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Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification
ORIGINAL RESEARCH published: 10 March 2017 doi: 10.3389/fmicb.2017.00380 Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification Arshan Nasir 1, 2 and Gustavo Caetano-Anollés 1* 1 Department of Crop Sciences, Evolutionary Bioinformatics Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA, 2 Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan The viral supergroup includes the entire collection of known and unknown viruses that roam our planet and infect life forms. The supergroup is remarkably diverse both in its genetics and morphology and has historically remained difficult to study and classify. The accumulation of protein structure data in the past few years now provides an excellent opportunity to re-examine the classification and evolution of viruses. Here we scan completely sequenced viral proteomes from all genome types and identify protein folds involved in the formation of viral capsids and virion architectures. Viruses encoding similar capsid/coat related folds were pooled into lineages, after benchmarking against published literature. Remarkably, the in silico exercise reproduced all previously described members of known structure-based viral lineages, along with several proposals for new Edited by: additions, suggesting it could be a useful supplement to experimental approaches and Ricardo Flores, to aid qualitative assessment of viral diversity in metagenome samples. Polytechnic University of Valencia, Spain Keywords: capsid, virion, protein structure, virus taxonomy, SCOP, fold superfamily Reviewed by: Mario A. Fares, Consejo Superior de Investigaciones INTRODUCTION Científicas(CSIC), Spain Janne J. Ravantti, The last few years have dramatically increased our knowledge about viral systematics and University of Helsinki, Finland evolution. -
Annual Conference Abstracts
ANNUAL CONFERENCE 14-17 April 2014 Arena and Convention Centre, Liverpool ABSTRACTS SGM ANNUAL CONFERENCE APRIL 2014 ABSTRACTS (LI00Mo1210) – SGM Prize Medal Lecture (LI00Tu1210) – Marjory Stephenson Climate Change, Oceans, and Infectious Disease Prize Lecture Dr. Rita R. Colwell Understanding the basis of antibiotic resistance University of Maryland, College Park, MD, USA as a platform for early drug discovery During the mid-1980s, satellite sensors were developed to monitor Laura JV Piddock land and oceans for purposes of understanding climate, weather, School of Immunity & Infection and Institute of Microbiology and and vegetation distribution and seasonal variations. Subsequently Infection, University of Birmingham, UK inter-relationships of the environment and infectious diseases Antibiotic resistant bacteria are one of the greatest threats to human were investigated, both qualitatively and quantitatively, with health. Resistance can be mediated by numerous mechanisms documentation of the seasonality of diseases, notably malaria including mutations conferring changes to the genes encoding the and cholera by epidemiologists. The new research revealed a very target proteins as well as RND efflux pumps, which confer innate close interaction of the environment and many other infectious multi-drug resistance (MDR) to bacteria. The production of efflux diseases. With satellite sensors, these relationships were pumps can be increased, usually due to mutations in regulatory quantified and comparatively analyzed. More recent studies of genes, and this confers resistance to antibiotics that are often used epidemic diseases have provided models, both retrospective and to treat infections by Gram negative bacteria. RND MDR efflux prospective, for understanding and predicting disease epidemics, systems not only confer antibiotic resistance, but altered expression notably vector borne diseases. -
Primordial Capsid and Spooled Ssdna Genome Structures Penetrate
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.14.435335; this version posted March 14, 2021. 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 Primordial capsid and spooled ssDNA genome structures penetrate 2 ancestral events of eukaryotic viruses 3 4 Anna Munke1*#, Kei Kimura2, Yuji Tomaru3, Han Wang1, Kazuhiro Yoshida4, Seiya Mito5, Yuki 5 Hongo6, and Kenta Okamoto1* 6 1. The Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala 7 University, Uppsala, Sweden 8 2. Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan 9 3. Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Hatsukaichi, 10 Hiroshima, Japan 11 4. Graduate School of Agriculture, Saga University, Saga, Japan 12 5. Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan 13 6. Bioinformatics and Biosciences Division, Fisheries Resources Institute, Japan Fisheries Research 14 and Education Agency, Fukuura, Kanazawa, Yokohama, Kanagawa, Japan 15 16 17 *Corresponding authors 18 Corresponding author 1: [email protected] 19 Corresponding author 2: [email protected] 20 21 22 #Present address: Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 23 Hamburg 22607, Germany 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.14.435335; this version posted March 14, 2021. 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. 24 Abstract 25 Marine algae viruses are important for controlling microorganism communities in the marine 26 ecosystem, and played a fundamental role during the early events of viral evolution. -
Table of Contents
Table of Contents Verbal Presentations Verbal Presentations – Monday………………………………………………………...................... Page 2 Verbal Presentations – Tuesday……………………………………………………………………… Page 17 Verbal Presentations – Wednesday………………………………………………………..…….….. Page 32 Verbal Presentations – Thursday……………………….……………………………….………..…. Page 46 Poster Presentations Poster Presentations – Monday…………………………………………………………………..…. Page 52 Poster Presentations – Tuesday……………………………………………………………..……… Page 64 Poster Presentations – Wednesday……………………………………………………….……….. Page 77 Poster Presentations – Thursday……………………………………….………………….……….. Page 90 Page 1 of 99 Verbal Presentations Monday, May 15th 8:30 – 10 AM Grumman A Microsimulation Approach to Estimating Annual Risk in QMRA. Coping with Non-Random Variation in Risk Amongst Populations Paul Hunter, The Norwich Medical School, University of East Anglia Additional Author: James Maas Most QMRA studies have focused on refining the estimation of the daily risk comparatively little thought has been given to estimating the annual risk. As pointed out by Karavarsamis and Hamilton most studies have used a relatively simple method of estimating annual risk from the distribution of daily risks, namely 1-(1-Pd)^365 (1). This approach essentially assumes that the daily risk is constant through the year and Karavarsamis and Hamilton, with justification, refer to this approach as "Naϊve". Instead they propose a stochastic approach that essentially samples the distribution of daily risks and then calculates the annual risk as 1-the product of (1- 365 randomly sampled daily risk), calling this the "Gold Standard Approach". We argue that Karavarsamis and Hamilton's gold standard approach is also naϊve. Daily risks in any one individual are neither constant through a year nor are they entirely random. For example, across a population some people drink a lot of water each day and others drink very little. Other factors like the concentration of pathogen in a supply may vary much more randomly. -
Holding Hands with Bacteria the Life and Work of Marjory Stephenson
SPRINGER BRIEFS IN MOLECULAR SCIENCE HISTORY OF CHEMISTRY Soňa Štrbáňová Holding Hands with Bacteria The Life and Work of Marjory Stephenson 123 SpringerBriefs in Molecular Science History of Chemistry Series editor Seth C. Rasmussen, Fargo, North Dakota, USA More information about this series at http://www.springer.com/series/10127 Soňa Štrbáňová Holding Hands with Bacteria The Life and Work of Marjory Stephenson 1 3 Soňa Štrbáňová Academy of Sciences of the Czech Republic Prague Czech Republic ISSN 2191-5407 ISSN 2191-5415 (electronic) SpringerBriefs in Molecular Science ISSN 2212-991X SpringerBriefs in History of Chemistry ISBN 978-3-662-49734-0 ISBN 978-3-662-49736-4 (eBook) DOI 10.1007/978-3-662-49736-4 Library of Congress Control Number: 2016934952 © The Author(s) 2016 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. -
Structure of Sputnik, a Virophage, at 3.5-Å Resolution
Structure of Sputnik, a virophage, at 3.5-Å resolution Xinzheng Zhanga, Siyang Suna, Ye Xianga, Jimson Wonga, Thomas Klosea, Didier Raoultb, and Michael G. Rossmanna,1 aDepartment of Biological Sciences, Purdue University, West Lafayette, IN 47907; and bUnité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Unité Mixte de Recherche 6236 Centre National de la Recherche Scientifique, L’Institut de Recherche pour le Développement 198, Faculté de Médecine, Université de la Méditerranée, 13385 Marseille Cedex 5, France Edited by Nikolaus Grigorieff, Howard Hughes Medical Institute, Brandeis University, Waltham, MA, and accepted by the Editorial Board September 26, 2012 (received for review July 10, 2012) “Sputnik” is a dsDNA virus, referred to as a virophage, that is Chlorella virus 1 (PBCV-1) MCP (Vp54) fitted well into the 10.7- coassembled with Mimivirus in the host amoeba. We have used Å resolution cryo-EM density map of Sputnik (9). A mushroom- cryo-EM to produce an electron density map of the icosahedral like fiber was found associated with the center of each hexon, Sputnik virus at 3.5-Å resolution, sufficient to verify the identity although the icosahedrally averaged density suggested that the of most amino acids in the capsid proteins and to establish the fiber had only partial occupancy. The capsid protein appeared to identity of the pentameric protein forming the fivefold vertices. surround a membrane that enclosed the genome, consistent with It was also shown that the virus lacks an internal membrane. The the presence of lipid in the virus. capsid is organized into a T = 27 lattice in which there are 260 The capsid structure of numerous icosahedral viruses consists trimeric capsomers and 12 pentameric capsomers. -
Microbiology Society Activities
MICROBIOLOGY TODAY 48:1 May 2021 Microbiology Today 48:1 May 2021 Life on a Changing Planet Life on a Changing Planet Exploring the relationship between climate change and the microbial world Forest Fire in Dixie National Forest, Utah, USA. santirf/iStock which in turn increase the risk of COVID-19 complications. impact on respiratory health of affected communities. Curr Opin Pulm Wildfire smoke exposure might also increase the likelihood of Med 2019;25:179–187. comorbidities, including cardiovascular diseases, respiratory Wu X, Nethery RC, Sabath MB, Braun D, Dominici F. Air pollution and diseases, diabetes and hypertension, leading to an increased COVID-19 mortality in the United States: strengths and limitations of an ecological regression analysis. Sci Adv 2020;6:eabd4049. COVID-19 risk. Higher daily average PM2.5 concentrations during the wildfire season in western US states were positively Gosling SN, Bryce EK, Dixon PG, Gabriel KMA, Gosling EY et al. associated with increased influenza rates the following A glossary for biometeorology. Int J Biometeorol 2014;58:277–308. winter, indicating strong evidence for delayed effects of wildfire exposure. Research on understanding the underlying mechanisms between wildfire exposure and respiratory Rosa von Borries infection is an area of active investigation. Consultant at World Meteorological Organization, In particular, vulnerable population groups such as socio- Bernhard-Lichtenberg-Str 15, 10407 Berlin, economically disadvantaged populations, individuals with Germany comorbidities and the elderly face higher risks of experiencing [email protected] the combined consequences of COVID-19 and wildfires. @rosavborries In the US, migrant farmworkers who were continuously linkedin.com/in/rosa-von-borries-5b4987197 exposed to wildfire smoke and deemed essential workers during the pandemic faced much higher risks of severe Rosa von Borries holds an MSc in Public Health from London School health consequences from wildfire smoke and COVID-19. -
82033571.Pdf
CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Cell, Vol. 120, 761–772, March 25, 2005, Copyright ©2005 by Elsevier Inc. DOI 10.1016/j.cell.2005.01.009 The Birnavirus Crystal Structure Reveals Structural Relationships among Icosahedral Viruses Fasséli Coulibaly,1 Christophe Chevalier,2 sified in two major categories according to their ge- Irina Gutsche,1 Joan Pous,1 Jorge Navaza,1 nome type: +sRNA and dsRNA. Among +sRNA eukary- Stéphane Bressanelli,1 Bernard Delmas,2,* otic viruses, the building block of the capsid—the “coat and Félix A. Rey1,* protein”—exhibits a special fold, the “jelly roll” β barrel 1Laboratoire de Virologie Moléculaire et Structurale (Rossmann and Johnson, 1989). This protein forms a UMR 2472/1157 CNRS-INRA and IFR 115 tightly closed protein shell protecting the viral RNA, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex with the jelly roll β barrel oriented such that the β 2 Unité de Virologie et Immunologie Moléculaires strands run tangentially to the particle surface. Except INRA for the very small satellite +sRNA viruses—in which the Domaine de Vilvert, 78350 Jouy-en-Josas capsid contains only 60 copies of the coat protein— France most virus capsids contain 60 copies of a multimer (Harrison, 2001b), organized in an icosahedral surface lattice following the rules of quasiequivalence (Caspar Summary and Klug, 1962). Such an arrangement leads to al- ternating 5-fold (I5 for “icosahedral 5-fold”) and quasi- Double-stranded RNA virions are transcriptionally 6-fold (Q6) contacts among coat proteins, distributed competent icosahedral particles that must translo- according to the triangulation of the surface lattice cate across a lipid bilayer to function within the cyto- (Johnson and Speir, 1997). -
The Foot-And-Mouth Disease Virus Replication Complex
The Foot-and-Mouth Disease Virus Replication Complex: Dissecting the Role of the Viral Polymerase (3Dpol) and Investigating Interactions with Phosphatidylinositol-4-kinase (PI4K) Eleni-Anna Loundras Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds School of Molecular and Cellular Biology August 2017 The candidate confirms that the work submitted is her own, except where work which has formed part of jointly authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly indicated below. The candidate confirms that appropriate credit has been given within the thesis where reference has been made to the work of others. The work appearing in Chapter 3 and Chapter 4 of the thesis has appeared in publications as follow: • Employing transposon mutagenesis in investigate foot-and-mouth disease virus replication. Journal of Virology (2015), 96 (12), pp 3507-3518., DOI: 10.1099/jgv.0.000306. Morgan R. Herod (MRH), Eleni-Anna Loundras (EAL), Joseph C. Ward, Fiona Tulloch, David J. Rowlands (DJR), Nicola J. Stonehouse (NJS). The author (EAL) was responsible for assisting with preparation of experiments and production of experimental data. MRH, as primary author drafted the manuscript and designed the experiments. NJS and DJR conceived the idea, supervised the project, and edited the manuscript. • Both cis and trans activities of foot-and-mouth disease virus 3D polymerase are essential for viral replication. Journal of Virology (2016), 90 (15), pp 6864-688., DOI: 10.1128/JVI.00469-16. Morgan R. Herod, Cristina Ferrer-Orta, Eleni-Anna Loundras, Joseph C. -
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F r-nierobiologytodcly i W; vol33i oug06 ,: qumrter{y rn{-}#r.}rin*nf thw s**:imty f'*r 6*[":*l"C*l rnicrr:hl*i*E5r I f vcl33(3) [*j'l-l l.-ili:i i" t'.ir'iliL.i i{:}li 90 News 128 Cradline 134 Reviews 122 Meetings 130 Hotoff the press 139 Addresses 124 Schoolzone132 Coingpublic it'l i:)'i-:il;I i i i::ji-i-l:; 117 Usingmicroscopy to enhanceundergraduate teaching 127 Letter 136 obituaries i:l l'Tl{,-li:}S 96 Fluorescencemicroscopy Canyou seethe asa researchtool in bacterial light? cellbiology lain Hagan , AgnesCrallert & Jeff Errington SteveBagley The revolution of new views of the subcellularorganization Simpleand affordable steps to exploitrecent of bacteria. advancesin ffuorescenceimaging. 100 |nvestigating a bacterial killer usingatomic force microscopy 118 HenryBaker: author of the MeganNufiez & EileenSpain first m icroscopy labo ratory Learnabout the secretlife of the predatorykiller, Bdellovibrio. manual Virusesand intracellular RichardBurns This18th century polymath played a big partin popularizing movement earlymicroscopes. TomWileman How do virusesmanaSe to move within and between the cellsof their host? Comment - Openoption for SCM 108 Studyingsingle molecules in journals microbialsystems RonFraser & RobinDunford ChristophBaumann Openaccess demands by grant-awardingbodies Individualmolecules in livingcells can now be observed. arecausing problems for publishers. {ovr:r inoge Microscopelenses. Tony Craddock / SciencePhoto Library Theviews expressed fditr.rrDrCavinThomas[lcii|*riili{l*"lrdDr5ueAssinder'Professor|ainHagan,ProfessorBertRlma -
70Th Anniversary Collection of the Microbiology Society: Journal of General Virology Robin A
Journal of General Virology (2015), 00, 1–3 DOI 10.1099/jgv.0.000286 Commentary 70th Anniversary Collection of the Microbiology Society: Journal of General Virology Robin A. Weiss Correspondence Division of Infection & Immunity, University College London, London WC1E 6BT, UK Robin A. Weiss [email protected] To mark the 70th anniversary of the founding of the Society From its inception, the Journal of General Virology took for General Microbiology (now renamed the Microbiology papers on the structure and design of virus particles, Society) it was decided to showcase 70 salient publications such as human adenovirus type 5. In a superb biochemical from the archives of its various journals. The Journal of Gen- and structural analysis comprising three consecutive eral Virology was allocated 15 papers. I was invited to curate papers, the second paper by Russell et al. (1967) showed them and given a carte blanche which ones to choose. True that when heated to 56 8C, the icosahedral capsid ruptured to the name of the journal, I picked a broad range of viruses at the penton bases and liberated viral DNA. They also cor- and a paper on prion disease. If readers are disappointed not rectly predicted that unknown nucleocore proteins exist to see their own most cherished contribution featured that in later years became important for understanding among them, please consider the odds: only 15 from over cell transformation and early steps in virus replication. 15 000 Journal of General Virology articles could be selected The only paper among the 15 selected that does not present and I gave more weight to older papers to recall contri- primary research data is the commentary on virus diversity butions by the pioneers of virology. -
Microbiologytoday Biology and Pathogenesis Current Technology and Author: Naveed Khan Molecular Biology Applications
Caister Academic Press New Books for 2009 www.caister.com Acanthamoeba Lactobacillus Real-Time PCR microbiologytoday Biology and Pathogenesis Current Technology and Author: Naveed Khan Molecular Biology Applications ... available now! c. 220 pp., February 2009 From Genomics to Probiotics Edited by: J. Logan, K. Edwards and N. Saunders ISBN: 978-1-904455-43-1 $310 / £150 Edited by: Åsa Ljungh and Torkel Wadström x + 284 pp., January 2009 The first comprehensive review of c. 220 pp., January 2009 ISBN 978-1-904455-39-4 $310 / £150 Acanthamoeba research to be published. ISBN 978-1-904455-41-7 $310 / £150 A comprehensive guide to the latest PCR The current state of research on every aspect An essential reference for all dairy of this organism, detailing major advances platforms, fluorescent chemistries, validation technologists, microbiologists and in areas such as genomics, molecular and software, data analysis, internal and external cellular biology, life cycles, geographical biotechnologists. Includes phylogenetics, controls and a wide range of applications: distribution, role in ecosystem, morphology, taxonomy, comparative genomics, functional clinical diagnostics, biodefense, RNA vol35|nov08 genomics, the intestinal microflora, surface motility, phylogenetics, genotyping, metabolism, expression studies, validation of array data, quarterly regulation of morphogenesis, host-parasite proteins, stress responses, interaction with mutation detection, food authenticity and interactions, the molecular and immunological the immune system, probiotics, anti-cancer legislation, NASBA, and molecular halotyping. basis of pathogenesis, methods of transmission, potential, and much more. Essential reading for magazine of epidemiology, clinical manifestation, diagnosis, all scientists involved with lactic acid bacteria treatment, new target development and drug or probiotic research and a recommended book the society resistance.