Identification of an RNA Silencing Suppressor Encoded by A
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies
viruses Review Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies Varvara I. Maliogka 1,* ID , Angelantonio Minafra 2 ID , Pasquale Saldarelli 2, Ana B. Ruiz-García 3, Miroslav Glasa 4 ID , Nikolaos Katis 1 and Antonio Olmos 3 ID 1 Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; [email protected] 2 Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy; [email protected] (A.M.); [email protected] (P.S.) 3 Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain; [email protected] (A.B.R.-G.); [email protected] (A.O.) 4 Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic; [email protected] * Correspondence: [email protected]; Tel.: +30-2310-998716 Received: 23 July 2018; Accepted: 13 August 2018; Published: 17 August 2018 Abstract: Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. -
The Viruses of Wild Pigeon Droppings
The Viruses of Wild Pigeon Droppings Tung Gia Phan1,2, Nguyen Phung Vo1,3,A´ kos Boros4,Pe´ter Pankovics4,Ga´bor Reuter4, Olive T. W. Li6, Chunling Wang5, Xutao Deng1, Leo L. M. Poon6, Eric Delwart1,2* 1 Blood Systems Research Institute, San Francisco, California, United States of America, 2 Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America, 3 Pharmacology Department, School of Pharmacy, Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh, Vietnam, 4 Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, A´ NTSZ Regional Institute of State Public Health Service, Pe´cs, Hungary, 5 Stanford Genome Technology Center, Stanford, California, United States of America, 6 Centre of Influenza Research and School of Public Health, University of Hong Kong, Hong Kong SAR Abstract Birds are frequent sources of emerging human infectious diseases. Viral particles were enriched from the feces of 51 wild urban pigeons (Columba livia) from Hong Kong and Hungary, their nucleic acids randomly amplified and then sequenced. We identified sequences from known and novel species from the viral families Circoviridae, Parvoviridae, Picornaviridae, Reoviridae, Adenovirus, Astroviridae, and Caliciviridae (listed in decreasing number of reads), as well as plant and insect viruses likely originating from consumed food. The near full genome of a new species of a proposed parvovirus genus provisionally called Aviparvovirus contained an unusually long middle ORF showing weak similarity to an ORF of unknown function from a fowl adenovirus. Picornaviruses found in both Asia and Europe that are distantly related to the turkey megrivirus and contained a highly divergent 2A1 region were named mesiviruses. -
Emerging Viral Diseases of Fish and Shrimp Peter J
Emerging viral diseases of fish and shrimp Peter J. Walker, James R. Winton To cite this version: Peter J. Walker, James R. Winton. Emerging viral diseases of fish and shrimp. Veterinary Research, BioMed Central, 2010, 41 (6), 10.1051/vetres/2010022. hal-00903183 HAL Id: hal-00903183 https://hal.archives-ouvertes.fr/hal-00903183 Submitted on 1 Jan 2010 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Vet. Res. (2010) 41:51 www.vetres.org DOI: 10.1051/vetres/2010022 Ó INRA, EDP Sciences, 2010 Review article Emerging viral diseases of fish and shrimp 1 2 Peter J. WALKER *, James R. WINTON 1 CSIRO Livestock Industries, Australian Animal Health Laboratory (AAHL), 5 Portarlington Road, Geelong, Victoria, Australia 2 USGS Western Fisheries Research Center, 6505 NE 65th Street, Seattle, Washington, USA (Received 7 December 2009; accepted 19 April 2010) Abstract – The rise of aquaculture has been one of the most profound changes in global food production of the past 100 years. Driven by population growth, rising demand for seafood and a levelling of production from capture fisheries, the practice of farming aquatic animals has expanded rapidly to become a major global industry. -
Tically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2021 doi:10.20944/preprints202106.0526.v1 Review Towards the forest virome: next-generation-sequencing dras- tically expands our understanding on virosphere in temperate forest ecosystems Artemis Rumbou 1,*, Eeva J. Vainio 2 and Carmen Büttner 1 1 Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Ber- lin, Germany; [email protected], [email protected] 2 Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland; [email protected] * Correspondence: [email protected] Abstract: Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont. Symbiotic mi- crobiota and pathogens engage in a permanent interplay, which influences the host. Thanks to the development of NGS technol- ogies, a vast amount of genetic information on the virosphere of temperate forests has been gained the last seven years. To estimate the qualitative/quantitative impact of NGS in forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of NGS methods is ex- tremely significant for forest virology. Reviewed data about viral presence in holobionts, allowed us to address the role of the virome in the holobionts. Genetic variation is a crucial aspect in hologenome, significantly reinforced by horizontal gene transfer among all interacting actors. Through virus-virus interplays synergistic or antagonistic relations may evolve, which may drasti- cally affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protec- tion based on endophytes and mycovirus biocontrol agents. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
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 . -
Yellow Head Virus: Transmission and Genome Analyses
The University of Southern Mississippi The Aquila Digital Community Dissertations Fall 12-2008 Yellow Head Virus: Transmission and Genome Analyses Hongwei Ma University of Southern Mississippi Follow this and additional works at: https://aquila.usm.edu/dissertations Part of the Aquaculture and Fisheries Commons, Biology Commons, and the Marine Biology Commons Recommended Citation Ma, Hongwei, "Yellow Head Virus: Transmission and Genome Analyses" (2008). Dissertations. 1149. https://aquila.usm.edu/dissertations/1149 This Dissertation is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Dissertations by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. The University of Southern Mississippi YELLOW HEAD VIRUS: TRANSMISSION AND GENOME ANALYSES by Hongwei Ma Abstract of a Dissertation Submitted to the Graduate Studies Office of The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2008 COPYRIGHT BY HONGWEI MA 2008 The University of Southern Mississippi YELLOW HEAD VIRUS: TRANSMISSION AND GENOME ANALYSES by Hongwei Ma A Dissertation Submitted to the Graduate Studies Office of The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Approved: December 2008 ABSTRACT YELLOW HEAD VIRUS: TRANSMISSION AND GENOME ANALYSES by I Iongwei Ma December 2008 Yellow head virus (YHV) is an important pathogen to shrimp aquaculture. Among 13 species of naturally YHV-negative crustaceans in the Mississippi coastal area, the daggerblade grass shrimp, Palaemonetes pugio, and the blue crab, Callinectes sapidus, were tested for potential reservoir and carrier hosts of YHV using PCR and real time PCR. -
Partitiviruses Infecting Drosophila Melanogaster and Aedes Aegypti Exhibit Efficient 2 Biparental Vertical Transmission 3 4 Shaun T
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.01.128819; this version posted June 2, 2020. 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 4.0 International license. 1 Partitiviruses infecting Drosophila melanogaster and Aedes aegypti exhibit efficient 2 biparental vertical transmission 3 4 Shaun T. Cross1, Bernadette L. Maertens1, Tillie J. Dunham1, Case P. Rodgers1, Ali L. Brehm1, 5 Megan R. Miller1, Alissa M. Williams2, Brian D. Foy, Mark D. Stenglein1,* 6 7 1. Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine 8 and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA 9 2. Department of Biology, Colorado State University, Fort Collins, CO, USA 10 * Correspondence to: [email protected] 11 12 Abstract 13 14 Partitiviruses are segmented, multipartite dsRNA viruses that until recently were only known to 15 infect fungi, plants, and protozoans. Metagenomic surveys have revealed that partitivirus-like 16 sequences are also commonly associated with arthropods. One arthropod-associated partitivirus, 17 galbut virus, is extraordinarily common in wild populations of Drosophila melanogaster fruit 18 flies. To begin to understand the processes that underlie this virus’s high global prevalence, we 19 established colonies of wild-caught infected flies. Infection remained at stably high levels over 20 three years, with between 63-100% of individual flies infected. Galbut virus infects fly cells and 21 replicates in tissues throughout infected adults, including reproductive tissues and the gut 22 epithelium. -
Genomic and Functional Analysis of Viruses from Giardia Duodenalis Isolates
biomedicines Article Re-Discovery of Giardiavirus: Genomic and Functional Analysis of Viruses from Giardia duodenalis Isolates Gianluca Marucci 1, Ilaria Zullino 1, Lucia Bertuccini 2 , Serena Camerini 2, Serena Cecchetti 2 , Agostina Pietrantoni 2, Marialuisa Casella 2, Paolo Vatta 1, Alex D. Greenwood 3,4 , Annarita Fiorillo 5 and Marco Lalle 1,* 1 Unit of Foodborne and Neglected Parasitic Disease, Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; [email protected] (G.M.); [email protected] (I.Z.); [email protected] (P.V.) 2 Core Facilities, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; [email protected] (L.B.); [email protected] (S.C.); [email protected] (S.C.); [email protected] (A.P.); [email protected] (M.C.) 3 Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany; [email protected] 4 Department of Veterinary Medicine, Freie Universität Berlin, 14195 Berlin, Germany 5 Department of Biochemical Science “A. Rossi-Fanelli”, Sapienza University, 00185 Rome, Italy; annarita.fi[email protected] * Correspondence: [email protected]; Tel.: +39-06-4990-2670 Abstract: Giardiasis, caused by the protozoan parasite Giardia duodenalis, is an intestinal diarrheal disease affecting almost one billion people worldwide. A small endosymbiotic dsRNA viruses, G. Citation: Marucci, G.; Zullino, I.; lamblia virus (GLV), genus Giardiavirus, family Totiviridae, might inhabit human and animal isolates Bertuccini, L.; Camerini, S.; Cecchetti, S.; Pietrantoni, A.; Casella, M.; Vatta, of G. duodenalis. Three GLV genomes have been sequenced so far, and only one was intensively P.; Greenwood, A.D.; Fiorillo, A.; et al. -
Feasibility of Cowpea Chlorotic Mottle Virus-Like Particles As Scaffold for Epitope Presentations
Hassani-Mehraban et al. BMC Biotechnology (2015) 15:80 DOI 10.1186/s12896-015-0180-6 RESEARCH ARTICLE Open Access Feasibility of Cowpea chlorotic mottle virus-like particles as scaffold for epitope presentations Afshin Hassani-Mehraban, Sjoerd Creutzburg, Luc van Heereveld and Richard Kormelink* Abstract Background & Methods: Within the last decade Virus-Like Particles (VLPs) have increasingly received attention from scientists for their use as a carrier of (peptide) molecules or as scaffold to present epitopes for use in subunit vaccines. To test the feasibility of Cowpea chlorotic mottle virus (CCMV) particles as a scaffold for epitope presentation and identify sites for epitope fusion or insertion that would not interfere with virus-like-particle formation, chimeric CCMV coat protein (CP) gene constructs were engineered, followed by expression in E. coli and assessment of VLP formation. Various constructs were made encoding a 6x-His-tag, or selected epitopes from Influenza A virus [IAV] (M2e, HA) or Foot and Mouth Disease Virus [FMDV] (VP1 and 2C). The epitopes were either inserted 1) in predicted exposed loop structures of the CCMV CP protein, 2) fused to the amino- (N) or carboxyl-terminal (C) ends, or 3) to a N-terminal 24 amino acid (aa) deletion mutant (NΔ24-CP) of the CP protein. Results: High levels of insoluble protein expression, relative to proteins from the entire cell lysate, were obtained for CCMV CP and all chimeric derivatives. A straightforward protocol was used that, without the use of purification columns, successfully enabled CCMV CP protein solubilization, reassembly and subsequent collection of CCMV CP VLPs. While insertions of His-tag or M2e (7-23 aa) into the predicted external loop structures did abolish VLP formation, high yields of VLPs were obtained with all fusions of His-tag or various epitopes (13- 27 aa) from IAV and FMDV at the N- or C-terminal ends of CCMV CP or NΔ24-CP. -
1 Chapter I Overall Issues of Virus and Host Evolution
CHAPTER I OVERALL ISSUES OF VIRUS AND HOST EVOLUTION tree of life. Yet viruses do have the This book seeks to present the evolution of characteristics of life, can be killed, can become viruses from the perspective of the evolution extinct and adhere to the rules of evolutionary of their host. Since viruses essentially infect biology and Darwinian selection. In addition, all life forms, the book will broadly cover all viruses have enormous impact on the evolution life. Such an organization of the virus of their host. Viruses are ancient life forms, their literature will thus differ considerably from numbers are vast and their role in the fabric of the usual pattern of presenting viruses life is fundamental and unending. They according to either the virus type or the type represent the leading edge of evolution of all of host disease they are associated with. In living entities and they must no longer be left out so doing, it presents the broad patterns of the of the tree of life. evolution of life and evaluates the role of viruses in host evolution as well as the role Definitions. The concept of a virus has old of host in virus evolution. This book also origins, yet our modern understanding or seeks to broadly consider and present the definition of a virus is relatively recent and role of persistent viruses in evolution. directly associated with our unraveling the nature Although we have come to realize that viral of genes and nucleic acids in biological systems. persistence is indeed a common relationship As it will be important to avoid the perpetuation between virus and host, it is usually of some of the vague and sometimes inaccurate considered as a variation of a host infection views of viruses, below we present some pattern and not the basis from which to definitions that apply to modern virology. -
RNA Silencing Functions As an Antiviral Defense Mechanism in Fungi
Evidence that RNA silencing functions as an antiviral defense mechanism in fungi Gert C. Segers*, Xuemin Zhang, Fuyou Deng, Qihong Sun, and Donald L. Nuss† Center for Biosystems Research, University of Maryland Biotechnology Institute, Shady Grove Campus, Rockville, MD 20850 Edited by Reed B. Wickner, National Institutes of Health, Bethesda, MD, and approved June 21, 2007 (received for review March 19, 2007) The role of RNA silencing as an antiviral defense mechanism in involved in incorporating siRNA into the RNA-induced silenc- fungi was examined by testing the effect of dicer gene disruptions ing complex, a RecQ helicase, QDE-3, and two Dicer orthologs, on mycovirus infection of the chestnut blight fungus Cryphonectria DCL-1 and DCL-2 (15–20). However, efforts to demonstrate a parasitica. C. parasitica dicer-like genes dcl-1 and dcl-2 were cloned role for RNA silencing in antiviral defense in N. crassa have been and shown to share a high level of predicted amino acid sequence limited by the absence of a well developed mycovirus experi- identity with the corresponding dicer-like genes from Neurospora mental system. crassa [Ncdcl-1 (50.5%); Ncdcl-2 (38.0%)] and Magnaporthe oryzae The chestnut blight fungus Cryphonectria parasitica is phylo- [MDL-1 (45.6%); MDL-2 (38.0%)], respectively. Disruption of dcl-1 genetically related to N. crassa and genetically tractable because and dcl-2 resulted in no observable phenotypic changes relative to of the haploid nature of its genome and the availability of a wild-type C. parasitica. Infection of ⌬dcl-1 strains with hypovirus robust DNA transformation protocol (21, 22).