.asp?_ ug=dbs+7%2C8o/o2C20+ln+en ... 2 page(s) will be printed. Record: 58 Title: A deadly virus escapes. Subject(s): MEDICAL laboratories- Accidents; COMMUNICABLE diseases -Transmission; YALE University (New Haven, Conn.).- Arbovirus Research Unit; CONNECTICUT; NEW Haven (Conn.) Source: Time, 9/5194, Vol. 1441ssue 10, p63, 1p, 2c Author(s): Lemonick, Michael D.; Park, Alice Abstract: States that concerns about lab security have arisen after a mysterious disease from Brazil struck a researcher at the Yale Arbovirus Research Unit. How the unnamed researcher became infected with the Sabia virus; Exposure of others before his illness was stopped. AN: 9408317724 ISSN: 0040-781X Full Text Word Count: 989 Database: Academic Search Premier MEDICINE A DEADLY VIRUS ESCAPES Concerns about lab security arise as a mysterious disease from Brazil strikes a Yale researcher The accident must have come as a horrifying shock, even for an experienced scientist. One minute, a sample was spinning in a high-speed centrifuge. Then, suddenly, the container cracked, and the sample - tissue contaminated by a rare, potentially lethal virus- spattered the inside of the centrifuge. Fortunately, the Yale University researcher working with the deadly germs was wearing a lab gown, latex gloves and a mask, as required under federal guidelines. He also knew the proper procedure for dealing with a deadly spill: rub every surface with bleach, sterilize all instruments that have been exposed, then wipe everything down again with alcohol. There was just one rule he failed to follow. Having decided the danger was over, he didn't bother to report the accident, and a few days later he left town to visit an old friend in Boston. -
Host-Microbe Relations: a Phylogenomics-Driven Bioinformatic Approach to the Characterization of Microbial DNA from Heterogeneous Sequence Data
Host-Microbe Relations: A Phylogenomics-Driven Bioinformatic Approach to the Characterization of Microbial DNA from Heterogeneous Sequence Data Timothy Patrick Driscoll Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Genetics, Bioinformatics, and Computational Biology Joseph J Gillespie David R Bevan Madhav V Marathe T M Murali May 1st, 2013 Blacksburg, Virginia Keywords: phylogenomics, genome-mining, host-microbe interactions, genomics, bioinformatics, symbiosis, bacteria, lateral gene transfer Copyright 2013 Host-Microbe Relations: A Phylogenomics-Driven Bioinformatic Approach to the Characterization of Microbial DNA from Heterogeneous Sequence Data Timothy Patrick Driscoll ABSTRACT Plants and animals are characterized by intimate, enduring, often indispensable, and always complex associations with microbes. Therefore, it should come as no surprise that when the genome of a eukaryote is sequenced, a medley of bacterial sequences are produced as well. These sequences can be highly informative about the interactions between the eukaryote and its bacterial cohorts; unfortunately, they often comprise a vanishingly small constituent within a heterogeneous mixture of microbial and host sequences. Genomic analyses typically avoid the bacterial sequences in order to obtain a genome sequence for the host. Metagenomic analysis typically avoid the host sequences in order to analyze community composition and functional diversity of the bacterial component. This dissertation describes the development of a novel approach at the intersection of genomics and metagenomics, aimed at the extraction and characterization of bacterial sequences from heterogeneous sequence data using phylogenomic and bioinformatic tools. To achieve this objective, three interoperable workflows were constructed as modular computational pipelines, with built-in checkpoints for periodic interpretation and refinement.