Virus Detection in Banana a Laboratory Manual
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Elisabeth Mendes Martins De Moura Diversidade De Vírus DNA
Elisabeth Mendes Martins de Moura Diversidade de vírus DNA autóctones e alóctones de mananciais e de esgoto da região metropolitana de São Paulo Tese apresentada ao Programa de Pós- Graduação em Microbiologia do Instituto de Ciências Biomédicas da Universidade de São Paulo, para obtenção do Titulo de Doutor em Ciências. Área de concentração: Microbiologia Orienta: Prof (a). Dr (a). Dolores Ursula Mehnert versão original São Paulo 2017 RESUMO MOURA, E. M. M. Diversidade de vírus DNA autóctones e alóctones de mananciais e de esgoto da região metropolitana de São Paulo. 2017. 134f. Tese (Doutorado em Microbiologia) - Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, 2017. A água doce no Brasil, assim como o seu consumo é extremamente importante para as diversas atividades criadas pelo ser humano. Por esta razão o consumo deste bem é muito grande e consequentemente, provocando o seu impacto. Os mananciais são normalmente usados para abastecimento doméstico, comercial, industrial e outros fins. Os estudos na área de ecologia de micro-organismos nos ecossistemas aquáticos (mananciais) e em esgotos vêm sendo realizados com mais intensidade nos últimos anos. Nas últimas décadas foi introduzido o conceito de virioplâncton com base na abundância e diversidade de partículas virais presentes no ambiente aquático. O virioplâncton influencia muitos processos ecológicos e biogeoquímicos, como ciclagem de nutriente, taxa de sedimentação de partículas, diversidade e distribuição de espécies de algas e bactérias, controle de florações de fitoplâncton e transferência genética horizontal. Os estudos nesta área da virologia molecular ainda estão muito restritos no país, bem como muito pouco se conhece sobre a diversidade viral na água no Brasil. -
Changes to Virus Taxonomy 2004
Arch Virol (2005) 150: 189–198 DOI 10.1007/s00705-004-0429-1 Changes to virus taxonomy 2004 M. A. Mayo (ICTV Secretary) Scottish Crop Research Institute, Invergowrie, Dundee, U.K. Received July 30, 2004; accepted September 25, 2004 Published online November 10, 2004 c Springer-Verlag 2004 This note presents a compilation of recent changes to virus taxonomy decided by voting by the ICTV membership following recommendations from the ICTV Executive Committee. The changes are presented in the Table as decisions promoted by the Subcommittees of the EC and are grouped according to the major hosts of the viruses involved. These new taxa will be presented in more detail in the 8th ICTV Report scheduled to be published near the end of 2004 (Fauquet et al., 2004). Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (eds) (2004). Virus Taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp. 1258. Recent changes to virus taxonomy Viruses of vertebrates Family Arenaviridae • Designate Cupixi virus as a species in the genus Arenavirus • Designate Bear Canyon virus as a species in the genus Arenavirus • Designate Allpahuayo virus as a species in the genus Arenavirus Family Birnaviridae • Assign Blotched snakehead virus as an unassigned species in family Birnaviridae Family Circoviridae • Create a new genus (Anellovirus) with Torque teno virus as type species Family Coronaviridae • Recognize a new species Severe acute respiratory syndrome coronavirus in the genus Coro- navirus, family Coronaviridae, order Nidovirales -
A Novel Species of RNA Virus Associated with Root Lesion Nematode Pratylenchus Penetrans
SHORT COMMUNICATION Vieira and Nemchinov, Journal of General Virology 2019;100:704–708 DOI 10.1099/jgv.0.001246 A novel species of RNA virus associated with root lesion nematode Pratylenchus penetrans Paulo Vieira1,2 and Lev G. Nemchinov1,* Abstract The root lesion nematode Pratylenchus penetrans is a migratory species that attacks a broad range of plants. While analysing transcriptomic datasets of P. penetrans, we have identified a full-length genome of an unknown positive-sense single- stranded RNA virus, provisionally named root lesion nematode virus 1 (RLNV1). The 8614-nucleotide genome sequence encodes a single large polyprotein with conserved domains characteristic for the families Picornaviridae, Iflaviridae and Secoviridae of the order Picornavirales. Phylogenetic, BLAST and domain search analyses showed that RLNV1 is a novel species, most closely related to the recently identified sugar beet cyst nematode virus 1 and potato cyst nematode picorna- like virus. In situ hybridization with a DIG-labelled DNA probe confirmed the presence of the virus within the nematodes. A negative-strand-specific RT-PCR assay detected RLNV1 RNA in nematode total RNA samples, thus indicating that viral replication occurs in P. penetrans. To the best of our knowledge, RLNV1 is the first virus identified in Pratylenchus spp. In recent years, several new viruses infecting plant-parasitic assembly from high-throughput sequence data was supple- nematodes have been described [1–5]. Thus far, the viruses mented by sequencing of the 5¢ RACE-amplified cDNA have been identified in sedentary nematode species, such as ends of the virus. 5¢RACE reactions were performed with the soybean cyst nematode (SCN; Heterodera glycines), two the virus-specific primers GSP1, GSP2 and LN715 potato cyst nematode (PCN) species, Globodera pallida and (Table S1, available in the online version of this article) in G. -
Comparison of Plant‐Adapted Rhabdovirus Protein Localization and Interactions
University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2011 COMPARISON OF PLANT‐ADAPTED RHABDOVIRUS PROTEIN LOCALIZATION AND INTERACTIONS Kathleen Marie Martin University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Martin, Kathleen Marie, "COMPARISON OF PLANT‐ADAPTED RHABDOVIRUS PROTEIN LOCALIZATION AND INTERACTIONS" (2011). University of Kentucky Doctoral Dissertations. 172. https://uknowledge.uky.edu/gradschool_diss/172 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Kathleen Marie Martin The Graduate School University of Kentucky 2011 COMPARISON OF PLANT‐ADAPTED RHABDOVIRUS PROTEIN LOCALIZATION AND INTERACTIONS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Kathleen Marie Martin Lexington, Kentucky Director: Dr. Michael M Goodin, Associate Professor of Plant Pathology Lexington, Kentucky 2011 Copyright © Kathleen Marie Martin 2011 ABSTRACT OF DISSERTATION COMPARISON OF PLANT‐ADAPTED RHABDOVIRUS PROTEIN LOCALIZATION AND INTERACTIONS Sonchus yellow net virus (SYNV), Potato yellow dwarf virus (PYDV) and Lettuce Necrotic yellows virus (LNYV) are members of the Rhabdoviridae family that infect plants. SYNV and PYDV are Nucleorhabdoviruses that replicate in the nuclei of infected cells and LNYV is a Cytorhabdovirus that replicates in the cytoplasm. LNYV and SYNV share a similar genome organization with a gene order of Nucleoprotein (N), Phosphoprotein (P), putative movement protein (Mv), Matrix protein (M), Glycoprotein (G) and Polymerase protein (L). -
Diversity of Plant Virus Movement Proteins: What Do They Have in Common?
processes Review Diversity of Plant Virus Movement Proteins: What Do They Have in Common? Yuri L. Dorokhov 1,2,* , Ekaterina V. Sheshukova 1, Tatiana E. Byalik 3 and Tatiana V. Komarova 1,2 1 Vavilov Institute of General Genetics Russian Academy of Sciences, 119991 Moscow, Russia; [email protected] (E.V.S.); [email protected] (T.V.K.) 2 Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia 3 Department of Oncology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia; [email protected] * Correspondence: [email protected] Received: 11 November 2020; Accepted: 24 November 2020; Published: 26 November 2020 Abstract: The modern view of the mechanism of intercellular movement of viruses is based largely on data from the study of the tobacco mosaic virus (TMV) 30-kDa movement protein (MP). The discovered properties and abilities of TMV MP, namely, (a) in vitro binding of single-stranded RNA in a non-sequence-specific manner, (b) participation in the intracellular trafficking of genomic RNA to the plasmodesmata (Pd), and (c) localization in Pd and enhancement of Pd permeability, have been used as a reference in the search and analysis of candidate proteins from other plant viruses. Nevertheless, although almost four decades have passed since the introduction of the term “movement protein” into scientific circulation, the mechanism underlying its function remains unclear. It is unclear why, despite the absence of homology, different MPs are able to functionally replace each other in trans-complementation tests. Here, we consider the complexity and contradictions of the approaches for assessment of the ability of plant viral proteins to perform their movement function. -
Characterization and Genome Organization of New Luteoviruses and Nanoviruses Infecting Cool Season Food Legumes
Adane Abraham (Autor) Characterization and Genome Organization of New Luteoviruses and Nanoviruses Infecting Cool Season Food Legumes https://cuvillier.de/de/shop/publications/2549 Copyright: Cuvillier Verlag, Inhaberin Annette Jentzsch-Cuvillier, Nonnenstieg 8, 37075 Göttingen, Germany Telefon: +49 (0)551 54724-0, E-Mail: [email protected], Website: https://cuvillier.de CHAPTER 1 General Introduction Viruses and virus diseases of cool season food legumes Legume crops play a major role worldwide as source of human food, feed and also in crop rotation. Faba bean (Vicia faba L.), field pea (Pisum sativum L.), lentil (Lens culinaris Medik.), chickpea (Cicer arietinum L.), and grasspea (Lathyrus sativus L.), collectively re- ferred to as cool season food legumes (Summerfield et al. 1988) are of particular importance in developing countries of Asia, North and Northeast Africa where they provide a cheap source of seed protein for the predominantly poor population. Diseases including those caused by viruses are among the main constraints reducing their yield. Bos et al. (1988) listed some 44 viruses as naturally infecting faba bean, chickpea, field pea and lentil worldwide. Since then, a number of new viruses were described from these crops including Faba bean necrotic yellows virus (FBNYV) (Katul et al. 1993) and Chickpea chlorotic dwarf virus (CpCDV) (Horn et al. 1993), which are widespread and economically important. Most of the viruses of cool season food legumes are known to naturally infect more than one host within this group of crops (Bos et al. 1988, Brunt et al. 1996 and Makkouk et al. 2003a). Virus symptoms in cool season food legumes vary depending on the virus or its strain, host species or cultivar and the prevailing environmental conditions. -
Characterization of P1 Leader Proteases of the Potyviridae Family
Characterization of P1 leader proteases of the Potyviridae family and identification of the host factors involved in their proteolytic activity during viral infection Hongying Shan Ph.D. Dissertation Madrid 2018 UNIVERSIDAD AUTONOMA DE MADRID Facultad de Ciencias Departamento de Biología Molecular Characterization of P1 leader proteases of the Potyviridae family and identification of the host factors involved in their proteolytic activity during viral infection Hongying Shan This thesis is performed in Departamento de Genética Molecular de Plantas of Centro Nacional de Biotecnología (CNB-CSIC) under the supervision of Dr. Juan Antonio García and Dr. Bernardo Rodamilans Ramos Madrid 2018 Acknowledgements First of all, I want to express my appreciation to thesis supervisors Bernardo Rodamilans and Juan Antonio García, who gave the dedicated guidance to this thesis. I also want to say thanks to Carmen Simón-Mateo, Fabio Pasin, Raquel Piqueras, Beatriz García, Mingmin, Zhengnan, Wenli, Linlin, Ruiqiang, Runhong and Yuwei, who helped me and provided interesting suggestions for the thesis as well as technical support. Thanks to the people in the greenhouse (Tomás Heras, Alejandro Barrasa and Esperanza Parrilla), in vitro plant culture facility (María Luisa Peinado and Beatriz Casal), advanced light microscopy (Sylvia Gutiérrez and Ana Oña), photography service (Inés Poveda) and proteomics facility (Sergio Ciordia and María Carmen Mena). Thanks a lot to all the assistance from lab313 colleagues. Thanks a lot to the whole CNB. Thanks a lot to the Chinese Scholarship Council. Thanks a lot to all my friends. Thanks a lot to my family. Madrid 20/03/2018 Index I CONTENTS Abbreviations………………………………………….……………………….……...VII Viruses cited…………………………………………………………………..……...XIII Summary…………………………………………………………………...….…….XVII Resumen…………………………………………………………......…...…………..XXI I. -
Corona and Other Virus: Their Useful and Harmful Aspects
Current Trends on Biotechnology & Microbiology DOI: ISSN: 2641-6875 10.32474/CTBM.2020.02.000129Review Article Corona and Other Virus: Their Useful and Harmful Aspects Birhanu Gizaw* Microbial Biodiversity Directorate, Ethiopian Biodiversity Institute, Ethiopia *Corresponding author: Birhanu Gizaw, Microbial Biodiversity Directorate, Ethiopian Biodiversity Institute, P.O. Box 30726, Addis Ababa, Ethiopia Received: June 15, 2020 Published: September 22, 2020 Abstract How the single virus is forceful and shakes the world is eyewitness during this contemporary COVID 19 pandemic time. People primarily think of viruses such as HIV, Ebola, Zika, Influenza, Tobacco mosaic virus or whatever new outbreak like SARS, Corona are Understandingall viruses worst the and microbial non-beneficial. world isHowever, very critical not all and viruses crucial are thing detrimental that they and are influential driving force to human, and governing animal and the plantphysical health. world In fact, some viruses have beneficial properties for their hosts in a symbiotic relationship and scientific research in many disciplines. industry,and biosphere agriculture, at all. Thehealth virus and and environment other microbial are the life application those of bacteria, of microbes fungi, andprion, their viroid, products virion are are too requiring high for great human attention being and researchenvironment. to enhance Without their microbes utilization all lifefrom would majority be cease of useful on earth.aspects However, of microbial some genetic microbes resource. are very The dangerous secret behind like of Corona every virus, HIV, Ebola, Mycobacterium and others that destroy human life, but majority of microorganisms are too useful to promote virusdevelopment. in respect Through with health, building environment, and strengthening agriculture microbial and biotechnological culture collection application centers during and through this Covid19 strong pandemic conservation time strategy, to raise awarenessit is possible about to exploit virus atmore all. -
Viruses Virus Diseases Poaceae(Gramineae)
Viruses and virus diseases of Poaceae (Gramineae) Viruses The Poaceae are one of the most important plant families in terms of the number of species, worldwide distribution, ecosystems and as ingredients of human and animal food. It is not surprising that they support many parasites including and more than 100 severely pathogenic virus species, of which new ones are being virus diseases regularly described. This book results from the contributions of 150 well-known specialists and presents of for the first time an in-depth look at all the viruses (including the retrotransposons) Poaceae(Gramineae) infesting one plant family. Ta xonomic and agronomic descriptions of the Poaceae are presented, followed by data on molecular and biological characteristics of the viruses and descriptions up to species level. Virus diseases of field grasses (barley, maize, rice, rye, sorghum, sugarcane, triticale and wheats), forage, ornamental, aromatic, wild and lawn Gramineae are largely described and illustrated (32 colour plates). A detailed index Sciences de la vie e) of viruses and taxonomic lists will help readers in their search for information. Foreworded by Marc Van Regenmortel, this book is essential for anyone with an interest in plant pathology especially plant virology, entomology, breeding minea and forecasting. Agronomists will also find this book invaluable. ra The book was coordinated by Hervé Lapierre, previously a researcher at the Institut H. Lapierre, P.-A. Signoret, editors National de la Recherche Agronomique (Versailles-France) and Pierre A. Signoret emeritus eae (G professor and formerly head of the plant pathology department at Ecole Nationale Supérieure ac Agronomique (Montpellier-France). Both have worked from the late 1960’s on virus diseases Po of Poaceae . -
Determinants of Taxonomic Composition of Plant Viruses at the Nature Conservancy’S Tallgrass Prairie Preserve, Oklahoma Vaskar Thapa,1,2 Daniel J
Virus Evolution, 2015, 1(1): vev007 doi: 10.1093/ve/vev007 Research article Determinants of taxonomic composition of plant viruses at the Nature Conservancy’s Tallgrass Prairie Preserve, Oklahoma Vaskar Thapa,1,2 Daniel J. McGlinn,2,† Ulrich Melcher,3 Michael W. Palmer,2 and Marilyn J. Roossinck1,*,†,‡ 1Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA, 2Department of Botany, Oklahoma State University, Stillwater, OK 74078, USA and 3Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA *Corresponding author: E-mail: [email protected] †Present address: Biology Department, College of Charleston, Charleston, SC, USA. ‡http://orcid.org/0000-0002-1743-0627 Abstract The role of biotic and abiotic factors in shaping the diversity and composition of communities of plant viruses remain understudied, particularly in natural settings. In this study, we test the effects of host identity, location, and sampling year on the taxonomic composition of plant viruses in six native plant species [Ambrosia psilostachya (Asteraceae), Vernonia baldwinii (Asteraceae), Asclepias viridis (Asclepiadaceae), Ruellia humilis (Acanthaceae), Panicum virgatum (Poaceae) and Sorghastrum nutans (Poaceae)] from the Nature Conservancy’s Tallgrass Prairie Preserve in northeastern Oklahoma. We sampled over 400 specimens of the target host plants from twenty sites (plots) in the Tallgrass Prairie Preserve over 4 years and tested them for the presence of plant viruses applying virus-like particle and double-stranded RNA enrichment meth- ods. Many of the viral sequences identified could not be readily assigned to species, either due to their novelty or the short- ness of the sequence. -
ICTV Code Assigned: 2011.001Ag Officers)
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2011.001aG officers) Short title: Change existing virus species names to non-Latinized binomials (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Van Regenmortel Marc, [email protected] Burke Donald, [email protected] Calisher Charles, [email protected] Dietzgen Ralf, [email protected] Fauquet Claude, [email protected] Ghabrial Said, [email protected] Jahrling Peter, [email protected] Johnson Karl, [email protected] Holbrook Michael, [email protected] Horzinek Marian, [email protected] Keil Guenther, [email protected] Kuhn Jens, [email protected] Mahy Brian, [email protected] Martelli Giovanni, [email protected] Pringle Craig, [email protected] Rybicki Ed, [email protected] Skern Tim, [email protected] Tesh Robert, [email protected] Wahl-Jensen Victoria, [email protected] Walker Peter, [email protected] Weaver Scott, [email protected] List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . -
Small Hydrophobic Viral Proteins Involved in Intercellular Movement of Diverse Plant Virus Genomes Sergey Y
AIMS Microbiology, 6(3): 305–329. DOI: 10.3934/microbiol.2020019 Received: 23 July 2020 Accepted: 13 September 2020 Published: 21 September 2020 http://www.aimspress.com/journal/microbiology Review Small hydrophobic viral proteins involved in intercellular movement of diverse plant virus genomes Sergey Y. Morozov1,2,* and Andrey G. Solovyev1,2,3 1 A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia 2 Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia 3 Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia * Correspondence: E-mail: [email protected]; Tel: +74959393198. Abstract: Most plant viruses code for movement proteins (MPs) targeting plasmodesmata to enable cell-to-cell and systemic spread in infected plants. Small membrane-embedded MPs have been first identified in two viral transport gene modules, triple gene block (TGB) coding for an RNA-binding helicase TGB1 and two small hydrophobic proteins TGB2 and TGB3 and double gene block (DGB) encoding two small polypeptides representing an RNA-binding protein and a membrane protein. These findings indicated that movement gene modules composed of two or more cistrons may encode the nucleic acid-binding protein and at least one membrane-bound movement protein. The same rule was revealed for small DNA-containing plant viruses, namely, viruses belonging to genus Mastrevirus (family Geminiviridae) and the family Nanoviridae. In multi-component transport modules the nucleic acid-binding MP can be viral capsid protein(s), as in RNA-containing viruses of the families Closteroviridae and Potyviridae. However, membrane proteins are always found among MPs of these multicomponent viral transport systems.