Discovery of Viroids
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Chapitre Quatre La Spécificité D'hôtes Des Virophages Sputnik
AIX-MARSEILLE UNIVERSITE FACULTE DE MEDECINE DE MARSEILLE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTE THESE DE DOCTORAT Présentée par Morgan GAÏA Né le 24 Octobre 1987 à Aubagne, France Pour obtenir le grade de DOCTEUR de l’UNIVERSITE AIX -MARSEILLE SPECIALITE : Pathologie Humaine, Maladies Infectieuses Les virophages de Mimiviridae The Mimiviridae virophages Présentée et publiquement soutenue devant la FACULTE DE MEDECINE de MARSEILLE le 10 décembre 2013 Membres du jury de la thèse : Pr. Bernard La Scola Directeur de thèse Pr. Jean -Marc Rolain Président du jury Pr. Bruno Pozzetto Rapporteur Dr. Hervé Lecoq Rapporteur Faculté de Médecine, 13385 Marseille Cedex 05, France URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Directeur : Pr. Didier RAOULT Avant-propos Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe permettant un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail. -
Grapevine Virus Diseases: Economic Impact and Current Advances in Viral Prospection and Management1
1/22 ISSN 0100-2945 http://dx.doi.org/10.1590/0100-29452017411 GRAPEVINE VIRUS DISEASES: ECONOMIC IMPACT AND CURRENT ADVANCES IN VIRAL PROSPECTION AND MANAGEMENT1 MARCOS FERNANDO BASSO2, THOR VINÍCIUS MArtins FAJARDO3, PASQUALE SALDARELLI4 ABSTRACT-Grapevine (Vitis spp.) is a major vegetative propagated fruit crop with high socioeconomic importance worldwide. It is susceptible to several graft-transmitted agents that cause several diseases and substantial crop losses, reducing fruit quality and plant vigor, and shorten the longevity of vines. The vegetative propagation and frequent exchanges of propagative material among countries contribute to spread these pathogens, favoring the emergence of complex diseases. Its perennial life cycle further accelerates the mixing and introduction of several viral agents into a single plant. Currently, approximately 65 viruses belonging to different families have been reported infecting grapevines, but not all cause economically relevant diseases. The grapevine leafroll, rugose wood complex, leaf degeneration and fleck diseases are the four main disorders having worldwide economic importance. In addition, new viral species and strains have been identified and associated with economically important constraints to grape production. In Brazilian vineyards, eighteen viruses, three viroids and two virus-like diseases had already their occurrence reported and were molecularly characterized. Here, we review the current knowledge of these viruses, report advances in their diagnosis and prospection of new species, and give indications about the management of the associated grapevine diseases. Index terms: Vegetative propagation, plant viruses, crop losses, berry quality, next-generation sequencing. VIROSES EM VIDEIRAS: IMPACTO ECONÔMICO E RECENTES AVANÇOS NA PROSPECÇÃO DE VÍRUS E MANEJO DAS DOENÇAS DE ORIGEM VIRAL RESUMO-A videira (Vitis spp.) é propagada vegetativamente e considerada uma das principais culturas frutíferas por sua importância socioeconômica mundial. -
Alpha-Satellite RNA Transcripts Are Repressed by Centromere
RESEARCH ARTICLE Alpha-satellite RNA transcripts are repressed by centromere–nucleolus associations Leah Bury1†, Brittania Moodie1†, Jimmy Ly1,2, Liliana S McKay1, Karen HH Miga3, Iain M Cheeseman1,2* 1Whitehead Institute for Biomedical Research, Cambridge, United States; 2Department of Biology, Massachusetts Institute of Technology, Cambridge, United States; 3UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, United States Abstract Although originally thought to be silent chromosomal regions, centromeres are instead actively transcribed. However, the behavior and contributions of centromere-derived RNAs have remained unclear. Here, we used single-molecule fluorescence in-situ hybridization (smFISH) to detect alpha-satellite RNA transcripts in intact human cells. We find that alpha-satellite RNA- smFISH foci levels vary across cell lines and over the cell cycle, but do not remain associated with centromeres, displaying localization consistent with other long non-coding RNAs. Alpha-satellite expression occurs through RNA polymerase II-dependent transcription, but does not require established centromere or cell division components. Instead, our work implicates centromere– nucleolar interactions as repressing alpha-satellite expression. The fraction of nucleolar-localized centromeres inversely correlates with alpha-satellite transcripts levels across cell lines and transcript levels increase substantially when the nucleolus is disrupted. The control of alpha-satellite transcripts by centromere-nucleolar contacts provides a mechanism to modulate centromere transcription and chromatin dynamics across diverse cell states and conditions. *For correspondence: [email protected] †These authors contributed equally to this work Introduction Chromosome segregation requires the function of a macromolecular kinetochore structure to con- Competing interests: The nect chromosomal DNA and spindle microtubule polymers. -
The Variability of Hop Latent Viroid As Induced Upon Heat Treatment
Virology 287, 349–358 (2001) doi:10.1006/viro.2001.1044, available online at http://www.idealibrary.com on View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector The Variability of Hop Latent Viroid as Induced upon Heat Treatment Jaroslav Matousˇek,* Josef Patzak,† Lidmila Orctova´,* Jo¨rg Schubert,‡ Luka´sˇ Vrba,* Gerhard Steger,§ and Detlev Riesner§,1 *Department of Molecular Genetics, Institute of Plant Molecular Biology Czech Academy of Sciences, Branisˇovska´31, 37005 Cˇ eske´Bude˘jovice, Czech Republic; †Department of Virology, Institute of Hop Research and Breeding, Kadanˇska´2525, 438 46 Zˇatec, Czech Republic; ‡Federal Centre for Breeding Research, Institute for Resistance Research and Pathogen Diagnostics, Theodor-Roemer-Weg 4, 06449 Aschersleben, Germany; and §Institute of Physical Biology, Heinrich-Heine Universita¨t Du¨sseldorf, Universita¨tsstraße 1, D-40225 Du¨sseldorf, Germany Received March 28, 2001; returned to author for revision March 30, 2001; accepted June 11, 2001; published online August 2, 2001 We have previously shown that heat treatment of hop plants infected by hop latent viroid (HLVd) reduces viroid levels. Here we investigate whether such heat treatment leads to the accumulation of sequence variability in HLVd. We observed a negligible level of mutated variants in HLVd under standard cultivation conditions. In contrast, the heat treatment of hop led to HLVd degradation and, simultaneously, to a significant increase in sequence variations, as judged from temperature gradient–gel electrophoresis analysis and cDNA library screening by DNA heteroduplex analysis. Thirty-one cDNA clones (9.8%) were identified as deviating forms. -
The Expression of Human Endogenous Retroviruses Is Modulated by the Tat Protein of HIV‐1
The Expression of Human Endogenous Retroviruses is modulated by the Tat protein of HIV‐1 by Marta Jeannette Gonzalez‐Hernandez A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Immunology) in The University of Michigan 2012 Doctoral Committee Professor David M. Markovitz, Chair Professor Gary Huffnagle Professor Michael J. Imperiale Associate Professor David J. Miller Assistant Professor Akira Ono Assistant Professor Christiane E. Wobus © Marta Jeannette Gonzalez‐Hernandez 2012 For my family and friends, the most fantastic teachers I have ever had. ii Acknowledgements First, and foremost, I would like to thank David Markovitz for his patience and his scientific and mentoring endeavor. My time in the laboratory has been an honor and a pleasure. Special thanks are also due to all the members of the Markovitz laboratory, past and present. It has been a privilege, and a lot of fun, to work near such excellent scientists and friends. You all have a special place in my heart. I would like to thank all the members of my thesis committee for all the valuable advice, help and jokes whenever needed. Our collaborators from the Bioinformatics Core, particularly James Cavalcoli, Fan Meng, Manhong Dai, Maureen Sartor and Gil Omenn gave generous support, technical expertise and scientific insight to a very important part of this project. Thank you. Thanks also go to Mariana Kaplan’s and Akira Ono’s laboratory for help with experimental designs and for being especially generous with time and reagents. iii Table of Contents Dedication ............................................................................................................................ ii Acknowledgements ............................................................................................................. iii List of Figures ................................................................................................................... -
Replication-Defective Chimeric Helper Proviruses and Factors Affecting Generation of Competent Virus
MOLECULAR AND CELLULAR BIOLOGY, May 1987, p. 1797-1806 Vol. 7, No. 5 0270-7306/87/051797-10$02.00/0 Copyright © 1987, American Society for Microbiology Replication-Defective Chimeric Helper Proviruses and Factors Affecting Generation of Competent Virus: Expression of Moloney Murine Leukemia Virus Structural Genes via the Metallothionein Promoter ROBERT A. BOSSELMAN,* ROU-YIN HSU, JOAN BRUSZEWSKI, SYLVIA HU, FRANK MARTIN, AND MARGERY NICOLSON Amgen, Thousand Oaks, California 91320 Received 15 October 1986/Accepted 28 January 1987 Two chimeric helper proviruses were derived from the provirus of the ecotropic Moloney murine leukemia virus by replacing the 5' long terminal repeat and adjacent proviral sequences with the mouse metallothionein I promoter. One of these chimeric proviruses was designed to express the gag-pol genes of the virus, whereas the other was designed to express only the env gene. When transfected into NIH 3T3 cells, these helper proviruses failed to generate competent virus but did express Zn2 -inducible trans-acting viral functions needed to assemble infectious vectors. One helper cell line (clone 32) supported vector assembly at levels comparable to those supported by the Psi-2 and PA317 cell lines transfected with the same vector. Defective proviruses which carry the neomycin phosphotransferase gene and which lack overlapping sequence homology with the 5' end of the chimeric helper proviruses could be transfected into the helper cell line without generation of replication-competent virus. Mass cultures of transfected helper cells produced titers of about 104 G418r CFU/ml, whereas individual clones produced titers between 0 and 2.6 x 104 CFU/ml. -
Characteristics of Virophages and Giant Viruses Beata Tokarz-Deptuła1*, Paulina Czupryńska2, Agata Poniewierska-Baran1 and Wiesław Deptuła2
Vol. 65, No 4/2018 487–496 https://doi.org/10.18388/abp.2018_2631 Review Characteristics of virophages and giant viruses Beata Tokarz-Deptuła1*, Paulina Czupryńska2, Agata Poniewierska-Baran1 and Wiesław Deptuła2 1Department of Immunology, 2Department of Microbiology, Faculty of Biology, University of Szczecin, Szczecin, Poland Five years after being discovered in 2003, some giant genus, Mimiviridae family (Table 3). It was found in the viruses were demonstrated to play a role of the hosts protozoan A. polyphaga in a water-cooling tower in Brad- for virophages, their parasites, setting out a novel and ford (Table 1). Sputnik has a spherical dsDNA genome yet unknown regulatory mechanism of the giant virus- closed in a capsid with icosahedral symmetry, 50–74 nm es presence in an aqueous. So far, 20 virophages have in size, inside which there is a lipid membrane made of been registered and 13 of them have been described as phosphatidylserine, which probably protects the genetic a metagenomic material, which indirectly impacts the material of the virophage (Claverie et al., 2009; Desnues number of single- and multi-cell organisms, the environ- et al., 2012). Sputnik’s genome has 18343 base pairs with ment where giant viruses replicate. 21 ORFs that encode proteins of 88 to 779 amino ac- ids. They compose the capsids and are responsible for Key words: virophages, giant viruses, MIMIVIRE, Sputnik N-terminal acetylation of amino acids and transposases Received: 14 June, 2018; revised: 21 August, 2018; accepted: (Claverie et al., 2009; Desnues et al., 2012; Tokarz-Dep- 09 September, 2018; available on-line: 23 October, 2018 tula et al., 2015). -
Hops – a Guide for New Growers 2017
Hops – a guide for new growers 2017 growers new – a guide for Hops Hops a guide for new growers FIRST EDITION 2017 first edition 2017 Author: Kevin Dodds www.dpi.nsw.gov.au Hops a guide for new growers Kevin Dodds Development Officer – Temperate Fruits NSW Department of Primary industries ©NSW Department of Primary Industries 2017 Published by NSW Department of Primary Industries, a part of NSW Department of Industry, Skills and Regional Development You may copy, distribute, display, download and otherwise freely deal with this publication for any purpose, provided that you attribute NSW Department of Industry, Skills and Regional Development as the owner. However, you must obtain permission if you wish to charge others for access to the publication (other than at cost); include the publication advertising or a product for sale; modify the publication; or republish the publication on a website. You may freely link to the publication on a departmental website. First published March 2017 ISBN print: 978‑1‑76058‑007‑0 web: 978‑1‑76058‑008‑7 Always read the label Users of agricultural chemical products must always read the Job number 14293 label and any permit before using the product and strictly comply with the directions on the label and the conditions of Author any permit. Users are not absolved from any compliance with Kevin Dodds, Development Officer Temperate Fruits the directions on the label or the conditions of the permit NSW Department of Primary Industries by reason of any statement made or omitted to be made in 64 Fitzroy Street TUMUT NSW 2720 this publication. -
Virus, Viroids and Mycoplasma
By: Dr. Bibha Kumari Dept. of Zoology Magadh Mahila College, Patna Email: [email protected] Virus •The viruses are non-cellular organisms. • They, in fact, have an inert crystalline structure outside the living cell. • Once they infect a cell, they take over the machinery of the host cell to replicate themselves, killing the host. •Pasteur. D.J. Ivanowsky (1892) gave the name virus. • It means venom or poisonous fluid. • According to his research, certain microbes caused the mosaic disease of tobacco. •These organisms were smaller than bacteria because they passed through bacteria-proof filters. • M.W. Beijerinek (1898) demonstrated that the extract of the infected plants of tobacco could cause infection in healthy plants. • He named the fluid as Contagium vivum fluidum (infectious living fluid). •W.M. Stanley (1935) discovered that viruses could be crystallized. These virus crystals are composed largely of proteins. •They are inert outside their specific host cell. Viruses are nothing but obligate parasites. Genetic Material of Viruses: •In addition to proteins, viruses also contain genetic material, that could be either RNA or DNA. • No virus contains both RNA and DNA. A virus is a nucleoprotein and the genetic material is infectious. •Speaking in strictly general terms, viruses infecting plants have single- stranded RNA. • On the other hand, viruses that infect animals have either single or double-stranded RNA or they might have double-stranded DNA •Bacterial viruses or bacteriophages usually have a double-stranded DNA structure. By bacteriophages, we mean viruses that infect the bacteria. • The protein coat, capsid made of small subunits (capsomeres) protects the nucleic acid. -
Viral Envelope Are Controlled by the Helper Virus Used to Activate The
DETERMINING FACTOR IN THE CAPACITY OF ROUS SARCOMA VIRUS TO INDUCE TUMORS IN MAMMALS* By HIDESABURO HANAFUSA AND TERUKO HANAFUSA COLLMGE DE FRANCE, LABORATOIRE DE MIDECINE EXPARIMENTALE, PARIS Communidated by Ahdre Lwoff, January 24, 1966 Since Zilber and Kriukoval and Svet-Moldavsky' demonstrated that some strains of Rous sarcoma virus (RSV) are capable of inducing hemorrhagic cysts or sarcomas in newborn rats, numerous attempts have been made to induce tumors by RSVin various species of mammals.3-9 One of the remarkable aspects revealed by these investigations is the strain differences in RSV for this capacity.6-9 Certain strains, such as the Schmidt-Ruppin strain, are active, while others, such as the Bryan strain, are generally inactive in mammals. The cause of such strain differ- ences has not been elucidated. Our previous studies have shown that the Bryan high-titer strain of RSV is a defective virus which cannot reproduce without the help of any one of the avian leukosis viruses.'0 The defectiveness derives from the inability of this strain of RSV to induce the synthesis of its own viral envelope."I An essential role played by the helper virus is to provide the envelope to the RSV genome, whose replica- tion occurs in the infected cells without the aid of helper virus. Thus, several properties of RSV which presumably depend in some way on the character of the viral envelope are controlled by the helper virus used to activate the RSV.11-13 These properties include the antigenicity, the sensitivity to the interference induced by the helper virus, and the host range among genetically different chick embryos. -
Satellite RNA-Mediated Resistance to Turnip Crinkle Virus in Arabidopsis Lnvolves a Reduction in Virus Movement
The Plant Cell, Vol. 9, 2051-2063, November 1997 O 1997 American Society of Plant Physiologists Satellite RNA-Mediated Resistance to Turnip Crinkle Virus in Arabidopsis lnvolves a Reduction in Virus Movement Qingzhong Kong, Jianlong Wang, and Anne E. Simon’ Department of Biochemistry and Molecular Biology and Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts O1 003-4505 Satellite RNAs (sat-RNAs) are parasites of viruses that can mediate resistance to the helper virus. We previously showed that a sat-RNA (sat-RNA C) of turnip crinkle virus (TCV), which normally intensifies symptoms of TCV, is able to attenuate symptoms when TCV contains the coat protein (CP) of cardamine chlorotic fleck virus (TCV-CPccw).We have now determined that sat-RNA C also attenuates symptoms of TCV containing an alteration in the initiating AUG of the CP open reading frame (TCV-CPm). TCV-CPm, which is able to move systemically in both the TCV-susceptible ecotype Columbia (Col-O) and the TCV-resistant ecotype Dijon (Di-O), produced a reduced level of CP and no detectable virions in infected plants. Sat-RNA C reduced the accumulation of TCV-CPm by <25% in protoplasts while reducing the level of TCV-CPm by 90 to 100% in uninoculated leaves of COLO and Di-O. Our results suggest that in the presence of a re- duced level of a possibly altered CP, sat-RNA C reduces virus long-distance movement in a manner that is independent of the salicylic acid-dependent defense pathway. INTRODUCTION Plants exhibit different types of resistance to plant viruses, on virus association for replication and spread in plants. -
Hammerhead Ribozymes Against Virus and Viroid Rnas
Hammerhead Ribozymes Against Virus and Viroid RNAs Alberto Carbonell, Ricardo Flores, and Selma Gago Contents 1 A Historical Overview: Hammerhead Ribozymes in Their Natural Context ................................................................... 412 2 Manipulating Cis-Acting Hammerheads to Act in Trans ................................. 414 3 A Critical Issue: Colocalization of Ribozyme and Substrate . .. .. ... .. .. .. .. .. ... .. .. .. .. 416 4 An Unanticipated Participant: Interactions Between Peripheral Loops of Natural Hammerheads Greatly Increase Their Self-Cleavage Activity ........................... 417 5 A New Generation of Trans-Acting Hammerheads Operating In Vitro and In Vivo at Physiological Concentrations of Magnesium . ...... 419 6 Trans-Cleavage In Vitro of Short RNA Substrates by Discontinuous and Extended Hammerheads ........................................... 420 7 Trans-Cleavage In Vitro of a Highly Structured RNA by Discontinuous and Extended Hammerheads ........................................... 421 8 Trans-Cleavage In Vivo of a Viroid RNA by an Extended PLMVd-Derived Hammerhead ........................................... 422 9 Concluding Remarks and Outlooks ........................................................ 424 References ....................................................................................... 425 Abstract The hammerhead ribozyme, a small catalytic motif that promotes self- cleavage of the RNAs in which it is found naturally embedded, can be manipulated to recognize and cleave specifically