SUPPLEMENTARY DATA TABLE S1. Hybridization with Single Probes Specific to Plant Virus Species
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
UC Riverside UC Riverside Previously Published Works
UC Riverside UC Riverside Previously Published Works Title Viral RNAs are unusually compact. Permalink https://escholarship.org/uc/item/6b40r0rp Journal PloS one, 9(9) ISSN 1932-6203 Authors Gopal, Ajaykumar Egecioglu, Defne E Yoffe, Aron M et al. Publication Date 2014 DOI 10.1371/journal.pone.0105875 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Viral RNAs Are Unusually Compact Ajaykumar Gopal1, Defne E. Egecioglu1, Aron M. Yoffe1, Avinoam Ben-Shaul2, Ayala L. N. Rao3, Charles M. Knobler1, William M. Gelbart1* 1 Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America, 2 Institute of Chemistry & The Fritz Haber Research Center, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel, 3 Department of Plant Pathology, University of California Riverside, Riverside, California, United States of America Abstract A majority of viruses are composed of long single-stranded genomic RNA molecules encapsulated by protein shells with diameters of just a few tens of nanometers. We examine the extent to which these viral RNAs have evolved to be physically compact molecules to facilitate encapsulation. Measurements of equal-length viral, non-viral, coding and non-coding RNAs show viral RNAs to have among the smallest sizes in solution, i.e., the highest gel-electrophoretic mobilities and the smallest hydrodynamic radii. Using graph-theoretical analyses we demonstrate that their sizes correlate with the compactness of branching patterns in predicted secondary structure ensembles. The density of branching is determined by the number and relative positions of 3-helix junctions, and is highly sensitive to the presence of rare higher-order junctions with 4 or more helices. -
Virus Particle Structures
Virus Particle Structures Virus Particle Structures Palmenberg, A.C. and Sgro, J.-Y. COLOR PLATE LEGENDS These color plates depict the relative sizes and comparative virion structures of multiple types of viruses. The renderings are based on data from published atomic coordinates as determined by X-ray crystallography. The international online repository for 3D coordinates is the Protein Databank (www.rcsb.org/pdb/), maintained by the Research Collaboratory for Structural Bioinformatics (RCSB). The VIPER web site (mmtsb.scripps.edu/viper), maintains a parallel collection of PDB coordinates for icosahedral viruses and additionally offers a version of each data file permuted into the same relative 3D orientation (Reddy, V., Natarajan, P., Okerberg, B., Li, K., Damodaran, K., Morton, R., Brooks, C. and Johnson, J. (2001). J. Virol., 75, 11943-11947). VIPER also contains an excellent repository of instructional materials pertaining to icosahedral symmetry and viral structures. All images presented here, except for the filamentous viruses, used the standard VIPER orientation along the icosahedral 2-fold axis. With the exception of Plate 3 as described below, these images were generated from their atomic coordinates using a novel radial depth-cue colorization technique and the program Rasmol (Sayle, R.A., Milner-White, E.J. (1995). RASMOL: biomolecular graphics for all. Trends Biochem Sci., 20, 374-376). First, the Temperature Factor column for every atom in a PDB coordinate file was edited to record a measure of the radial distance from the virion center. The files were rendered using the Rasmol spacefill menu, with specular and shadow options according to the Van de Waals radius of each atom. -
To Build a Virus on a Nucleic Acid Substrate
CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Biophysical Journal Volume 104 April 2013 1595–1604 1595 To Build a Virus on a Nucleic Acid Substrate Adam Zlotnick,†‡* J. Zachary Porterfield,†‡ and Joseph Che-Yen Wang† † ‡ Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana; and Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma ABSTRACT Many viruses package their genomes concomitant with assembly. Here, we show that this reaction can be described by three coefficients: association of capsid protein (CP) to nucleic acid (NA), KNA; CP-CP interaction, u; and a, propor- tional to the work required to package NA. The value of a can vary as NA is packaged. A phase diagram of average lna versus lnu identifies conditions where assembly is likely to fail or succeed. NA morphology can favor (lna > 0) or impede (lna < 0) assembly. As lnu becomes larger, capsids become more stable and assembly becomes more cooperative. Where (lna þ lnu) < 0, the CP is unable to contain the NA, so that assembly results in aberrant particles. This phase diagram is consis- tent with quantitative studies of cowpea chlorotic mottle virus, hepatitis B virus, and simian virus 40 assembling on ssRNA and dsDNA substrates. Thus, the formalism we develop is suitable for describing and predicting behavior of experimental studies of CP assembly on NA. INTRODUCTION Viruses are self-replicating molecular machines and obli- (6)). In an x-ray structure of Pariacoto virus, the viral ssRNA gate parasites that package a genome and deliver it to is clearly visualized as a dodecahedral cage with dsRNA a host. -
Icosahedral Viruses Defined by Their Positively Charged Domains: a Signature for Viral Identity and Capsid Assembly Strategy
Support Information for: Icosahedral viruses defined by their positively charged domains: a signature for viral identity and capsid assembly strategy Rodrigo D. Requião1, Rodolfo L. Carneiro 1, Mariana Hoyer Moreira1, Marcelo Ribeiro- Alves2, Silvana Rossetto3, Fernando L. Palhano*1 and Tatiana Domitrovic*4 1 Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil. 2 Laboratório de Pesquisa Clínica em DST/Aids, Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, RJ, 21040-900, Brazil 3 Programa de Pós-Graduação em Informática, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil. 4 Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil. *Corresponding author: [email protected] or [email protected] MATERIALS AND METHODS Software and Source Identifier Algorithms Calculation of net charge (1) Calculation of R/K ratio This paper https://github.com/mhoyerm/Total_ratio Identify proteins of This paper https://github.com/mhoyerm/Modulate_RK determined net charge and R/K ratio Identify proteins of This paper https://github.com/mhoyerm/Modulate_KR determined net charge and K/R ratio Data sources For all viral proteins, we used UniRef with the advanced search options (uniprot:(proteome:(taxonomy:"Viruses [10239]") reviewed:yes) AND identity:1.0). For viral capsid proteins, we used the advanced search options (proteome:(taxonomy:"Viruses [10239]") goa:("viral capsid [19028]") AND reviewed:yes) followed by a manual selection of major capsid proteins. Advanced search options for H. -
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 . -
Exploring the Tymovirids Landscape Through Metatranscriptomics Data
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.15.452586; this version posted July 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Exploring the tymovirids landscape through metatranscriptomics data 2 Nicolás Bejerman1,2, Humberto Debat1,2 3 4 1 Instituto de Patología Vegetal – Centro de Investigaciones Agropecuarias – Instituto Nacional de 5 Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5 (X5020ICA), Córdoba, 6 Argentina 7 2 Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización 8 Agrícola, Camino 60 Cuadras Km 5,5 (X5020ICA), Córdoba, Argentina 9 10 Corresponding author: Nicolás Bejerman, [email protected] 11 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.15.452586; this version posted July 16, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 12 Abstract 13 Tymovirales is an order of viruses with positive-sense, single-stranded RNA genomes that mostly infect 14 plants, but also fungi and insects. The number of tymovirid sequences has been growing in the last few 15 years with the extensive use of high-throughput sequencing platforms. Here we report the discovery of 31 16 novel tymovirid genomes associated with 27 different host plant species, which were hidden in public 17 databases. -
First Insight Into the Viral Community of the Cnidarian Model Metaorganism Aiptasia Using RNA-Seq Data
First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data Jan D. Brüwer and Christian R. Voolstra Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, Saudi Arabia ABSTRACT Current research posits that all multicellular organisms live in symbioses with asso- ciated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems. To gain first insight into viruses associated with the coral model system Aiptasia (sensu Exaiptasia pallida), we analyzed an existing RNA-Seq dataset of aposymbiotic, partially populated, and fully symbiotic Aiptasia CC7 anemones with Symbiodinium. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (∼3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences could be assigned as of viral origin. Taxonomic annotation of these sequences suggests that Aiptasia is associated with a diverse viral community, comprising 116 viral taxa covering 40 families. The viral assemblage was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral assemblage, we found that some viral taxa exhibited significant changes in their relative abundance when Aiptasia engaged in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present across all conditions revealed a core virome of 15 viral taxa from 11 viral families, encompassing many viruses previously reported as members of coral viromes. -
Note to Users
NOTE TO USERS This reproduction is the best copy available. UMI* SUB-CELLULAR LOCALIZATION OF THE GRAPEVINE RUPESTRIS STEMPITTING-ASSOCIATED VIRUS REPLICASE A Thesis Presented to The Faculty of Graduate Studies of The University of Guelph By SEAN PROSSER In partial fulfillment of requirements for the degree of Master of Science November, 2009 ©Sean Prosser, 2009 Library and Archives Bibliotheque et 1*1 Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A 0N4 OttawaONK1A0N4 Canada Canada Vour Tile Votre reference ISBN: 978-0-494-58413-2 Our file Notre reference ISBN: 978-0-494-58413-2 NOTICE: AVIS: The author has granted a non L'auteur a accorde une licence non exclusive exclusive license allowing Library and permettant a la Bibliotheque et Archives Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par I'lnternet, preter, telecommunication or on the Internet, distribuer et vendre des theses partout dans le loan, distribute and sell theses monde, a des fins commerciales ou autres, sur worldwide, for commercial or non support microforme, papier, electronique et/ou commercial purposes, in microform, autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in this et des droits moraux qui protege cette these. Ni thesis. Neither the thesis nor la these ni des extraits substantiels de celle-ci substantial extracts from it may be ne doivent etre imprimes ou autrement printed or otherwise reproduced reproduits sans son autorisation. -
Part but Systemic Virus Spread Was Not Observed in C
GRAPEVINE VIRUS DISEASES AND CLEAN GRAPE STOCK PROGRAM IN HUNGARY Lázár, J.1 Mikulás, J.1 Hajdú, E.1 Kölber, M.2 Sznyegi, S.2 1 Research Institute for Viticulture and Enology of Ministry of Agriculture and Rural Development, Kecskemét, Hungary 2 Plant Health and Soil Conservation Station of Ministry of Agriculture and Rural Development, Budapest, Hungary In Hungarian viticulture the use of clones developed of cultivated vine varieties is well justified in order to establish variety true, healthy and productive plantations. Use of virus-free propagation material is an important factor to improve quality and quantity of grape production. In Hungary the exploration of the grape virus and virus-like diseases began in 1960’s in the Research Institute for Viticulture and Enology by Dr. János Lehoczky and his collegues (1). In this time fifteen virus and virus-like diseases of Vitis vinifera are known to occure in Hungary (Table 1). Some of the viruses, for example fanleaf and leafroll cause great crop losses and/or lower fruit quality. Other virus diseases for example Rugose wood complex can cause untimely death of stocks. A few viruses are latent. Their effects on grapevines are less known, however occurrence of these diseases are quite frequent, so they appear to have high economic importance. Table 1. Identified grapevine virus and virus-like diseases in Hungary _________________________________________________________________________________ Virus disease Identified viruses Year _________________________________________________________________________________ -
Ancient Recombination Events and the Origins of Hepatitis E Virus Andrew G
Kelly et al. BMC Evolutionary Biology (2016) 16:210 DOI 10.1186/s12862-016-0785-y RESEARCH ARTICLE Open Access Ancient recombination events and the origins of hepatitis E virus Andrew G. Kelly, Natalie E. Netzler and Peter A. White* Abstract Background: Hepatitis E virus (HEV) is an enteric, single-stranded, positive sense RNA virus and a significant etiological agent of hepatitis, causing sporadic infections and outbreaks globally. Tracing the evolutionary ancestry of HEV has proved difficult since its identification in 1992, it has been reclassified several times, and confusion remains surrounding its origins and ancestry. Results: To reveal close protein relatives of the Hepeviridae family, similarity searching of the GenBank database was carried out using a complete Orthohepevirus A, HEV genotype I (GI) ORF1 protein sequence and individual proteins. The closest non-Hepeviridae homologues to the HEV ORF1 encoded polyprotein were found to be those from the lepidopteran-infecting Alphatetraviridae family members. A consistent relationship to this was found using a phylogenetic approach; the Hepeviridae RdRp clustered with those of the Alphatetraviridae and Benyviridae families. This puts the Hepeviridae ORF1 region within the “Alpha-like” super-group of viruses. In marked contrast, the HEV GI capsid was found to be most closely related to the chicken astrovirus capsid, with phylogenetic trees clustering the Hepeviridae capsid together with those from the Astroviridae family, and surprisingly within the “Picorna-like” supergroup. These results indicate an ancient recombination event has occurred at the junction of the non-structural and structure encoding regions, which led to the emergence of the entire Hepeviridae family. -
Evidence to Support Safe Return to Clinical Practice by Oral Health Professionals in Canada During the COVID-19 Pandemic: a Repo
Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. November 2020 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Paul Allison, Faculty of Dentistry, McGill University Raphael Freitas de Souza, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University November 30th, 2020 1 Contents Page Introduction 3 Project goal and specific objectives 3 Methods used to identify and include relevant literature 4 Report structure 5 Summary of update report 5 Report results a) Which patients are at greater risk of the consequences of COVID-19 and so 7 consideration should be given to delaying elective in-person oral health care? b) What are the signs and symptoms of COVID-19 that oral health professionals 9 should screen for prior to providing in-person health care? c) What evidence exists to support patient scheduling, waiting and other non- treatment management measures for in-person oral health care? 10 d) What evidence exists to support the use of various forms of personal protective equipment (PPE) while providing in-person oral health care? 13 e) What evidence exists to support the decontamination and re-use of PPE? 15 f) What evidence exists concerning the provision of aerosol-generating 16 procedures (AGP) as part of in-person