Lily Virus X (LVX) ELISA Kit
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Ordine Tymovirales
Ordine Tymovirales Classificazione Dominium/Dominio: Acytota o Aphanobionta Gruppo: IV (Virus a ssRNA+) Ordo/Ordine: Tymovirales Il nome deriva dal genere Tymovirus (e dalla famiglia Tymoviridae). Questo è stato scelto perché le altre famiglie costituenti hanno nomi che riflettono i loro virioni flessi (non una caratteristica di tutti i membri del’'ordine). Tymovirales è un ordine di virus proposto nel 2007 e ufficialmente approvato dall’International Committee on Taxonomy of Viruses nel 2009. Quest’ordine possiede un genoma ad RNA a singolo filamento a senso positivo, di conseguenza fanno parte del gruppo IV secondo la classificazione di Baltimore. I virus appartenenti a quest’ordine hanno, come ospite, le piante. I Tymovirales hanno capside senza pericapside, filamentoso e flessibile o isometrico a simmetria icosaedrica e possiedono tutti una poliproteina di replicazione alpha-like. I Tymovirales, hanno una singola molecola di ssRNA senso positivo e sono uniti dalle somiglianze nelle loro poliproteine associate alla replicazione. I virioni all’interno delle famiglie Alphaflexiviridae, Betaflexiviridae e Gammaflexiviridae sono filamenti flessuosi ed hanno solitamente un diametro di 12-13 nm e una lunghezza compresa tra circa 470 e 1000 nm, a seconda del genere. Hanno una simmetria elicoidale e in alcuni generi c’è un crossbanding ben visibile. Quasi tutti i membri hanno una singola proteina di rivestimento (CP) di 18-44 kDa e nel caso dei generi Lolavirus e alcuni Marafivirus, ci sono due proteine strutturali, che sono di forme diverse dallo stesso genere. La più grande proteina codificata è una poliproteina associata alla replicazione di circa 150-250 kDa vicino all'estremità 5' del genoma e che è tradotta direttamente dall’RNA genomico. -
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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
Edna-Host: Detection of Global Plant Viromes Using High Throughput Sequencing
EDNA-HOST: DETECTION OF GLOBAL PLANT VIROMES USING HIGH THROUGHPUT SEQUENCING By LIZBETH DANIELA PENA-ZUNIGA Bachelor of Science in Biotechnology Escuela Politecnica de las Fuerzas Armadas (ESPE) Sangolqui, Ecuador 2014 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 May 2020 EDNA-HOST: DETECTION OF GLOBAL PLANT VIROMES USING HIGH THROUGHPUT SEQUENCING Dissertation Approved: Francisco Ochoa-Corona, Ph.D. Dissertation Adviser Committee member Akhtar, Ali, Ph.D. Committee member Hassan Melouk, Ph.D. Committee member Andres Espindola, Ph.D. Outside Committee Member Daren Hagen, Ph.D. ii ACKNOWLEDGEMENTS I would like to express sincere thanks to my major adviser Dr. Francisco Ochoa –Corona for his guidance from the beginning of my journey believing and trust that I am capable of developing a career as a scientist. I am thankful for his support and encouragement during hard times in research as well as in personal life. I truly appreciate the helpfulness of my advisory committee for their constructive input and guidance, thanks to: Dr. Akhtar Ali for his support in this research project and his kindness all the time, Dr. Hassan Melouk for his assistance, encouragement and his helpfulness in this study, Dr. Andres Espindola, developer of EDNA MiFi™, he was extremely helpful in every step of EDNA research, and for his willingness to give his time and advise; to Dr. Darren Hagen for his support and advise with bioinformatics and for his encouragement to develop a new set of research skills. I deeply appreciate Dr. -
Blackberry Virus E: an Unusual flexivirus
Arch Virol (2011) 156:1665–1669 DOI 10.1007/s00705-011-1015-y BRIEF REPORT Blackberry virus E: an unusual flexivirus Sead Sabanadzovic • Nina Abou Ghanem-Sabanadzovic • Ioannis E. Tzanetakis Received: 5 November 2010 / Accepted: 30 April 2011 / Published online: 9 June 2011 Ó Springer-Verlag 2011 Abstract A virus, named blackberry virus E (BVE), was disease (BYVD), a serious disorder observed in the south- recently discovered in blackberries and characterized. The ern United States [19]. Disease symptoms are not specific to virus genome is 7,718 nt long, excluding the poly-A tail, any given virus combination, and different virus combina- contains five open reading frames (ORFs) and resembles that tions are found associated with identical symptoms [19]. of flexiviruses. Phylogenetic analysis revealed relationships This study was initiated with four blackberry plants to allexiviruses, which are known to infect plants of the showing BYVD-like symptoms observed in northeastern family Alliaceae. BVE lacks the 3’end-proximal ORF, Mississippi (Fig. 1A). They were tested by ELISA using which encodes a nucleotide-binding protein, a putative antibodies specific for 12 viruses and a ‘‘universal potyvirus’’ silencing suppressor in allexiviruses. The overall results of kit (Agdia Inc., USA). Additionally, they were tested by this study suggest that this virus is an atypical and as yet reverse transcription polymerase chain reaction (RT-PCR) undescribed flexivirus that is closely related to allexiviruses. using specific primers for viruses identified recently in BYVD-affected plants, or one still being characterized and Keywords Blackberry Á Virus Á dsRNA Á lacking serological diagnostics (authors, unpublished data). Alphaflexiviridae Á RT-PCR All four specimens were infected with blackberry virus Y, a virus known to be asymptomatic in single infections [17], leading to the assumption that one or more additional viruses Rubus species (blackberry, raspberry and their hybrids) are are involved in the observed symptomatology. -
Short 5′ UTR Enables Optimal Translation of Plant Virus Tricistronic RNA Via Leaky Scanning
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.14.444105; this version posted May 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 4.0 International license. Title Short 5′ UTR enables optimal translation of plant virus tricistronic RNA via leaky scanning Authors Yuji Fujimoto1, Takuya Keima1, Masayoshi Hashimoto1, Yuka Hagiwara-Komoda2, Naoi Hosoe1, Shuko Nishida1, Takamichi Nijo1, Kenro Oshima3, Jeanmarie Verchot4, Shigetou Namba1, and Yasuyuki Yamaji1* 1Graduate School of Agricultural and Life Sciences, The University of Tokyo, 113-8657 Tokyo, Japan 2Department of Sustainable Agriculture, College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, 069-8501 Ebetsu Hokkaido, Japan 3Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei-shi, 184-8584 Tokyo, Japan 4Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77802, USA. Correspondence *To whom correspondence should be addressed. Tel: +81-3-5841-5092. Fax: +81-3-5841-5090. E-mail: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.05.14.444105; this version posted May 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 4.0 International license. Abstract Regardless of the general model of translation in eukaryotic cells, a number of studies suggested that many of mRNAs encode multiple proteins. -
Hypera Postica) and Its Host Plant, Alfalfa (Medicago Sativa
Article Characterisation of the Viral Community Associated with the Alfalfa Weevil (Hypera postica) and Its Host Plant, Alfalfa (Medicago sativa) Sarah François 1,2,*, Aymeric Antoine-Lorquin 2, Maximilien Kulikowski 2, Marie Frayssinet 2, Denis Filloux 3,4, Emmanuel Fernandez 3,4, Philippe Roumagnac 3,4, Rémy Froissart 5 and Mylène Ogliastro 2,* 1 Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, South Park Road, Oxford OX1 3SY, UK 2 DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE 34095 Montpellier, France; [email protected] (A.A.-L.); [email protected] (M.K.); [email protected] (M.F.) 3 CIRAD, UMR PHIM, 34090 Montpellier, France; [email protected] (D.F.); [email protected] (E.F.); [email protected] (P.R.) 4 PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD 34090 Montpellier, France 5 MIVEGEC Infectious and Vector Diseases: Ecology, Genetics, Evolution and Control, University of Montpellier, CNRS, IRD 34394 Montpellier, France; [email protected] Citation: François, S.; * Correspondence: [email protected] (S.F.); [email protected] (M.O.) Antoine-Lorquin, A.; Kulikowski, M.; Frayssinet, M.; Abstract: Advances in viral metagenomics have paved the way of virus discovery by making the Filloux, D.; Fernandez, E.; exploration of viruses in any ecosystem possible. Applied to agroecosystems, such an approach Roumagnac, P.; Froissart, R.; opens new possibilities to explore how viruses circulate between insects and plants, which may help Ogliastro, M. Characterisation of the to optimise their management. It could also lead to identifying novel entomopathogenic viral re- Viral Community Associated with sources potentially suitable for biocontrol strategies. -
011P 2008.008P 2008.009P 2008.010P
Taxonomic proposal to the ICTV Executive Committee This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). 2008.008- Code(s) assigned: (to be completed by ICTV officers) 011P Short title: Creation of genus Lolavirus in the family Alphaflexiviridae for Lolium latent virus (e.g. 6 new species in the genus Zetavirus; re-classification of the family Zetaviridae etc.) Modules attached 1 2 3 4 5 (please check all that apply): 6 7 Author(s) with e-mail address(es) of the proposer: John Hammond ([email protected]) Anna Maria Vaira ([email protected]) Clarissa Maroon-Lango ([email protected]) ICTV-EC or Study Group comments and response of the proposer: The EC requested a phylogenetic tree that provided information on genetic distances between the sequences. This has been added to the proposal as Figure 3 by the chair of the plant virus subcommittee to further support the proposal. MODULE 4: NEW GENUS (if more than one genus is to be created, please complete additional copies of this section) Code 2008.008P (assigned by ICTV officers) To create a new genus assigned as follows: Subfamily: Fill in all that apply. Ideally, a genus should be placed within a higher taxon, Family: Alphaflexiviridae but if not put “unassigned” here. Order: Tymovirales Code 2008.009P (assigned by ICTV officers) To name the new genus: Lolavirus Code 2008.010P (assigned by ICTV officers) To assign the following as species in the new genus: Lolium latent virus -
The Characterisation of Ornithogalum Mosaic Virus
/ THE CHARACTERISATION OF ORNITHOGALUM MOSAIC VIRUS Johan Theodorus Burger University of Cape Town A dissertation submitted in fulfilment of the requiremements for the Degree of Doctor of Philosophy in the Faculty of Science, University of Cape Town. Cape Town, November, 1990 ·F-~~-=-~:.r:-":':."·.-:_~-~·;-.~--:-~·_::--:"_-.:-:::·_, ·_-:-... _... ';' _-:_: = -~-- -·-:--~ -~u 7 1! ~h: ~;;;-:f)~;_i~y :~(.\ ~~ ~~'·:~~ .. ~;.;s-~::;3:,_~:~:~~ '] c~v~1 ~:.:~.- -· . ·' -:~. ;: The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town CERTIFICATION OF SUPERVISOR' In terms of paragraph GP 8 in " General rules for the Degree of Doctor of Philosophy (PhD)", I as supervisor of the candidate, Johan Theodorus Burger, certify that I approve of- the incorporation in this dissertation of material that has already been submitted or accepted for publication. Associated Professor M. B. Von Wechmar Department of Microbiology University of Cape Town i CONTENTS ACKNOWLEDGEMENTS .................................... · ii ABBREVIATIONS . iii LIST OF FIGURES . vi LIST OFTABLES ................................ ; . ix ABSTRACT............................................ X CHAPTER 1: Introduction .......... "'· . 1 CHAPTER 2: The purification and physicochemical characterisation of ornithogalum mosaic virus. 33 CHAPTER 3: Serology of ornithogalum mosaic virus . 48 CHAPTER 4: Biological aspects of ornithogalum mosaic virus . 70 CHAPTER 5: Molecular cloning and nucleotide sequencing of ornithogalum mosaic virus. 88 CHAPTER 6: The expression of ornithogalum mosaic virus coat protein in E.