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Virology Journal Biomed Central
Virology Journal BioMed Central Research Open Access The complete genomes of three viruses assembled from shotgun libraries of marine RNA virus communities Alexander I Culley1, Andrew S Lang2 and Curtis A Suttle*1,3 Address: 1University of British Columbia, Department of Botany, 3529-6270 University Blvd, Vancouver, B.C. V6T 1Z4, Canada, 2Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada and 3University of British Columbia, Department of Earth and Ocean Sciences, Department of Microbiology and Immunology, 1461-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada Email: Alexander I Culley - [email protected]; Andrew S Lang - [email protected]; Curtis A Suttle* - [email protected] * Corresponding author Published: 6 July 2007 Received: 10 May 2007 Accepted: 6 July 2007 Virology Journal 2007, 4:69 doi:10.1186/1743-422X-4-69 This article is available from: http://www.virologyj.com/content/4/1/69 © 2007 Culley et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: RNA viruses have been isolated that infect marine organisms ranging from bacteria to whales, but little is known about the composition and population structure of the in situ marine RNA virus community. In a recent study, the majority of three genomes of previously unknown positive-sense single-stranded (ss) RNA viruses were assembled from reverse-transcribed whole- genome shotgun libraries. -
Mgr. Marie Vilánková
www.novinky.cz www.rozhlas.cz VIRY Mgr. Marie Vilánková © ECC s.r.o. www.stefajir.cz Všechna práva vyhrazena Viry • Jejich zařazení do živé přírody • Virus jako informace • Jejich členění, • způsoby pronikání do lidského organismu, • nejčastější zdravotní problémy s nimi spojené • Možnosti řešení, včetně akutních infekcí, preparáty Joalis • Proč preparát Antivex je velmi důležitý © ECC s.r.o. Všechna práva vyhrazena Země • Životní prostředí – živé organismy - rostliny, živočichové… – tvořeny buňkami • Rostliny – počátek potravního řetězce, umí zachytávat sluneční energii a ukládat do chemických vazeb • Zvířata – zdroj potravy – rostliny nebo jiná zvířata • Houby a plísně – rozklad hmoty na základní prvky • Bakterie – také rozklad, velký význam v oběhu živin, prospěšné svazky s jinými organismy, mohou také škodit - Různé vztahy mezi organismy – boj o potravu, získání životního prostoru, přežití… © ECC s.r.o. Všechna práva vyhrazena Živé organismy • Živé organismy tvořeny buňkami – jednobuněčné (bakterie, prvoci, některé plísně), vícebuněčné • Buňka – tvořena ze specializovaných částí organel - cytoplasma, jádro, mitochondrie, endoplasmatické retikulum … • Buněčná membrána: dvojitá vrstva fosfolipidů s molekulami bílkovin – velmi důležité NENAsycené mastné kyseliny – VÝŽIVA!!! • Každá buňka – samostatný organismus – přijímá potravu, vylučuje, rozmnožuje se, reaguje na okolí, má nějakou fci -stavební produkuje stavební materiál (bílkoviny), transportní bariérová – přenáší částice přes bariéru, pohybová – natahuje a smršťuje se, signalizační © ECC s.r.o. Všechna práva vyhrazena Organismus = společnost buněk Soubor buněk = základní funkční jednotka • Propojeny pojivem – mezibuněčná hmota – produkt buněk vazivo, chrupavky, kosti, tekutiny • Tkáně: soubor buněk stejného typu (nervová, svalová, epitel...) • Orgány: skládají se z tkání, tvoří soustavy orgánů • Tělo: je složeno z buněk – 3,5 x 1013 buněk (lidí na Zemi 109) • Délka těla= 1,7 m, průměrná velikost buňky 10 - 20 mikrometru, měřítko 10-6 - člověk se dívá na svět z družice © ECC s.r.o. -
Marine Surface Microlayer As a Source of Enteric Viruses
MARINE SURFACE MICROLAYER AS A SOURCE OF ENTERIC VIRUSES Ana Catarina Bispo Prata Tese de Doutoramento em Ciências do Mar e do Ambiente 2014 Ana Catarina Bispo Prata MARINE SURFACE MICROLAYER AS A SOURCE OF ENTERIC VIRUSES Tese de Candidatura ao grau de Doutor em Ciências do Mar e do Ambiente Especialidade em Oceanografia e Ecossistemas Marinhos submetida ao Instituto de Ciências Biomédicas de Abel Salazar da Universidade do Porto. Programa Doutoral da Universidade do Porto (Instituto de Ciências Biomédicas de Abel Salazar e Faculdade de Ciências) e da Universidade de Aveiro. Orientador – Doutor Adelaide Almeida Categoria – Professora Auxiliar Afiliação – Departamento de Biologia da Universidade de Aveiro Co-orientador – Doutor Newton Carlos Marcial Gomes Categoria – Investigador Principal do CESAM Afiliação – Departamento de Biologia da Universidade de Aveiro LEGAL DETAILS In compliance with what is stated in the legislation in vigor, it is hereby declared that the author of this thesis participated in the creation and execution of the experimental work leading to the results here stated, as well as in their interpretation and writing of the respective manuscripts. This thesis includes one scientific paper published in an international journal and three articles in preparation originated from part of the results obtained in the experimental work referenced as: • Prata C, Ribeiro A, Cunha A , Gomes NCM, Almeida A, 2012, Ultracentrifugation as a direct method to concentrate viruses in environmental waters: virus-like particles enumeration as a new approach to determine the efficiency of recovery, Journal of Environmental Monitoring, 14 (1), 64-70. • Prata C, Cunha A, Gomes N, Almeida A, Surface Microlayer as a source of health relevant enteric viruses in Ria de Aveiro. -
Identification and Complete Genomic Sequence of a Novel Sadwavirus
Archives of Virology https://doi.org/10.1007/s00705-020-04592-9 ANNOTATED SEQUENCE RECORD Identifcation and complete genomic sequence of a novel sadwavirus discovered in pineapple (Ananas comosus) Adriana Larrea‑Sarmiento1 · Alejandro Olmedo‑Velarde1 · James C. Green1 · Maher Al Rwahnih2 · Xupeng Wang1 · Yun‑He Li3 · Weihuai Wu4 · Jingxin Zhang5 · Tracie K. Matsumoto6 · Jon Y. Suzuki6 · Marisa M. Wall6 · Wayne Borth1 · Michael J. Melzer1 · John S. Hu1 Received: 19 December 2019 / Accepted: 15 February 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020 Abstract The complete genomic sequence of a putative novel member of the family Secoviridae was determined by high-throughput sequencing of a pineapple accession obtained from the National Plant Germplasm Repository in Hilo, Hawaii. The predicted genome of the putative virus was composed of two RNA molecules of 6,128 and 4,161 nucleotides in length, excluding the poly-A tails. Each genome segment contained one large open reading frame (ORF) that shares homology and phylogenetic identity with members of the family Secoviridae. The presence of this new virus in pineapple was confrmed using RT-PCR and Sanger sequencing from six samples collected in Oahu, Hawaii. The name “pineapple secovirus A” (PSVA) is proposed for this putative new sadwavirus. Members of the family Secoviridae are non-enveloped has a poly-A tract at its 3’- end. Secovirids form isometric viruses containing linear positive-sense single-stranded viral particles and are classifed within eight genera: Nepo- RNA [(+)-ssRNA] genomes that are monopartite or bipar- virus, Comovirus, Fabavirus, Sadwavirus, Cheravirus, Tor- tite. Each genome segment encodes a large polyprotein, is radovirus, Sequivirus, and Waikavirus [1]. -
Keizo Nagasaki and Gunnar Bratbak. Isolation of Viruses Infecting
MANUAL of MAVE Chapter 10, 2010, 92–101 AQUATIC VIRAL ECOLOGY © 2010, by the American Society of Limnology and Oceanography, Inc. Isolation of viruses infecting photosynthetic and nonphotosynthetic protists Keizo Nagasaki1* and Gunnar Bratbak2† 1National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan 2University of Bergen, Department of Biology, Box 7800, N-5020 Bergen, Norway Abstract Viruses are the most abundant biological entities in aquatic environments and our understanding of their eco- logical significance has increased tremendously since the first discovery of their high abundance in natural waters. About 40 viruses infecting eukaryotic algae and 4 viruses infecting nonphotosynthetic protists have so far been isolated and characterized to different extents. The isolated viruses infecting phytoplankton (Chlorophyceae, Prasinophyceae, Haptophyceae, Dinophyceae, Pelagophyceae, Raphidophyceae, and Bacillariophyceae) and heterotrophic protists (Bicosoecophyceae, Acanthamoebidae, and Thraustochytriaceae) are all lytic. Some of the brown algal phaeoviruses, which infect host spores or gametes, have also been found in a latent form (lysogeny) in vegetative cells. Viruses infecting eukaryotic photosynthetic and nonphotosynthetic protists are highly diverse both in size (ca. 20–220 nm in diameter), genome type (double-strand deoxyribonu- cleic acid [dsDNA], single-strand [ss]DNA, ds–ribonucleic acid [dsRNA], ssRNA), and genome size [4.4–560 kb]). Availability of host–virus laboratory cultures is a necessary prerequisite for characterization of the viruses and for investigation of host–virus interactions. In this report we summarize and comment on the techniques used for preparation of host cultures and for screening, cloning, culturing, and maintaining viruses in the laboratory. -
Diversity and Classification of Reoviruses in Crustaceans: a Proposal
Journal of Invertebrate Pathology 182 (2021) 107568 Contents lists available at ScienceDirect Journal of Invertebrate Pathology journal homepage: www.elsevier.com/locate/jip Diversity and classification of reoviruses in crustaceans: A proposal Mingli Zhao a, Camila Prestes dos Santos Tavares b, Eric J. Schott c,* a Institute of Marine and Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD 21202, USA b Integrated Group of Aquaculture and Environmental Studies, Federal University of Parana,´ Rua dos Funcionarios´ 1540, Curitiba, PR 80035-050, Brazil c Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA ARTICLE INFO ABSTRACT Keywords: A variety of reoviruses have been described in crustacean hosts, including shrimp, crayfish,prawn, and especially P virus in crabs. However, only one genus of crustacean reovirus - Cardoreovirus - has been formally recognized by ICTV CsRV1 (International Committee on Taxonomy of Viruses) and most crustacean reoviruses remain unclassified. This Cardoreovirus arises in part from ambiguous or incomplete information on which to categorize them. In recent years, increased Crabreovirus availability of crustacean reovirus genomic sequences is making the discovery and classification of crustacean Brachyuran Phylogenetic analysis reoviruses faster and more certain. This minireview describes the properties of the reoviruses infecting crusta ceans and suggests an overall classification of brachyuran crustacean reoviruses based on a combination of morphology, host, genome organization pattern and phylogenetic sequence analysis. 1. Introduction fish, crustaceans, marine protists, insects, ticks, arachnids, plants and fungi (Attoui et al., 2005; Shields et al., 2015). Host range and disease 1.1. Genera of Reoviridae family symptoms are also important indicators that help to identify viruses of different genera (Attoui et al., 2012). -
Plant Virus Evolution
Marilyn J. Roossinck Editor Plant Virus Evolution Plant Virus Evolution Marilyn J. Roossinck Editor Plant Virus Evolution Dr. Marilyn J. Roossinck The Samuel Roberts Noble Foundation Plant Biology Division P.O. Box 2180 Ardmore, OK 73402 USA Cover Photo: Integrated sequences of Petunia vein cleaning virus (in red) are seen in a chromosome spread of Petunia hybrida (see Chapter 4). ISBN: 978-3-540-75762-7 e-ISBN: 978-3-540-75763-4 Library of Congress Control Number: 2007940847 © 2008 Springer-Verlag Berlin Heidelberg This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, 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. Cover design: WMXDesign GmbH, Heidelberg, Germany Printed on acid-free paper 9 8 7 6 5 4 3 2 1 springer.com Preface The evolution of viruses has been a topic of intense investigation and theoretical development over the past several decades. Numerous workshops, review articles, and books have been devoted to the subject. -
Joseph G. Sinkovics RNA/DNA and Cancer RNA/DNA and Cancer Joseph G
Joseph G. Sinkovics RNA/DNA and Cancer RNA/DNA and Cancer Joseph G. Sinkovics RNA/DNA and Cancer 123 Joseph G. Sinkovics Retired Professor, M.D. Anderson Hospital Comprehensive Cancer Center The University of Texas Houston, TX USA Retired External Professor and Honorary Member H.L. Moffitt Comprehensive Cancer Center The University of South Florida Tampa, FL USA External Professor, Department of Molecular Medicine The University of South Florida Morsani College of Medicine Tampa, FL USA Retired Medical Director; Senior Scientific Medical Advisor, The Cancer Institute St. Joseph’s Hospital Tampa, FL USA ISBN 978-3-319-22278-3 ISBN 978-3-319-22279-0 (eBook) DOI 10.1007/978-3-319-22279-0 Library of Congress Control Number: 2015946582 Springer Cham Heidelberg New York Dordrecht London © Springer International Publishing Switzerland 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. -
Taxonomy of Picornaviridae: Current Situation and Future Proposals
EUROPIC 2008 TaxonomyTaxonomy ofof PicornaviridaePicornaviridae:: C1 CurrentCurrent SituationSituation andand FutureFuture ProposalsProposals Nick J. Knowles1, Tapani Hovi2, Timo Hyypiä3, Andrew M.Q. King4, A. Michael Lindberg5, Philip D. Minor6, Mark A. Pallansch7, Ann C. Palmenberg8, Tim Skern9, Glyn Stanway10, Teruo Yamashita11 and Roland Zell12 (1) Institute for Animal Health, Pirbright, UK; (2) Enterovirus Laboratory, KTL, Helsinki, Finland; (3) Dept. of Virology, Univ. Turku, Finland; 4) ‘Sunfield’, Dawney Hill, Pirbright, Woking, Surrey, UK; (5) School of Pure and Applied Natural Sciences, University of Kalmar, Sweden; (6) NIBSC, South Mimms, UK; (7) CDC, Atlanta, USA; (8) Institute for Molecular Virology, Wisconsin, USA; (9) Max F. Perutz Laboratories, Medical Univ. Vienna, Austria; (10) Dept. of Biological Sci., Univ. Essex, UK; (11) Aichi Prefectural Institute of Public Health, Aichi, Japan; (12) Institut fuer Virologie und Antivirale Therapie, Jena, Germany. RECENT ICTV‐APPROVED CHANGES (ICTV LEVEL 05) “Sapelovirus” Teschovirus Porcine teschovirus "Avian sapelovirus" Four taxonomic proposals have recently been approved by the ICTV: i) to combine the "Porcine sapelovirus" "Human rhinovirus C" "Simian sapelovirus" Cardiovirus Enterovirus and Rhinovirus genera, keeping the existing name Enterovirus; ii) to combine Encephalomyocarditis virus the species Poliovirus and Human enterovirus C, retaining the latter name; iii) to assign Human rhinovirus A Theilovirus Human enterovirus C as the type species of the enterovirus genus; iv) -
Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda Africana Bat Flies in South Africa
viruses Article Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa Petrus Jansen van Vuren 1,2, Michael Wiley 3, Gustavo Palacios 3, Nadia Storm 1,2, Stewart McCulloch 2, Wanda Markotter 2, Monica Birkhead 1, Alan Kemp 1 and Janusz T. Paweska 1,2,4,* 1 Centre for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham 2131, South Africa; [email protected] (P.J.v.V.); [email protected] (N.S.); [email protected] (M.B.); [email protected] (A.K.) 2 Department of Microbiology and Plant Pathology, Faculty of Natural and Agricultural Science, University of Pretoria, Pretoria 0028, South Africa; [email protected] (S.M.); [email protected] (W.K.) 3 Center for Genomic Science, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; [email protected] (M.W.); [email protected] (G.P.) 4 Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa * Correspondence: [email protected]; Tel.: +27-11-3866382 Academic Editor: Andrew Mehle Received: 27 November 2015; Accepted: 23 February 2016; Published: 29 February 2016 Abstract: We report on the isolation of a novel fusogenic orthoreovirus from bat flies (Eucampsipoda africana) associated with Egyptian fruit bats (Rousettus aegyptiacus) collected in South Africa. Complete sequences of the ten dsRNA genome segments of the virus, tentatively named Mahlapitsi virus (MAHLV), were determined. Phylogenetic analysis places this virus into a distinct clade with Baboon orthoreovirus, Bush viper reovirus and the bat-associated Broome virus. -
Discrimination and Trancriptional Response
DISCRIMINATION AND TRANCRIPTIONAL RESPONSE ANALYSIS OF HEMIPTERAN PHYTOPATHOGEN VECTORS By SHARON ANDREASON Bachelor of Science in Biology University of Texas at Tyler Tyler, Texas 2009 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY July, 2016 DISCRIMINATION AND TRANSCRIPTIONAL RESPONSE ANALYSIS OF HEMIPTERAN PHYTOPATHOGEN VECTORS Dissertation Approved: Astri Wayadande, Ph.D. Dissertation Adviser Jacqueline Fletcher, Ph.D. Francisco Ochoa-Corona, Ph.D. Ulrich Melcher, Ph.D. ii ACKNOWLEDGEMENTS I would first like to extend my deepest thanks to my advisor, Dr. Astri Wayadande, for all of her years of support. Always full of positivity, encouragement, and advice, her enthusiasm for research and effort devoted to others are attributes that I aspire to cultivate in my future career. I am forever grateful for her guidance throughout earning my degree. I would also like to thank my committee members, Drs. Jacqueline Fletcher, Francisco Ochoa-Corona, and Ulrich Melcher, each of whom have not only offered me thoughtful advice through my research, but have also educated and inspired me in unique and invaluable ways. I am deeply appreciative of their guidance over the years. I want to thank Dr. Judith Brown, without whom I would not have had the opportunity to work on such an important vector system. I am sincerely grateful to Dr. Mohammad Arif, who provided exceptional expertise and advice through my whitefly projects. I would also like to extend my thanks to Dr. Trenna Blagden for all her help and guidance on my projects, particularly during my work with EDNA, as well as for the professional advice she has provided. -
University of Oklahoma Graduate College Direct Metagenomic Detection and Analysis of Plant Viruses Using an Unbiased High-Throug
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE DIRECT METAGENOMIC DETECTION AND ANALYSIS OF PLANT VIRUSES USING AN UNBIASED HIGH-THROUGHPUT SEQUENCING APPROACH A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By GRAHAM BURNS WILEY Norman, Oklahoma 2009 DIRECT METAGENOMIC DETECTION AND ANALYSIS OF PLANT VIRUSES USING AN UNBIASED HIGH-THROUGHPUT SEQUENCING APPROACH A DISSERTATION APPROVED FOR THE DEPARTMENT OF CHEMISTRY AND BIOCHEMISTRY BY Dr. Bruce A. Roe, Chair Dr. Ann H. West Dr. Valentin Rybenkov Dr. George Richter-Addo Dr. Tyrell Conway ©Copyright by GRAHAM BURNS WILEY 2009 All Rights Reserved. Acknowledgments I would first like to thank my father, Randall Wiley, for his constant and unwavering support in my academic career. He truly is the “Winston Wolf” of my life. Secondly, I would like to thank my wife, Mandi Wiley, for her support, patience, and encouragement in the completion of this endeavor. I would also like to thank Dr. Fares Najar, Doug White, Jim White, and Steve Kenton for their friendship, insight, humor, programming knowledge, and daily morning coffee sessions. I would like to thank Hongshing Lai and Dr. Jiaxi Quan for their expertise and assistance in developing the TGPweb database. I would like to thank Dr. Marilyn Roossinck and Dr. Guoan Shen, both of the Noble Foundation, for their preparation of the samples for this project and Dr Rick Nelson and Dr. Byoung Min, also both of the Noble Foundation, for teaching me plant virus isolation techniques. I would like to thank Chunmei Qu, Ping Wang, Yanbo Xing, Dr.