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Fontdevila Pareta N, Khalili M, Maachi A, Rivarez MPS, Rollin J, Salavert F, Temple C, Aranda MA, Boonham N, Botermans M, Candresse T, Fox A, Hernando Y, Kutnjak D, Marais A, Petter F, Ravnikar M, Selmi I, Tahzima R, Trontin C, Wetzel T, Massart S. Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis. Front Microbiol 2023; 14:1181562. [PMID: 37323908 PMCID: PMC10265641 DOI: 10.3389/fmicb.2023.1181562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/25/2023] [Indexed: 06/17/2023] Open
Abstract
The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties.
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Affiliation(s)
| | - Maryam Khalili
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
- EGFV, Univ. Bordeaux, INRAE, ISVV, Villenave d’Ornon, France
| | | | - Mark Paul S. Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- College of Agriculture and Agri-Industries, Caraga State University, Butuan, Philippines
| | - Johan Rollin
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- DNAVision (Belgium), Charleroi, Belgium
| | - Ferran Salavert
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Coline Temple
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Miguel A. Aranda
- Department of Stress Biology and Plant Pathology, Center for Edaphology and Applied Biology of Segura, Spanish National Research Council (CSIC), Murcia, Spain
| | - Neil Boonham
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), Wageningen, Netherlands
| | | | - Adrian Fox
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
- Fera Science Ltd, York Biotech Campus, York, United Kingdom
| | | | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | | | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ilhem Selmi
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Rachid Tahzima
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Plant Sciences Unit, Institute for Agricultural, Fisheries and Food Research (ILVO), Merelbeke, Belgium
| | - Charlotte Trontin
- European and Mediterranean Plant Protection Organization, Paris, France
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Sebastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Bioversity International, Montpellier, France
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Morán F, Olmos A, Glasa M, Silva MBD, Maliogka V, Wetzel T, Ruiz-García AB. A Novel and Highly Inclusive Quantitative Real-Time RT-PCR Method for the Broad and Efficient Detection of Grapevine Leafroll-Associated Virus 1. Plants (Basel) 2023; 12:876. [PMID: 36840223 PMCID: PMC9962094 DOI: 10.3390/plants12040876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/20/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Grapevine (Vitis vinifera L.) is one of the most important crops in the world due to its economic and social impact. Like many other crops, grapevine is susceptible to different types of diseases caused by pathogenic microorganisms. Grapevine leafroll-associated virus 1 (GLRaV-1) is a virus associated with grapevine leafroll disease and it is considered at the national and European level as a pathogen that must be absent in propagative plant material. For this reason, the availability of specific, sensitive and reliable detection techniques to ascertain the sanitary status of the plants is of great importance. The objective of this research was the development of a new GLRaV-1 detection method based on a TaqMan quantitative real-time RT-PCR targeted to the coat protein genomic region and including a host internal control in a duplex reaction. To this end, three new GLRaV-1 full genomes were recovered by HTS and aligned with all sequences available in the databases. The method has been validated following EPPO standards and applied for the diagnosis of field plant material and transmission vectors. The new protocol designed has turned out to be highly sensitive as well as much more specific than the current available methods for the detection and absolute quantitation of GLRaV-1 viral titer.
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Affiliation(s)
- Félix Morán
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, Moncada, 46113 Valencia, Spain
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, Moncada, 46113 Valencia, Spain
| | - Miroslav Glasa
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská Cesta 9, 84505 Bratislava, Slovakia
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia
| | - Marilia Bueno Da Silva
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, Moncada, 46113 Valencia, Spain
| | - Varvara Maliogka
- Plant Pathology Laboratory, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Breitenweg, 71, 67435 Neustadt an der Weinstrasse, Germany
| | - Ana Belén Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, Moncada, 46113 Valencia, Spain
- Departamento de Microbiología y Ecología, C/Doctor Moliner 50, Burjasot, 46100 Valencia, Spain
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Ben-Amar A, Daldoul S, Allel D, Wetzel T, Mliki A. Ectopic expression of a grapevine alkaline α-galactosidase seed imbibition protein VvSIP enhanced salinity tolerance in transgenic tobacco plants. Funct Integr Genomics 2022; 23:12. [PMID: 36547729 DOI: 10.1007/s10142-022-00945-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Alpha-galactosidase seed imbibition protein (VvSIP) isolated from Vitis vinifera is up-regulated upon salt stress and mediates osmotic stress responses in a tolerant grapevine cultivar. So far, little is known about the putative role of this stress-responsive gene. In the present study, VvSIP function was investigated in model tobacco plants via Agrobacterium-mediated genetic transformation. Our results showed that overexpression of VvSIP exhibited increased tolerance to salinity at germination and late vegetative stage in transgenic Nicotiana benthamiana compared to the nontransgenic plants based on the measurement of the germination rate and biomass production. High salt concentrations of 200 and 400 mM NaCl in greenhouse-grown pot assay resulted in better relative water content, higher leaf osmotic potential, and leaf water potential in transgenic lines when compared to the wild-type (WT) plants. These physiological changes attributed to efficient osmotic adjustment improved plant performance and tolerance to salinity compared to the WT. Moreover, the VvSIP-expressing lines SIP1 and SIP2 showed elevated amounts of chlorophyll with lower malondialdehyde content indicating a reduced lipid peroxidation required to maintain membrane stability. When subjected to high salinity conditions, the transgenic tobacco VvSIP exhibited higher soluble sugar content, which may suggest an enhancement of the carbohydrate metabolism. Our findings indicate that the VvSIP is involved in plant salt tolerance by functioning as a positive regulator of osmotic adjustment and sugar metabolism, both of which are responsible for stress mitigation. Such a candidate gene is highly suitable to alleviate environmental stresses and thus could be a promising candidate for crop improvement.
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Affiliation(s)
- Anis Ben-Amar
- Department of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Science and Technology Park, P.O. Box. 901, 2050, Hammam-Lif, Tunisia.
| | - Samia Daldoul
- Department of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Science and Technology Park, P.O. Box. 901, 2050, Hammam-Lif, Tunisia
| | - Dorsaf Allel
- Department of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Science and Technology Park, P.O. Box. 901, 2050, Hammam-Lif, Tunisia
| | - Thierry Wetzel
- Institute of Plant Protection, DLR Rheinpfalz, Breitenweg 71, 67435, Neustadt an Der Weinstrasse, Germany
| | - Ahmed Mliki
- Department of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, Science and Technology Park, P.O. Box. 901, 2050, Hammam-Lif, Tunisia
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Daldoul S, Hanzouli F, Hamdi Z, Chenenaoui S, Wetzel T, Nick P, Mliki A, Gargouri M. The root transcriptome dynamics reveals new valuable insights in the salt-resilience mechanism of wild grapevine ( Vitis vinifera subsp . sylvestris). Front Plant Sci 2022; 13:1077710. [PMID: 36570937 PMCID: PMC9780605 DOI: 10.3389/fpls.2022.1077710] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 11/16/2022] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Most of elite cultivated grapevine varieties (Vitis vinifera L.), conventionally grafted on rootstocks, are becoming more and more affected by climate changes, such as increase of salinity. Therefore, we revisited the valuable genetic resources of wild grapevines (V. sylvestris) to elaborate strategies for a sustainable viticulture. METHODS Here, we compared physiological and biochemical responses of two salt-tolerant species: a wild grapevine genotype "Tebaba" from our previous studies and the conventional rootstock "1103 Paulsen". Interestingly, our physio-biochemical results showed that under 150mM NaCl, "Tebaba" maintains higher leaf osmotic potential, lower Na+/K+ ratio and a significant peaked increase of polyphenol content at the first 8h of salinity stress. This behavior allowed to hypothesis a drastic repatterning of metabolism in "Tebaba's" roots following a biphasic response. In order to deepen our understanding on the "Tebaba" salt tolerance mechanism, we investigated a time-dependent transcriptomic analysis covering three sampling times, 8h, 24h and 48h. RESULTS The dynamic analysis indicated that "Tebaba" root cells detect and respond on a large scale within 8h to an accumulation of ROS by enhancing a translational reprogramming process and inducing the transcripts of glycolytic metabolism and flavonoids biosynthesis as a predominate non-enzymatic scavenging process. Afterwards, there is a transition to a largely gluconeogenic stage followed by a combined response mechanism based on cell wall remodeling and lignin biosynthesis with an efficient osmoregulation between 24 and 48 h. DISCUSSION This investigation explored for the first time in depth the established cross-talk between the physiological, biochemical and transcriptional regulators contributing to propose a hypothetical model of the dynamic salt mechanism tolerance of wild grapevines. In summary, these findings allowed further understanding of the genetic regulation mechanism of salt-tolerance in V. sylvestris and identified specific candidate genes valuable for appropriate breeding strategies.
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Affiliation(s)
- Samia Daldoul
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Faouzia Hanzouli
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
- Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Zohra Hamdi
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Synda Chenenaoui
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Peter Nick
- Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
| | - Mahmoud Gargouri
- Laboratory of Plant Molecular Physiology, Center of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia
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Fuchs M, Hily JM, Petrzik K, Sanfaçon H, Thompson JR, van der Vlugt R, Wetzel T, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Secoviridae 2022. J Gen Virol 2022; 103. [PMID: 36748634 DOI: 10.1099/jgv.0.001807] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Members of the family Secoviridae are non-enveloped plant viruses with mono- or bipartite linear positive-sense ssRNA genomes with a combined genome of 9 to 13.7 kb and icosahedral particles 25-30 nm in diameter. They are related to picornaviruses and are members of the order Picornavirales. Genera in the family are distinguished by the host range, vector, genomic features and phylogeny of the member viruses. Most members infect dicotyledonous plants, and many cause serious disease epidemics. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Secoviridae, which is available at ictv.global/report/secoviridae.
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Affiliation(s)
- Marc Fuchs
- School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Jean-Michel Hily
- Institut Français de la Vigne et du Vin, 30240 Le Grau du Roi, France
| | - Karel Petrzik
- Institute of Plant Molecular Biology, 370 05 České Budějovice, Czech Republic
| | | | | | | | - Thierry Wetzel
- DLR Rheinpfalz, Neustadt an der Weinstrasse 67435, Germany
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Jarausch B, Biancu S, Kugler S, Wetzel T, Baumann M, Winterhagen P, Jarausch W, Kortekamp A, Maixner M. First report of Flavescence dorée-related Phytoplasma in Grapevine in Germany. Plant Dis 2021; 105:3285. [PMID: 33823613 DOI: 10.1094/pdis-02-21-0330-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Flavescence dorée (FD) and Bois noir (BN) are the principal grapevine yellows diseases in Europe caused by distinct phytoplasmas: FD by 16SrV phytoplasmas (FDp), BN by Candidatus Phytoplasma solani. FDp is spread epidemically by the introduced Nearctic Deltocephalinae Scaphoideus titanus and is listed as a quarantine pest in the European Union (Regulation (EU) 2019/2072). Black Alder (Alnus glutinosa) is a common asymptotic host of 16SrV phytoplasmas in Europe and considered the original host of FDp (Malembic-Maher et al. 2020). Palatinate grapevine yellows (PGY) transmitted from alder to grapevine by the Macropsinae Oncopsis alni (Maixner et al. 2000) is not transmissible by S. titanus, unlike isolates transmitted by the autochthonous Deltocephalinae Allygus spp. and the invasive Orientus ishidae (Malembic-Maher et al. 2020). Germany is considered free from FD in grapevine and from its vector. A single case in a nursery in 2014 was eradicated (EPPO 2017). Since S. titanus was detected in 2016 in the neighboring French Region of Alsace, monitoring of FD was carried out in Germany. It was focused on vineyards within a distance of 100 m from stands of alder trees. A geodata-based risk map (Jalke 2020) was used to identify those plots. All symptomatic vines sampled until September 2020 proved to be infected by BN or, occasionally, by PGY. Eight vines with typical symptoms were sampled in vineyards adjacent to alder stands in the winegrowing region of Rheinhessen in September 2020. Symptoms comprised leaf rolling and discoloration, incomplete lignification, black pustules on shoots, dried inflorescences and shriveled berries. Diseased shoots were black and necrotic in December. Leaf midribs were sampled for total DNA extraction. The phytoplasma 16S rRNA gene was amplified by generic primers R16F2/R2-mod followed by a nested PCR using 16Sr(V) group-specific primers R16(V)F1/R1, and primers R16(I)F1/R1 (Lee et al. 1995) to detect 'Candidatus Phytoplasma solani', associated with BN. While BN was detected in seven vines, one sample tested positive for 16SrV phytoplasma. This result was confirmed by triplex real-time Taq-Man assay based on rpl14 gene sequences (IPADLAB), by multiplex real-time PCR of map locus as well as by Loop-mediated isothermal amplification (LAMP) according to the EPPO diagnostic standard PM 7/079(2) (EPPO 2016). PCR-products of the map- and the vmpA-Gene (Malembic-Maher et al., 2020) were sequenced and compared to reference sequences to distinguish between FD- and non-FD genotypes. The isolate from the diseased vine exhibited 100% identity with map-M38 (Accession No. LT221933), a genotype of the map-FD2 cluster. The same genotype was detected in A. glutinosa and Allygus spp. sampled at the infested site. A 234 bp sequence of the first repeat of the vmpA-gene showed 100% identity with the S. titanus transmitted isolate FD-92 (Accession No. LN680870) of the vmpA-II cluster. It can be concluded, that the 16SrV-isolate detected in a symptomatic grapevine is infected by FD and not PGY. This is the first report of FD in a vineyard in Germany. The infected vine of cv. Silvaner was 25 years old. While infected planting material is an unlikely source of the infection, a transmission of FDp from alder is highly probable. Finding a single FD-infection after several years of testing implies a low risk originating from the wild compartment, but the approach of the vector S. titanus justifies further monitoring activities. The infected vine was eradicated.
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Affiliation(s)
- Barbara Jarausch
- Julius Kühn-Institut Federal Research Institute for Plant Protection in Fruit Crops and Viticulture, Siebeldingen, Germany;
| | - Sandra Biancu
- Julius Kühn-Institut Federal Reserach Institute for Plant Protection in Fruit Crops and Viticulture, Siebeldingen, Germany;
| | - Sanela Kugler
- Julius Kühn-Institut Federal Institute for Plant Protection in Fruit Crops and Viticulture, Siebeldingen, Germany;
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Breitenweg 71, Neustadt an der Weinstrasse, Germany, 67435;
| | - Manuel Baumann
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany;
| | - Patrick Winterhagen
- Dienstleistungszentrum ländlicher Raum, 111096, Breitenweg 71, Neustadt, Germany, 67435;
| | | | - Andreas Kortekamp
- DLR Rheinpfalz, Institut für Phytomedizin , Neustadt an der Weinstrasse, Germany;
| | - Michael Maixner
- Julius Kühn-Institut (JKI) Federal Research Institute for Cultivated Plants, Siebeldingen, Germany;
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Pacio J, Daubner M, Fellmoser F, Wetzel T. Experimental study of the influence of inter-wrapper flow on liquid-metal cooled fuel assemblies. Nuclear Engineering and Design 2019. [DOI: 10.1016/j.nucengdes.2019.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Junge-Hoffmeister J, Bittner A, Kress V, Wetzel T, Weidner K. Traumatisierte Mütter – Einfluss auf die postpartale Psychopathologie und die Mutter-Kind-Interaktion. Geburtshilfe Frauenheilkd 2019. [DOI: 10.1055/s-0039-1678367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
| | - A Bittner
- Klinik für Psychotherapie und Psychosomatik, Universitätsklinikum Dresden
| | - V Kress
- Klinik für Psychotherapie und Psychosomatik, Universitätsklinikum Dresden
| | - T Wetzel
- Klinik für Psychotherapie und Psychosomatik, Universitätsklinikum Dresden
| | - K Weidner
- Klinik für Psychotherapie und Psychosomatik, Universitätsklinikum Dresden
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Nourinejhad Zarghani S, Hily JM, Glasa M, Marais A, Wetzel T, Faure C, Vigne E, Velt A, Lemaire O, Boursiquot JM, Okic A, Ruiz-Garcia AB, Olmos A, Lacombe T, Candresse T. Grapevine virus T diversity as revealed by full-length genome sequences assembled from high-throughput sequence data. PLoS One 2018; 13:e0206010. [PMID: 30376573 PMCID: PMC6207325 DOI: 10.1371/journal.pone.0206010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/04/2018] [Indexed: 12/13/2022] Open
Abstract
RNASeq or double-stranded RNA based approaches allowed the reconstruction of a total of 9 full-length or near full-length genomes of the recently discovered grapevine virus T (GVT). In addition, datamining of publicly available grapevine RNASeq transcriptome data allowed the reconstruction of a further 14 GVT genomes from five grapevine sources. Together with four GVT sequences available in Genbank, these novel sequences were used to analyse GVT diversity. GVT shows a very limited amount of indels variation but a high level of nucleotide and aminoacid polymorphism. This level is comparable to that shown in the closely related grapevine rupestris stem pitting-associated virus (GRSPaV). Further analyses showed that GVT mostly evolves under conservative selection pressure and that recombination has contributed to its evolutionary history. Phylogenetic analyses allow to identify at least seven clearly separated groups of GVT isolates. Analysis of the only reported PCR GVT-specific detection primer pair indicates that it is likely to fail to amplify some GVT isolates. Taken together these results point at the distinctiveness of GVT but also at the many points it shares with GRSPaV. They constitute the first pan-genomic analysis of the diversity of this novel virus.
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Affiliation(s)
- Shaheen Nourinejhad Zarghani
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
- Department of Plant Protection, College of Abouraihan, University of Tehran, Tehran, Iran
| | | | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Armelle Marais
- Equipe de Virologie, UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Chantal Faure
- Equipe de Virologie, UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | | | - Amandine Velt
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Olivier Lemaire
- Université de Strasbourg, INRA, SVQV UMR-A 1131, Colmar, France
| | - Jean Michel Boursiquot
- UMR 1334 AGAP, INRA, Montpellier SupAgro, Montpellier, France
- Centre de Ressources Biologiques de la Vigne, INRA, Marseillan-Plage, France
| | - Arnela Okic
- University of Sarajevo, Faculty of Agriculture and Food Science, Sarajevo, Bosnia and Herzegovina
| | | | - Antonio Olmos
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Thierry Lacombe
- UMR 1334 AGAP, INRA, Montpellier SupAgro, Montpellier, France
- Centre de Ressources Biologiques de la Vigne, INRA, Marseillan-Plage, France
| | - Thierry Candresse
- Equipe de Virologie, UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
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Daldoul S, Massart S, Ruiz-García AB, Olmos A, Wetzel T. First Report of Grapevine rupestris vein feathering virus in grapevine in Germany. Plant Dis 2018; 102:PDIS03180533PDN. [PMID: 30117786 DOI: 10.1094/pdis-03-18-0533-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- S Daldoul
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany, and Laboratory of Plant Molecular Physiology, Biotechnology Center of Borj Cedria, PB 901, 2050 Hammam-Lif, Tunisia
| | - S Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - A B Ruiz-García
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain
| | - A Olmos
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain
| | - T Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
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Glasa M, Predajňa L, Sihelská N, Šoltys K, Ruiz-García AB, Olmos A, Wetzel T, Sabanadzovic S. Grapevine virus T is relatively widespread in Slovakia and Czech Republic and genetically diverse. Virus Genes 2018; 54:737-741. [PMID: 29995199 DOI: 10.1007/s11262-018-1587-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/05/2018] [Indexed: 11/26/2022]
Abstract
A recently described putative foveavirus, grapevine virus T (GVT), was detected in a Slovak grapevine accession (SK704) using high-throughput sequencing, prompting further studies. Full-length genome sequence of isolate GVT-SK704 was determined. Analyses revealed 86.1% nucleotide identity with the Italian GVT isolate, currently the only available nearly complete sequence of GVT in GenBank. A virus-specific RT-PCR assay was developed, which enabled a survey of GVT incidence in grapevine samples from Slovakia and Czech Republic. Unexpectedly, GVT was present in ~ 30% of tested samples. Analysis of complete CP gene sequences of 20 Slovak and Czech GVT isolates detected in the survey revealed relatively high intra-species variability (up to 11.2% nucleotide divergence), suggesting multiple introductions from different sources, possibly over an extended period of time.
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Affiliation(s)
- Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505, Bratislava, Slovakia.
| | - Lukáš Predajňa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505, Bratislava, Slovakia
| | - Nina Sihelská
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505, Bratislava, Slovakia
| | - Katarína Šoltys
- Comenius University Science Park, Comenius University, Ilkovičova 8, 841 04, Bratislava, Slovakia
| | - Ana Belén Ruiz-García
- Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada a Náquera km 4.5, Moncada, 46113, Valencia, Spain
| | - Antonio Olmos
- Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada a Náquera km 4.5, Moncada, 46113, Valencia, Spain
| | - Thierry Wetzel
- Institute of Plant Protection, DLR Rheinpfalz, Breitenweg 71, 67435, Neustadt an der Weinstrasse, Germany
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, USA
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12
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Pacio J, Daubner M, Fellmoser F, Litfin K, Wetzel T. Heat transfer experiment in a partially (internally) blocked 19-rod bundle with wire spacers cooled by LBE. Nuclear Engineering and Design 2018. [DOI: 10.1016/j.nucengdes.2018.01.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Daldoul S, Amar AB, Gargouri M, Limam H, Mliki A, Wetzel T. A Grapevine-Inducible Gene Vv-α-gal/SIP Confers Salt and Desiccation Tolerance in Escherichia coli and Tobacco at Germinative Stage. Biochem Genet 2018; 56:78-92. [PMID: 29150723 DOI: 10.1007/s10528-017-9831-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 11/11/2017] [Indexed: 01/01/2023]
Abstract
Grapevine is an important fruit crop cultivated worldwide. Previously, we have reported the characterization of a salt stress-inducible gene Vv-α-gal/SIP isolated from the tolerant grapevine cultivar Razegui. In this study, we performed functional studies in both Escherichia coli and tobacco systems to gain more insights in the role of the Vv-α-gal/SIP gene. Our data revealed that the recombinant E. coli cells harboring the pET24b+ expression vector with the Vv-α-gal/SIP showed higher tolerance to desiccation and salinity compared to E. coli cells harboring the vector alone. In addition, the transgenic tobacco plants expressing the Vv-α-gal/SIP gene exhibited a higher percentage of seed germination and better growth under salt stress than the wild-type (WT) tobacco seedlings. This stress mitigation might be related to the putative function of this gene, which is thought to be involved in carbohydrate metabolism regulation. Collectively, these results suggest that Vv-α-gal/SIP is potentially a candidate gene for engineering drought and salt tolerance in cultivated plants.
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Affiliation(s)
- Samia Daldoul
- Laboratory of Plant Molecular Physiology, Biotechnology Center of Borj Cedria, PB.901, 2050, Hammam-Lif, Tunisia.
- DLR Rheinpfalz, Institute of Plant Protection, Breitenweg 71, 67435, Neustadt an Der Weinstraße, Germany.
| | - Anis Ben Amar
- Laboratory of Plant Molecular Physiology, Biotechnology Center of Borj Cedria, PB.901, 2050, Hammam-Lif, Tunisia
- DLR Rheinpfalz, Institute of Plant Protection, Breitenweg 71, 67435, Neustadt an Der Weinstraße, Germany
| | - Mahmoud Gargouri
- Laboratory of Plant Molecular Physiology, Biotechnology Center of Borj Cedria, PB.901, 2050, Hammam-Lif, Tunisia
| | - Hajer Limam
- Laboratory of Plant Molecular Physiology, Biotechnology Center of Borj Cedria, PB.901, 2050, Hammam-Lif, Tunisia
| | - Ahmed Mliki
- Laboratory of Plant Molecular Physiology, Biotechnology Center of Borj Cedria, PB.901, 2050, Hammam-Lif, Tunisia
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Breitenweg 71, 67435, Neustadt an Der Weinstraße, Germany
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14
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Flesch J, Niedermeier K, Fritsch A, Musaeva D, Marocco L, Uhlig R, Baake E, Buck R, Wetzel T. Liquid metals for solar power systems. ACTA ACUST UNITED AC 2017. [DOI: 10.1088/1757-899x/228/1/012012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Thompson JR, Dasgupta I, Fuchs M, Iwanami T, Karasev AV, Petrzik K, Sanfaçon H, Tzanetakis I, van der Vlugt R, Wetzel T, Yoshikawa N, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Secoviridae. J Gen Virol 2017; 98:529-531. [PMID: 28452295 PMCID: PMC5657025 DOI: 10.1099/jgv.0.000779] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the family Secoviridae are non-enveloped viruses with
mono- or bipartite (RNA-1 and RNA-2) linear positive-sense ssRNA genomes with
the size of the RNAs combined ranging from 9 to 13.7 kb.
They are related to picornaviruses and are classified in the order
Picornavirales. The majority of known members infect
dicotyledonous plants and many are important plant pathogens (e.g. grapevine
fanleaf virus and rice tungro spherical virus). This is a summary of the current
International Committee on Taxonomy of Viruses (ICTV) report on the taxonomy of
the family Secoviridae available at www.ictv.global/report/secoviridae.
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Affiliation(s)
- Jeremy R Thompson
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Marc Fuchs
- School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, USA
| | - Toru Iwanami
- Apple Research Station, NARO Institute of Fruit Tree and Tee Science, Nabeyashiki 92-24, Shimokuriyagawa, Morioka, Iwate 020-0123, Japan
| | | | - Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre AS CR, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic
| | - Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, P.O. Box 5000, 4200 Highway 97, Summerland, B.C., Canada V0H 1Z0
| | - Ioannis Tzanetakis
- Department of Plant Pathology, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - René van der Vlugt
- Wageningen Research, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Thierry Wetzel
- DLR Rheinpfalz - Institute of Plant Protection, Breitenweg 71, Neustadt an der Weinstrasse 67435, Germany
| | - Nobuyuki Yoshikawa
- Plant Pathology Lab, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka 020-8550, Japan
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16
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Pacio J, Wetzel T, Doolaard H, Roelofs F, Van Tichelen K. Thermal-hydraulic study of the LBE-cooled fuel assembly in the MYRRHA reactor: Experiments and simulations. Nuclear Engineering and Design 2017. [DOI: 10.1016/j.nucengdes.2016.08.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Glasa M, Predajňa L, Šoltys K, Sihelská N, Nagyová A, Wetzel T, Sabanadzovic S. Analysis of Grapevine rupestris stem pitting-associated virus in Slovakia Reveals Differences in Intra-Host Population Diversity and Naturally Occurring Recombination Events. Plant Pathol J 2017; 33:34-42. [PMID: 28167886 PMCID: PMC5291396 DOI: 10.5423/ppj.oa.07.2016.0158] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/30/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
Grapevine rupestris stem pitting-associated virus (GRSPaV) is a worldwide-distributed pathogen in grapevines with a high genetic variability. Our study revealed differences in the complexity of GRSPaV population in a single host. A single-variant GRSPaV infection was detected from the SK30 grapevine plant. On the contrary, SK704 grapevine was infected by three different GRSPaV variants. Variant-specific RT-PCR detection protocols have been developed in this work to study distribution of the three different variants in the same plant during the season. This study showed their randomized distribution in the infected SK704 grapevine plant. Comparative analysis of fulllength genome sequences of four Slovak GRSPaV isolates determined in this work and 14 database sequences showed that population of the virus cluster into four major phylogenetic lineages. Moreover, our analyses suggest that genetic recombination along with point mutations could play a significant role in shaping evolutionary history of GRSPaV and contributed to its extant genetic diversification.
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Affiliation(s)
- Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava 84505,
Slovakia
| | - Lukáš Predajňa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava 84505,
Slovakia
| | - Katarína Šoltys
- Comenius University Science Park, Comenius University, Bratislava 84216,
Slovakia
| | - Nina Sihelská
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava 84505,
Slovakia
| | - Alžbeta Nagyová
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Bratislava 84505,
Slovakia
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse 67435,
Germany
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39762,
USA
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18
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Massart S, Candresse T, Gil J, Lacomme C, Predajna L, Ravnikar M, Reynard JS, Rumbou A, Saldarelli P, Škorić D, Vainio EJ, Valkonen JPT, Vanderschuren H, Varveri C, Wetzel T. A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies. Front Microbiol 2017; 8:45. [PMID: 28174561 PMCID: PMC5258733 DOI: 10.3389/fmicb.2017.00045] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/06/2017] [Indexed: 01/14/2023] Open
Abstract
Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.
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Affiliation(s)
- Sebastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Thierry Candresse
- Institut National de la Recherche Agronomique (INRA), University of Bordeaux, CS20032 UMR 1332 BFP Villenave d'Ornon, France
| | - José Gil
- Plant Biology, Linnean Centre for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Christophe Lacomme
- Virology and Zoology, Science and Advice for Scottish Agriculture Edinbourgh, UK
| | - Lukas Predajna
- Department of Plant Virology, Institute of Virology, Biomedical Research Center, Slovak Academy of Science (SAS) Bratislava, Slovakia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology Ljubljana, Slovenia
| | | | - Artemis Rumbou
- Division Phytomedicine Lentzeallee, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-University of Berlin Berlin, Germany
| | - Pasquale Saldarelli
- National Research Council Institute for Sustainable Plant Protection Bari, Italy
| | - Dijana Škorić
- Department of Biology, Faculty of Science, University of Zagreb Zagreb, Croatia
| | - Eeva J Vainio
- Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke) Helsinki, Finland
| | - Jari P T Valkonen
- Department of Agricultural Sciences, University of Helsinki Helsinki, Finland
| | - Hervé Vanderschuren
- Plant Genetics, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Christina Varveri
- Department of Phytopathology, Benaki Phytopathological Institute Athens, Greece
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse Germany
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19
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Afonso CL, Amarasinghe GK, Bányai K, Bào Y, Basler CF, Bavari S, Bejerman N, Blasdell KR, Briand FX, Briese T, Bukreyev A, Calisher CH, Chandran K, Chéng J, Clawson AN, Collins PL, Dietzgen RG, Dolnik O, Domier LL, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Farkas SL, Freitas-Astúa J, Formenty P, Fouchier RAM, Fù Y, Ghedin E, Goodin MM, Hewson R, Horie M, Hyndman TH, Jiāng D, Kitajima EW, Kobinger GP, Kondo H, Kurath G, Lamb RA, Lenardon S, Leroy EM, Li CX, Lin XD, Liú L, Longdon B, Marton S, Maisner A, Mühlberger E, Netesov SV, Nowotny N, Patterson JL, Payne SL, Paweska JT, Randall RE, Rima BK, Rota P, Rubbenstroth D, Schwemmle M, Shi M, Smither SJ, Stenglein MD, Stone DM, Takada A, Terregino C, Tesh RB, Tian JH, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Verbeek M, Volchkov VE, Wahl-Jensen V, Walsh JA, Walker PJ, Wang D, Wang LF, Wetzel T, Whitfield AE, Xiè JT, Yuen KY, Zhang YZ, Kuhn JH. Taxonomy of the order Mononegavirales: update 2016. Arch Virol 2016; 161:2351-60. [PMID: 27216929 PMCID: PMC4947412 DOI: 10.1007/s00705-016-2880-1] [Citation(s) in RCA: 352] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 04/27/2016] [Indexed: 12/17/2022]
Abstract
In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Claudio L Afonso
- Southeast Poultry Research Laboratory, Agricultural Research Service, US Department of Agriculture, Athens, GA, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Yīmíng Bào
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Nicolás Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Kim R Blasdell
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - François-Xavier Briand
- Avian and Rabbit Virology Immunology and Parasitology Unit, French Agency for Food, Environmental and Occupational Health and Safety, Ploufragan, France
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Alexander Bukreyev
- Departments of Pathology and Microbiology & Immunology, Galveston National Laboratory, The University of Texas Medical Branch, Galveston, TX, USA
| | - Charles H Calisher
- Arthropod-Borne and Infectious Diseases Laboratory, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jiāsēn Chéng
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology of Húběi Province, College of Plant Science and Technology, Huázhōng Agricultural University, Wuhan, China
| | - Anna N Clawson
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Peter L Collins
- Respiratory Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, Champaign, IL, USA
| | | | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Rocky Mountain Laboratories Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Szilvia L Farkas
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | | | | | - Ron A M Fouchier
- Department of Viroscience, Postgraduate School Molecular Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yànpíng Fù
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology of Húběi Province, College of Plant Science and Technology, Huázhōng Agricultural University, Wuhan, China
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | | | - Roger Hewson
- Public Health England, Porton Down, Wiltshire, Salisbury, UK
| | - Masayuki Horie
- Joint Faculty of Veterinary Medicine, Transboundary Animal Diseases Research Center, Kagoshima University, Kagoshima, Japan
| | - Timothy H Hyndman
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology of Húběi Province, College of Plant Science and Technology, Huázhōng Agricultural University, Wuhan, China
| | - Elliot W Kitajima
- Núcleo de Apoio à Pesquisa em Microscopia Eletrônica Aplicada a Agricultura, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Gary P Kobinger
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
| | - Sergio Lenardon
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina
| | - Eric M Leroy
- Centre International de Recherches Médicales de Franceville, Institut de Recherche pour le Développement, Franceville, Gabon
| | - Ci-Xiu Li
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xian-Dan Lin
- Wēnzhōu Center for Disease Control and Prevention, Wenzhou, China
| | - Lìjiāng Liú
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology of Húběi Province, College of Plant Science and Technology, Huázhōng Agricultural University, Wuhan, China
| | - Ben Longdon
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Andrea Maisner
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratory, Boston University School of Medicine, Boston, MA, USA
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine, Vienna, Austria
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Jean L Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Susan L Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Janusz T Paweska
- Center for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Rick E Randall
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Scotland, UK
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute for Virology, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Martin Schwemmle
- Institute for Virology, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Mang Shi
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | | | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science Weymouth, Dorset, UK
| | - Ayato Takada
- Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
| | - Calogero Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie, Department of Comparative Biomedical Sciences, National/OIE Reference Laboratory for Newcastle Disease and Avian Influenza, FAO Reference Centre for Animal Influenza and Newcastle Disease, OIE Collaborating Centre for Diseases at the Human-Animal Interface, Legnaro, Padova, Italy
| | - Robert B Tesh
- Departments of Pathology and Microbiology & Immunology, Galveston National Laboratory, The University of Texas Medical Branch, Galveston, TX, USA
| | - Jun-Hua Tian
- Wǔhàn Center for Disease Control and Prevention, Wuhan, China
| | - Keizo Tomonaga
- Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur, Unité des Stratégies Antivirales, Paris, France
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nikos Vasilakis
- Center for Biodefense and Emerging Infectious Diseases, Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
- Center for Tropical Diseases, Institute for Human Infections and Immunity, The University of Texas Medical Branch, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Wageningen, The Netherlands
| | - Viktor E Volchkov
- Molecular Basis of Viral Pathogenicity, CIRI, INSERM U1111, CNRS UMR5308, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Victoria Wahl-Jensen
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - John A Walsh
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Peter J Walker
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - David Wang
- Departments of Molecular Microbiology and Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lin-Fa Wang
- Department of Agriculture and Fisheries, Biosecurity Queensland, Brisbane, QLD, Australia
- Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | | | - Ji Tāo Xiè
- State Key Laboratory of Agricultural Microbiology, The Provincial Key Lab of Plant Pathology of Húběi Province, College of Plant Science and Technology, Huázhōng Agricultural University, Wuhan, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Yong-Zhen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA.
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Meinicke S, Dietrich B, Wetzel T. Strukturdatenrekonstruktion und CFD-Simulation zur thermischen Charakterisierung fester Schwammstrukturen. CHEM-ING-TECH 2014. [DOI: 10.1002/cite.201450643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Dietrich B, Marocco L, Kind M, Wetzel T. Charakterisierung des Wärmetransports in festen Schwämmen bei Flüssigmetall-Durchströmung. CHEM-ING-TECH 2014. [DOI: 10.1002/cite.201450211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Nourinejhad Zarghani S, Dupuis-Maguiraga L, Bassler A, Wetzel T. Mapping of the exchangeable and dispensable domains of the RNA 2-encoded 2AHP protein of arabis mosaic nepovirus. Virology 2014; 458-459:106-13. [DOI: 10.1016/j.virol.2014.04.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/23/2013] [Accepted: 04/19/2014] [Indexed: 10/25/2022]
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Dietzgen RG, Kuhn JH, Clawson AN, Freitas-Astúa J, Goodin MM, Kitajima EW, Kondo H, Wetzel T, Whitfield AE. Dichorhavirus: a proposed new genus for Brevipalpus mite-transmitted, nuclear, bacilliform, bipartite, negative-strand RNA plant viruses. Arch Virol 2013; 159:607-19. [PMID: 24081823 DOI: 10.1007/s00705-013-1834-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 07/16/2013] [Indexed: 12/18/2022]
Abstract
Orchid fleck virus (OFV) is an unassigned negative-sense, single-stranded (-)ssRNA plant virus that was previously suggested to be included in the family Rhabdoviridae, order Mononegavirales. Although OFV shares some biological characteristics, including nuclear cytopathological effects, gene order, and sequence similarities, with nucleorhabdoviruses, its taxonomic status is unclear because unlike all mononegaviruses, OFV has a segmented genome and its particles are not enveloped. This article analyses the available biological, physico-chemical, and nucleotide sequence evidence that seems to indicate that OFV and several other Brevipalpus mite-transmitted short bacilliform (-)ssRNA viruses are likely related and may be classified taxonomically in novel species in a new free-floating genus Dichorhavirus.
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Affiliation(s)
- Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia,
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Wetzel T, Stieglitz R, Marocco L, Pacio J, Hering W, Dietrich B. Flüssigmetalle als Wärmeträgerfluide für Hochtemperaturprozesse. CHEM-ING-TECH 2013. [DOI: 10.1002/cite.201250703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Lamprecht RL, Spaltman M, Stephan D, Wetzel T, Burger JT. Complete nucleotide sequence of a South African isolate of Grapevine fanleaf virus and its associated satellite RNA. Viruses 2013; 5:1815-23. [PMID: 23867805 PMCID: PMC3738963 DOI: 10.3390/v5071815] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 07/08/2013] [Accepted: 07/10/2013] [Indexed: 11/29/2022] Open
Abstract
The complete sequences of RNA1, RNA2 and satellite RNA have been determined for a South African isolate of Grapevine fanleaf virus (GFLV-SACH44). The two RNAs of GFLV-SACH44 are 7,341 nucleotides (nt) and 3,816 nt in length, respectively, and its satellite RNA (satRNA) is 1,104 nt in length, all excluding the poly(A) tail. Multiple sequence alignment of these sequences showed that GFLV-SACH44 RNA1 and RNA2 were the closest to the South African isolate, GFLV-SAPCS3 (98.2% and 98.6% nt identity, respectively), followed by the French isolate, GFLV-F13 (87.3% and 90.1% nt identity, respectively). Interestingly, the GFLV-SACH44 satRNA is more similar to three Arabis mosaic virus satRNAs (85%–87.4% nt identity) than to the satRNA of GFLV-F13 (81.8% nt identity) and was most distantly related to the satRNA of GFLV-R2 (71.0% nt identity). Full-length infectious clones of GFLV-SACH44 satRNA were constructed. The infectivity of the clones was tested with three nepovirus isolates, GFLV-NW, Arabis mosaic virus (ArMV)-NW and GFLV-SAPCS3. The clones were mechanically inoculated in Chenopodium quinoa and were infectious when co-inoculated with the two GFLV helper viruses, but not when co-inoculated with ArMV-NW.
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Affiliation(s)
- Renate L. Lamprecht
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; E-Mails: (R.L.L.); (M.S.); (D.S.)
| | - Monique Spaltman
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; E-Mails: (R.L.L.); (M.S.); (D.S.)
| | - Dirk Stephan
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; E-Mails: (R.L.L.); (M.S.); (D.S.)
| | - Thierry Wetzel
- RLP Agroscience, AlPlanta–Institute for Plant Research, Breitenweg 71, Neustadt an der 67435 Weinstrasse, Germany; E-Mail:
| | - Johan T. Burger
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; E-Mails: (R.L.L.); (M.S.); (D.S.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +27-218-085-858; Fax: +27-218-085-833
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Werner D, Loges A, Wetzel T. Thermische Charakterisierung und Modellierung prismatischer Li-Ionen-Batteriezellen. CHEM-ING-TECH 2012. [DOI: 10.1002/cite.201250518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Loges A, Werner D, Wetzel T. Li-Ionen-Batterien - Bestimmung der Materialkennwerte und thermische Modellierung. CHEM-ING-TECH 2012. [DOI: 10.1002/cite.201250523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Wetzel M, Wetzel T. Strömungsverdampfen von CO2-Öl-Gemischen im horizontalen Rohr. CHEM-ING-TECH 2012. [DOI: 10.1002/cite.201250220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hanss S, Schaaf T, Wetzel T, Hahn C, Schrader T, Tolxdorff T. Integration of decentralized clinical data in a data warehouse: a service-oriented design and realization. Methods Inf Med 2009; 48:414-8. [PMID: 19657544 DOI: 10.3414/me9240] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVES In this paper we present a general concept and describe the difficulties for the integration of data from various clinical partners in one data warehouse using the Open European Nephrology Science Center (OpEN.SC) as an example. This includes a requirements analysis of the data integration process and also the design according to these requirements. METHODS This conceptual approach based on the Rational Unified Process (RUP) and paradigm of Service-Oriented Architecture (SOA). RESULTS Because we have to enhance the confidence of our partners in the OpEN.SC system and with this the willingness of them to participate, important requirements are controllability, transparency and security for all partners. Reusable and fine-grained components were found to be necessary when working with diverse data sources. With SOA the requested reusability is implemented easily. CONCLUSIONS A key step in the development of a data integration process within such a health information system like OpEN.SC is to analyze the requirements. And to show that this is not only a theoretical work, we present a design - developed with RUP and SOA - which fulfills these requirements.
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Affiliation(s)
- Sabine Hanss
- Institute of Medical Informatics, Charité - Universitätsmedizin Berlin, 12200 Berlin, Germany.
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Winterhagen P, Dubois C, Sinn M, Wetzel T, Reustle GM. Gene silencing and virus resistance based on defective interfering constructs in transgenic Nicotiana benthamiana is not linked to accumulation of siRNA. Plant Physiol Biochem 2009; 47:739-42. [PMID: 19419883 DOI: 10.1016/j.plaphy.2009.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Revised: 03/24/2009] [Accepted: 03/31/2009] [Indexed: 05/27/2023]
Abstract
RNA interference (RNAi) was established in Nicotiana benthamiana plants by introducing constructs containing a defective interfering (DI) sequence from Tomato bushy stunt virus (TBSV) in combination with a conserved sense-sequence from the target Grapevine fanleaf virus (GFLV). Silencing in plants was confirmed by Agrobacterium-mediated infiltration of a GFP-sensor containing the GFLV-derived target sequence. The transgene-induced RNAi led to silencing of the GFP-sensor and GFP fluorescence was absent post-infiltration. In plants without GFP fluorescence after infiltration with the GFP-sensor, siRNA specific to GFP and the target virus sequence could not be detected. In contrast, infiltrated leaves of wild type and transgenic plants showing GFP fluorescence after infiltration revealed accumulation of siRNA specific to the sequence of the sensor. Silencing could be inhibited by co-infiltration using a p19 silencing suppressor construct together with the GFP-sensor, which always resulted in bright GFP fluorescence. In parallel, virus resistance of transgenic Nicotiana benthamiana was investigated via challenge inoculation with GFLV. Our results indicate that efficient RNAi in transgenic plants does not necessarily lead to a detectable accumulation of siRNA.
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Affiliation(s)
- Patrick Winterhagen
- RLP AgroScience GmbH, AlPlanta - Institute for Plant Research, 67435 Neustadt, Germany.
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31
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Sanfaçon H, Wellink J, Le Gall O, Karasev A, van der Vlugt R, Wetzel T. Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus. Arch Virol 2009; 154:899-907. [DOI: 10.1007/s00705-009-0367-z] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Accepted: 03/16/2009] [Indexed: 11/24/2022]
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Jürgens P, Wetzel T, Schieferstein H, Sader R, Zeilhofer HF. O.462 Shape-memory-alloy staples for mandibula osteosynthesis. J Craniomaxillofac Surg 2008. [DOI: 10.1016/s1010-5182(08)71586-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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33
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Dupuis L, Cobanov P, Bassler A, Krczal G, Wetzel T. Complete genome sequence of a virulent isolate of Arabis mosaic virus from privet (Ligustrum vulgare). Arch Virol 2008; 153:1611-3. [DOI: 10.1007/s00705-008-0126-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Accepted: 04/25/2008] [Indexed: 11/29/2022]
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34
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Wetzel T, Chisholm J, Bassler A, Sanfaçon H. Characterization of proteinase cleavage sites in the N-terminal region of the RNA1-encoded polyprotein from Arabis mosaic virus (subgroup A nepovirus). Virology 2008; 375:159-69. [DOI: 10.1016/j.virol.2008.01.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 12/20/2007] [Accepted: 01/30/2008] [Indexed: 11/25/2022]
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35
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Heim F, Lot H, Delecolle B, Bassler A, Krczal G, Wetzel T. Complete nucleotide sequence of a putative new cytorhabdovirus infecting lettuce. Arch Virol 2007; 153:81-92. [PMID: 17943394 DOI: 10.1007/s00705-007-1071-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 08/30/2007] [Indexed: 10/22/2022]
Abstract
The full-length nucleotide sequence of the genomic RNA of a new cytorhabdovirus infecting lettuce was determined. Six open reading frames were found in the antigenomic sequence of the 12,926-nt negative-sense viral RNA genome. The genomic organisation was similar to that of lettuce necrotic yellows virus (LNYV), the type member of the genus Cytorhabdovirus: 3'-N-P-3-M-G-L-5', where N is the capsid protein gene, P the putative phosphoprotein gene, 3 a gene coding for a putative protein of unknown function, M the putative matrix protein gene, G the glycoprotein gene, and L the putative polymerase gene. Amino acid sequence comparison with the corresponding sequences of other rhabdoviruses revealed the closest relationship to LNYV, with identities ranging from 41% for the matrix proteins and 65% for the L polymerase proteins. These results indicate that this virus may be a member of a new cytorhabdovirus species, for which the name Lettuce yellow mottle virus (LYMoV) is proposed.
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Affiliation(s)
- F Heim
- RLP Agroscience, AlPlanta - Institute for Plant Research, Neustadt an der Weinstrasse, Germany
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36
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Le Gall O, Sanfaçon H, Ikegami M, Iwanami T, Jones T, Karasev A, Lehto K, Wellink J, Wetzel T, Yoshikawa N. Cheravirus and Sadwavirus: two unassigned genera of plant positive-sense single-stranded RNA viruses formerly considered atypical members of the genus Nepovirus (family Comoviridae). Arch Virol 2007; 152:1767-74. [PMID: 17585366 DOI: 10.1007/s00705-007-1015-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 05/15/2007] [Indexed: 11/26/2022]
Abstract
The genus Nepovirus (family Comoviridae) was known both for a good level of homogeneity and for the presence of atypical members. In particular, the atypical members of the genus differed by the number of capsid protein (CP) subunits. While typical nepoviruses have a single CP subunit with three structural domains, atypical nepoviruses have either three small CP subunits, probably corresponding to the three individual domains, or a large and a small subunit, probably containing two and one structural domains, respectively. These differences are corroborated by hierarchical clustering based on sequences derived from both genomic RNAs. Therefore, these atypical viruses are now classified in two distinct genera, Cheravirus (three CP subunits; type species Cherry rasp leaf virus) and Sadwavirus (two CP subunits; type species Satsuma dwarf virus).
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Affiliation(s)
- O Le Gall
- INRA Bordeaux-Aquitaine and Université Victor Segalen, Villenave d'Ornon, France
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Chen Y, Wetzel T, Aranovich GL, Donohue MD. Generalization of Kelvin's equation for compressible liquids in nanoconfinement. J Colloid Interface Sci 2006; 300:45-51. [PMID: 16631783 DOI: 10.1016/j.jcis.2006.03.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Revised: 02/07/2006] [Accepted: 03/11/2006] [Indexed: 11/16/2022]
Abstract
The Kelvin equation for a compressible liquid in nanoconfinement is written in a form that takes into account not only Laplace's pressure, but also the oscillatory compression pressure. This leads to a simple analytical equation for pressure in nanocapillaries. The corrected equation is used to analyze properties of aqueous systems, including the oscillatory structural forces between attractive surfaces and inert surfaces, repulsive "hydration" forces between hydrophilic surfaces, and attractive "hydrophobic" forces between hydrophobic surfaces. Relative vapor pressure in a nanocapillary also is discussed.
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Affiliation(s)
- Y Chen
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.
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Dietzgen RG, Callaghan B, Wetzel T, Dale JL. Completion of the genome sequence of Lettuce necrotic yellows virus, type species of the genus Cytorhabdovirus. Virus Res 2005; 118:16-22. [PMID: 16313992 DOI: 10.1016/j.virusres.2005.10.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 10/31/2005] [Accepted: 10/31/2005] [Indexed: 11/21/2022]
Abstract
We completed the genome sequence of Lettuce necrotic yellows virus (LNYV) by determining the nucleotide sequences of the 4a (putative phosphoprotein), 4b, M (matrix protein), G (glycoprotein) and L (polymerase) genes. The genome consists of 12,807 nucleotides and encodes six genes in the order 3' leader-N-4a(P)-4b-M-G-L-5' trailer. Sequences were derived from clones of a cDNA library from LNYV genomic RNA and from fragments amplified using reverse transcription-polymerase chain reaction. The 4a protein has a low isoelectric point characteristic for rhabdovirus phosphoproteins. The 4b protein has significant sequence similarities with the movement proteins of capillo- and trichoviruses and may be involved in cell-to-cell movement. The putative G protein sequence contains a predicted 25 amino acids signal peptide and endopeptidase cleavage site, three predicted glycosylation sites and a putative transmembrane domain. The deduced L protein sequence shows similarities with the L proteins of other plant rhabdoviruses and contains polymerase module motifs characteristic for RNA-dependent RNA polymerases of negative-strand RNA viruses. Phylogenetic analysis of this motif among rhabdoviruses placed LNYV in a group with other sequenced cytorhabdoviruses, most closely related to Strawberry crinkle virus.
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Affiliation(s)
- Ralf G Dietzgen
- Department of Primary Industries and Fisheries, Queensland Agricultural Biotechnology Centre, Queensland Bioscience Precinct, The University of Queensland, 306 Carmody Rd, St. Lucia, Qld. 4072, Australia.
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Wetzel T, Ebel R, Moury B, Le Gall O, Endisch S, Reustle GM, Krczal G. Sequence analysis of grapevine isolates of Raspberry ringspot nepovirus. Arch Virol 2005; 151:599-606. [PMID: 16328136 DOI: 10.1007/s00705-005-0665-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Accepted: 09/22/2005] [Indexed: 10/25/2022]
Abstract
The nucleotide sequences of RNAs 1 and 2 of a German isolate of Raspberry ringspot virus (RpRSV) infecting grapevine (RpRSV-Grapevine), as well as partial sequences of another grapevine isolate from Switzerland (RAC815) were determined. The sequences of the protease-polymerase region encoded by RNA1, and the movement protein and coat protein genes encoded by RNA 2, of these isolates were compared with those of other isolates available in databases. The coat proteins of the grapevine isolates formed a sister group to all those from other RpRSV isolates, but whether this resulted from divergence or recombination was uncertain.
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Affiliation(s)
- T Wetzel
- AlPlanta - Institute for Plant Research, RLP Agroscience, Neustadt an der Weinstrasse, Germany.
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Wetzel T, Njapo Ngangom HO, Chotewutmontri S, Krczal G. Nucleotide sequence of a new isolate of ribgrass mosaic tobamovirus infecting Impatiens New Guinea. Arch Virol 2005; 151:787-91. [PMID: 16292595 DOI: 10.1007/s00705-005-0677-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2005] [Accepted: 10/11/2005] [Indexed: 11/29/2022]
Abstract
The complete nucleotide sequence of a tobamovirus isolated from Impatiens New Guinea was determined. The genome was 6302 nt long, and its genomic organisation was similar to those of other crucufer tobamoviruses. Sequence comparisons with the corresponding sequences of other crucifer tobamoviruses revealed highest levels of identity with the ribgrass mosaic virus (Shanghai isolate). A small open reading frame putatively encoding a 4.5-kDa protein with a low degree of similarity to the ORF6 of tobacco mosaic virus was found nested in the movement protein gene.
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Affiliation(s)
- T Wetzel
- RLP Agrosciences GmbH, AlPlanta - Institute for Plant Research, Neustadt an der Weinstrasse, Germany.
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Wetzel T, Bassler A, Amren MAW, Krczal G. A RT/PCR-partial restriction enzymatic mapping (PREM) method for the molecular characterisation of the large satellite RNAs of Arabis mosaic virus isolates. J Virol Methods 2005; 132:97-103. [PMID: 16216344 DOI: 10.1016/j.jviromet.2005.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Revised: 09/01/2005] [Accepted: 09/06/2005] [Indexed: 10/25/2022]
Abstract
The satellite RNA of the grapevine isolate NW of Arabis mosaic virus (ArMV) was cloned and sequenced, and showed 75% identity at the nucleotide level to the satellite RNA of the lilac isolate of ArMV. In order to survey ArMV isolates from various geographical origins and natural hosts for the presence of large satellite RNAs and analyse their degree of variability, a RT/PCR-partial restriction enzymatic mapping (PREM) method was developed. The method is based on the incorporation of 5-methyl-dCTP in the RT/PCR reaction, and the subsequent digestion of the RT/PCR products by methyl-sensitive restriction enzymes. Satellites RNAs were detected by RT/PCR in eight isolates out of 47, six of them originating from grapevine, one from hop and one from lilac. The partial restriction digestion patterns allowed to distinguish six different types of satellites. Cloning and sequencing of the different satellites confirmed these results, the PREM proving able to discriminate sequences with 96% identity. The sizes of the different satellites varied between 1092 and 1139 nucleotides, their encoded proteins between 338 and 360 amino acids. Conserved domains were found in the amino and carboxy-termini between the sequences of the proteins encoded by the satellites of the different isolates of ArMV.
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Affiliation(s)
- T Wetzel
- RLP Agroscience, AlPlanta -- Institute for Plant Research, Breitenweg 71, 67435 Neustadt an der Weinstrasse, Germany.
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Sader R, Schieferstein H, Abeln A, Wetzel T, Keller T, Exner B, Jürgens P, Zeilhofer HF. Biomechanical and animal-experimental results of a new osteosynthesis material made from shape memory alloy. Int J Oral Maxillofac Surg 2005. [DOI: 10.1016/s0901-5027(05)81209-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
The complete nucleotide sequence of the RNAs 1 and 2 of the nepovirus Raspberry ringspot virus cherry isolate (RpRSV-ch) from grapevine was determined. The RNA 1 is 7935 nucleotides (nt) long excluding the poly(A) tail, and contains one long open reading frame (ORF) encoding a polypeptide of 2367 amino acids. This ORF is preceeded by a 136nt 5' non-coding region, and followed by a 695nt 3' non-coding region. Conserved amino acid motifs, characteristic of the viral protease cofactor, the NTP-binding protein, proteinase and polymerase, were found in the sequence of the RNA 1-encoded polyprotein. The RNA 2 is 3915nt long excluding the poly(A) tail, and contains one long ORF encoding a polypeptide of 1106 amino acids. This ORF is preceeded by a 203nt 5' non-coding region, and followed by a 390nt 3' non-coding region. When compared to the corresponding sequences of other nepoviruses, a maximum level of 34% identity was found between the RNA 1-encoded polypetides of RpRSV-ch and other nepoviruses. For the RNA 2-encoded polypeptide, 88% identity was found between RpRSV-ch and RpRSV-S, a Scottish isolate of RpRSV from raspberry, and a maximum 29% identity between RpRSV-ch and other nepoviruses.
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Affiliation(s)
- R Ebel
- Centrum Gruene Gentechnik, DLR Rheinpfalz, Breitenweg 71, 67435 Neustadt an der Weinstrasse, Germany
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44
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Wetzel T, Beck A, Wegener U, Krczal G. Complete nucleotide sequence of the RNA 1 of a grapevine isolate of Arabis mosaic virus. Arch Virol 2004; 149:989-95. [PMID: 15098112 DOI: 10.1007/s00705-003-0277-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2003] [Accepted: 11/12/2003] [Indexed: 11/28/2022]
Abstract
The complete nucleotide sequence of the genomic RNA 1 of the grapevine isolate NW (Neustadt an der Weinstrasse) of Arabis mosaic virus (ArMV) was determined. It is 7334 nucleotides long excluding the poly(A) tail, and contains one long open reading frame encoding a polypeptide of 2284 amino acids. The 5' and 3' non-coding regions were 227 and 252 nucleotides long respectively, and showed stretches of high identity with the corresponding 5' and 3' non-coding regions of ArMV-NW RNA 2. The analysis of the amino acid sequence of the polyprotein encoded by the RNA 1 of the ArMV-NW showed that the conserved amino acid motifs, characteristic for the viral protease co-factor, the NTP-binding protein, the cystein protease, and the RdRp core domains, were all present. Amino acid sequence comparisons between the polyproteins encoded by the RNAs 1 of ArMV-NW and other nepoviruses showed 75% identity with the GFLV-F13, and up to 36% with other nepoviruses.
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Affiliation(s)
- T Wetzel
- Centrum Gruene Gentechnik, DLR Rheinpfalz, Neustadt an der Weinstrasse, Germany.
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45
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Wetzel T, Janning G, Heuser L, Morgenroth K, Schmiegel W, Heuer H. [66-year-old patient with bilateral brachial claudication, blood pressure differences generally decreased energy level. Takayasu arteritis]. Internist (Berl) 2003; 44:81-7. [PMID: 12677709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Affiliation(s)
- T Wetzel
- Medizinische Klinik I, St.-Johannes-Hospital Dortmund.
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46
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Wetzel T, Janning G, Heuser L, Morgenroth K, Schmiegel W, Heuer H. 66-jährige Patientin mit bilateraler Claudicatio brachialis, Blutdruckdifferenz und allgemeinem Leistungsabfall. Internist (Berl) 2003. [DOI: 10.1007/s00108-002-0687-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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47
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Abstract
The RNA 2 of the nepovirus Arabis mosaic virus (ArMV) encodes a polyprotein from which protein 2A is released by proteolytic cleavage at the N-terminus. The 2A gene of 19 ArMV isolates from different geographical origin and 9 distinct natural hosts was amplified by RT/PCR and subsequently cloned and sequenced. These 19 isolates and those from databanks were classified into four groups based on the size of the protein 2A which ranged from 233 to 280 amino acids, and sequence identities. Sequence variability was mainly located in the N-terminus of the proteins, whereas the core region and the C-terminus were conserved.
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Affiliation(s)
- Thierry Wetzel
- Centrum Gruene Gentechnik, Staatliche Lehr- und Forschungsanstalt, Breitenweg 71, D-67435 Neustadt an der Weinstrasse, Germany.
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48
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Wetzel T, Jardak R, Meunier L, Ghorbel A, Reustle GM, Krczal G. Simultaneous RT/PCR detection and differentiation of arabis mosaic and grapevine fanleaf nepoviruses in grapevines with a single pair of primers. J Virol Methods 2002; 101:63-9. [PMID: 11849684 DOI: 10.1016/s0166-0934(01)00422-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The movement protein genes from several isolates of ArMV and GFLV of different geographical origins were amplified by RT/PCR using degenerate primers, cloned and sequenced. A single pair of degenerate primers was designed from these sequences to allow the simultaneous amplification of parts of the movement protein genes of ArMV and GFLV. Their use in an immunocapture-RT/PCR for the detection of ArMV or GFLV in infected grapevines proved to be ten times more sensitive than the corresponding ArMV or GFLV ELISA tests. A Sph1 restriction site found in the sequences corresponding to the amplified products from the GFLV isolates, but not in the amplified products from the ArMV isolates, allowed the differentiation between ArMV and GFLV in the infected grapevines by a Sph1 restriction digestion of the amplified products.
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Affiliation(s)
- T Wetzel
- Centrum Gruene Gentechnik, Staatliche Lehr- und Forschungsanstalt, Breitenweg 71, 67435, Neustadt an der Weinstrasse, Germany.
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49
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Wetzel T, Meunier L, Jaeger U, Reustle GM, Krczal G. Complete nucleotide sequences of the RNAs 2 of German isolates of grapevine fanleaf and Arabis mosaic nepoviruses. Virus Res 2001; 75:139-45. [PMID: 11325468 DOI: 10.1016/s0168-1702(01)00235-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The RNAs 2 of an Arabis mosaic virus (ArMV) and a grapevine fanleaf virus (GFLV) isolate, originating from South West of Germany near Neustadt an der Weinstrasse (NW), were sequenced. They are 3820 and 3775 nucleotides long respectively, and both contain one open reading frame encoding a polypeptide of 1110 amino acids. Their 5' non-coding regions contain conserved and repeated sequences, which are able to form stem-loop structures. Nucleotide sequence comparisons between the full-length RNAs 2 revealed homology levels of 84 and 82% between the ArMV-NW and the ArMV-L and -U, respectively, 90% between GFLV-NW and GFLV-F13, and 72% between ArMV-NW and GFLV-NW. Amino acid sequence comparisons showed that the greatest difference was found between the 2A proteins of the different ArMV isolates, the 2A protein of the ArMV-NW showing more similarity to the 2A protein of GFLV-NW than to those of ArMV-L2 or -U2.
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Affiliation(s)
- T Wetzel
- Centrum Gruene Gentechnik, Staatliche Lehr- und Forschungsanstalt, Breitenweg 71, 67435 Neustadtander, Weinstrasse, Germany.
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50
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Stephan J, Dörre K, Brakmann S, Winkler T, Wetzel T, Lapczyna M, Stuke M, Angerer B, Ankenbauer W, Földes-Papp Z, Rigler R, Eigen M. Towards a general procedure for sequencing single DNA molecules. J Biotechnol 2001; 86:255-67. [PMID: 11257535 DOI: 10.1016/s0168-1656(00)00417-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this paper we report on the latest technical advances towards single molecule sequencing, a useful method currently developed especially for fast and easy de novo sequencing. Different approaches for complete labeling of DNA with fluorescent dyes are described. In addition, the experimental set-up for the sequencing process is shown. We demonstrate the ability to purify the buffer and enzyme solutions. Inorganic buffers were purified down to at least 20 fM of remaining fluorescent impurities. The exonuclease buffer solution could be cleaned down to 0.8 pM whereby its full activity was kept. Finally, we show a selection procedure for beads and present the data of a model experiment, in which immobilized DNA is degraded by an exonuclease within a polymethylmethacrylate (PMMA) microstructure. Furthermore, the mathematical processing of the obtained raw data is described. A first complete experimental cycle is shown, combining all preparatory steps which are necessary for single molecule sequencing in microstructures.
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Affiliation(s)
- J Stephan
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Biochemische Kinetik, Am Fassberg 2, D-37077 Göttingen, Germany.
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