Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Vitis vinifera is the woody crop most susceptible to intracellular pathogens. Currently 70 pathogens infect grapevine, of which 63 are of viral origin. Grapevine leafroll-associated virus 3 (GLRaV-3) is the type species of the genus Ampelovirus, family Closteroviridae. It is considered to be the primary causative agent of Grapevine leafroll disease (GLD) globally; however, the etiology of GLD is not completely understood. Here we report on the viral populations present in GLD symptomatic grapevines across the Western Cape province, South Africa. A widespread survey was performed to screen 315 grapevines for 11 grapevine-infecting viruses using RT-PCR. Additionally, GLRaV-3 variant groups were distinguished with high-resolution melt (HRM) curve analysis used in conjunction with real-time RT-PCR. Members of the family Closteroviridae were detected with the highest frequency, particularly GLRaV-3 that was detected in 87% of tested plants. Nextgeneration sequencing (NGS) is capable of detecting known and novel viruses without prior knowledge of viral sequences and when used in a metagenomic approach is able to detected viral populations within diseased vines. A total of 17 grapevine samples were subjected to NGS using either an Illumina MiSeq or HiSeq 2500 instrument to determine the virome within GLD vines. Collectively, more than 190 million reads were generated through NGS. Read datasets were trimmed and filtered for quality and subjected to both read-mapping and de novo assembly. Contigs assembled de novo were analyzed with BLAST (Basic Local Alignment Search Tool) against the NCBI (National Centre for Biotechnology Information) database and it was determined that GLRaV-3 was the best-represented virus, comprising 97.5% of the assembled contigs. Grapevine virus F (GVF) was detected for the first time in South African vineyards through de novo assemblies and the complete genome sequence validated through direct Sanger sequencing. The complete genome of GVF isolate V5 spans 7 539 nucleotides and shares 89.11% nucleotide identity to existing GVF genomes. The data generated through this study will assist in further understanding the etiology of GLD, support the current hypothesis of GLRaV-3 as the primary contributor to GLD, aid in understanding virus associations in diseased vines and potentially develop systems in which to control disease spread and symptom severity. / AFRIKAANSE OPSOMMING: Vitis vinifera is die houtagtige oes wat die mees vatbaarste is vir intrasellulêre patogene. Tans word wingerde deur 70 patogene geïnfekteer, waarvan 63 van virale oorsprong is. Grapevine leafrollassociated virus 3 (GLRaV-3) is die tipe spesie van die genus Ampelovirus, familie Closteroviridae. Dit word globaal beskou as die primêre oorsaak van Wingerd krulblaar-siekte (GLD), alhoewel die etiologie van GLD nie heeltemal begryp word nie. In hierdie verslag word die virale populasies teenwoordig in GLD simptomatiese wingerde oor die Wes-Kaap provinsie in Suid-Afrika gerapporteer. ‘n Wydverspreide opname was uitgevoer om 315 wingerde met 11 wingerdinfekterende virusse te ondersoek, deur gebruik te maak van tru-transkripsie polimerase ketting reaksie (PKR). Verder is variantgroepe van GLRaV-3 onderskei met hoë-resolusie smeltingskurweanalise, tesame met die gebruik van in-tyd tru-transkripsie PKR. Die hoogste frekwensie was van die lede van die familie Closteroviridae, veral GLRaV-3 wat in 87% van die ondersoekte plante gevind is. Nuwe-generasie volgorderbepaling (NGS) beskik oor die vermoë om bekende en nuwe virusse te herken in virale populasies in geaffekteerde wingerde sonder vorige kennis van virale volgorderbepalings en wanneer dit in ‘n metagenomiese benadering gebruik word kan die virale bevolkings binne siek wingerde ontdek. ‘n Totaal van 17 wingerd-steekproewe was blootgestel aan NGS deur die gebruik van of ‘n Illumina MiSeq of ‘n HiSeq 2500 instrument om die virome te bepaal van GLD wingerde. In totaal is meer 190 miljoen lesings gegenereer deur NGS. Hierdie data lesings was verwerk en gefilter vir kwaliteit om onderwerp te word vir beide kartering en de novo samestellings. Contigs verkry deur de novo samestellings was geanaliseer met BLAST (Basic Local Alignment Search Tool) teenoor die NCBI (National Centre for Biotechnology Information) databasis en dit was vasgestel dat GLRaV-3 was die mees-verteenwoordigende virus, bestaande uit 97.5% van die saamgestelde contigs. Grapevine virus F (GVF) was vir die eerste keer in Suid- Afrikaanse wingerde waargeneem deur de novo samestellings en die volledige genoom volgordger is geverifieer deur middel van direkte Sanger volgorderbepaling. Die volledige genoom van GVF isoleer V5 spanwydte van 7539 nukleotiedes en deel 89.11% nukleotied identiteite van bestaande GVF genome. Die gegenereerde data van hierdie studie sal bykomende begrip van die etiologie van GLD bystaan, die huidige hipotese van GLRaV-3 as die primêre bydraer tot GLD ondersteun, verhoogde begrip van virus-assosiasies in wingerdsiektes verseker en potensiële sisteme ontwikkel om siektes en simptome te beheer.

GVB é um patógeno agrícola composto por RNA de fita simples de senso positivo, com extremidades 3’ poliadeniladas e tem seu diagnóstico feito por testes biológicos, imunológicos e moleculares. Juntamente com outros vírus, causa a síndrome do “complexo rugoso”, que impede a pega da enxertia, destruindo o floema e matando a planta precocemente. A produção de anticorpos contra uma proteína do capsídeo e o desenvolvimento de teste imunológico são os objetivos deste trabalho. A clonagem da região codificante da proteína do capsídeo do Grapevine Virus B foi obtida por PCR, utilizando primers específicos para região codificante e com sítios de restrição para endonucleases BamHI e NdeI, obtendo-se um amplicon de 594 pb. Este fragmento foi clonado no vetor de expressão pET19b e transformado em Escherichia coli BL21 Codon Plus (DE3) RP (Stratagene). Para a expressão da proteína rGVB1a (24 kDa com cauda de histidina), estabeleceu-se uma indução de 1 mM de IPTG (isopropyl-beta-Dthiogalactopyranoside), mantida sob agitação a 250C por 18 horas. A expressão foi analisada por SDS-PAGE 13% e a presença da rGVB1a foi confirmada por Western blot, usando anticorpo monoclonal anti-histidina. A rGVB1a expressada foi purificada por cromatografia de afinidade a cauda de histidina em resina sepharose-Ni2+. A proteína purificada foi utilizada para imunizar um coelho e sete lotes de três camundongos para obtenção de soro policlonal e monoclonal contra a proteína recombinante. A fusão de células de linfócitos B com mielomas SP2/0 foi realizada, obtendo-se um hibridoma produtor de anticorpo IgG2a que em testes de ELISA e Western blot reconhecem a proteína recombinante. Adicionalmente, testes de Western blot utilizando extrato total de plantas sintomáticas e assintomáticas foram realizados para verificar se estes soros reconheciam a proteína nativa. / GVB is an agricultural pathogen composed by a single-stranded positive sense RNA with poliadenilated 3’ end and its diagnosis is based on biological, immunological and molecular tests. Together with another virus, it causes the rugose wood complex disease which prevents grafting, destroying the phloem and killing the plant early. The objectives of this work are the production of antibodies against the coat protein and the development of an immunological test. Cloning of a coat protein coding gene from Grapevine Virus B was performed by PCR, using specific primers for the coding region with restriction sites for BamHl and Ndel endonucleases, obtaining an amplicon of 594 bp. This fragment was cloned into the pET19b expression vector and transformed with Escherichia coli BL21 Codon Plus (DE3) RP (Stratagene). For expression of rGVB1a protein (24 kDa with histidine tail) a protocol with 1 mM IPTG (isopropyl-beta-D-thiogalactopyranoside), and shaking for 18 hours at 25ºC was established. The expression was analyzed by SDS-PAGE 13% and the presence of rGVB1a was confirmed by Western-blot, using an anti-histidine monoclonal antibody.rGVB1a expressed was purified by histidine tail Ni2+ Sepharose affinity chromatography. Purified protein was used to immunize a rabbit and seven lots of mice to obtain policlonal serum and monoclonal antibody against the recombinant protein. Cell fusions of lymphocyte B and SP2/0 were performed and a hybridoma producer of IgG2a antibody was obtained. This hybridoma recognized the recombinant protein in ELISA and Western blot tests. Additionally, Western blot using the extract of symptomatic and assymptomatic plants were developed to investigate if these serum recognize the native protein.

Ce travail de recherche a eu pour objectif de caractériser l’influence du génotype de porte-greffes sur le développement du greffon notamment à travers l’étude des mécanismes relatifs à la signalisation azotée et hormonale. Dans ce contexte, deux porte-greffes, 1103 Paulsen (1103P) et Riparia Gloire de Montpellier (RGM), induisant respectivement une forte et faible vigueur du greffon, ont été étudiés. Une analyse du transcriptome racinaire a été effectuée chez des plants greffés impliquant ces deux génotypes dans un système split-root où la disponibilité en azote était hétérogène. Une réponse plus prononcée a été observée pour le génotype RGM, ainsi qu’une régulation temporelle différente entre les deux génotypes, notamment concernant des gènes clés de la réponse au nitrate intervenant dans la régulation de la croissance des racines ou dans la signalisation hormonale. D’un point de vue développemental, une régulation étroite de la production des racines latérales et des rameaux latéraux par la disponibilité en azote a été mise en évidence chez RGM. D’autre part, les propriétés intrinsèques de chaque porte-greffe semblent être conférées au greffon induisant notamment une ramification plus importante de celui-ci lorsque le porte-greffe 1103P est utilisé. La caractérisation fonctionnelle des gènes impliqués dans la voie de biosynthèse des strigolactones et la réalisation de bio-essais ont permis de mettre en évidence la production de composés de type strigolactones chez la Vigne. Ces travaux suggèrent aussi une balance contrastée entre les strigolactones et les cytokinines au sein des deux génotypes, corrélée à leur capacité de contrôle de la croissance du greffon. L’ensemble de ces résultats a permis de mettre en évidence une réponse transcriptomique et développementale à la disponibilité en azote toujours plus prononcée pour le génotype connu pour conférer le moins de vigueur au greffon, RGM. / This work aimed to characterize the impact of the rootstock genotype on the scion development especially through the study of the mechanisms related to nitrogen and hormonal signalling. In that context, two rootstocks were studied, 1103 Paulsen (1103P) and Riparia Gloire de Montpellier (RGM), inducing high and low scion vigour, respectively. A transcriptomic analysis was performed on roots of grafted plants involving both genotypes, cultivated in a split-root system where the nitrogen availability was heterogeneous. A more pronounced response was observed for RGM together with a different temporal regulation between both rootstocks, in particular concerning the expression of key genes of the nitrate response involved in root growth regulation or in hormonal signaling. Concerning plant development, a clear impact of the nitrogen availability on the production of lateral roots and shoot branching was highlighted for RGM. Moreover, the intrinsic properties of each rootstock seemed to be conferred to the scion inducing especially a higher shoot branching when the rootstock 1103P was used. The functional characterization of the genes involved in the strigolactone biosynthesis pathway and bioassays highlighted the production of strigolactone-like compounds in Grapevine. These experiments suggest also a contrasted balance between strigolactones and cytokinins within each rootstock genotype, correlated with their ability to control the scion growth. Taking together, these results showed a pronounced transcriptomic and developmental response to nitrogen availability for the genotype conferring the lowest scion vigour, RGM

Made available in DSpace on 2014-06-11T19:32:25Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-01-13Bitstream added on 2014-06-13T19:03:03Z : No. of bitstreams: 1 santos_cmg_dr_botfca.pdf: 789847 bytes, checksum: 537327b05e9f2df0d4e947da5809dbc4 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A vitivinicultura é uma atividade econômica, relativamente, recente no Brasil e a região semiárida do Submédio do Vale do São Francisco, utilizando-se de irrigação localizada, tem atraído muitos investidores internacionais para a produção de uvas e vinhos. O presente trabalho teve o objetivo de avaliar a fisiologia e o metabolismo da videira ‘Syrah’, sob três estratégias de irrigação (Irrigação com Défice Controlado-IDC, Irrigação Deficitária-ID e Irrigação Plena-IP,) no Submédio do Vale do São Francisco. A pesquisa foi desenvolvida na Embrapa Semiárido, especificamente, no Campo Experimental de Bebedouro, localizado no município de Petrolina-PE. O delineamento experimental foi em blocos casualizados, em três esquemas fatoriais: 3 x 5, três estratégias de irrigação e cinco avaliações para potencial hídrico foliar de base (Ψb), teor SPAD da clorofila e atividade da enzima nitrato redutase (NR); 3 x 6, três estratégias de irrigação e seis avaliações para trocas gasosas, açúcares solúveis totais, açúcares redutores, proteína solúvel total e atividade das invertases e 3 x 3, três estratégias de irrigação e três avaliações para as análises químicas de sólidos solúveis, acidez titulável, relação sólidos solúveis/acidez titulável e pH, sendo nove repetições para cada tratamento. A imposição da deficiência hídrica controlada a partir da fase fenológica de 'cacho fechado' em videira cv. Syrah resultou em plantas ao longo do ciclo com maior eficiência no uso da água e economia no recurso hídrico. O porta-enxerto ‘Paulsen 1103’ demonstra tolerância e/ou resistência ao défice hídrico e a cultivar copa Syrah, comportamento anisohídrico. A maior disponibilidade hídrica na irrigação plena promoveu as maiores... / Viticulture is a relatively recent economic activity in Brazil and the semiarid region of the Submedium of the San Francisco Valley, using drip irrigation, has attracted many international investors to grapes and wine production. The study aimed to evaluate the physiology and metabolism of grapevine ‘Syrah’ under three irrigation strategies (Regulated Deficit Irrigation-RDI, Deficit Irrigation-DI and Full Irrigation-FI,) in the Submedium of the San Francisco Valley. The research was conducted at Embrapa Semiarid, specifically in the Bebedouro Experimental Field, located in Petrolina, Pernambuco-Brazil. The statistical design was in randomized blocks, factorial in three regimens: 3 x 5, three irrigation strategies and five evaluations of leaf water potential (Ψb), SPAD chlorophyll content and activity of the nitrate reductase enzyme (NR); 3 x 6, three irrigation strategies and six evaluations for gas exchange, soluble sugars, reducing sugars, total soluble protein and invertase activity, and 3 x 3, three irrigation strategies and three evaluations for the chemical variables: soluble solids, titratable acidity, soluble solids / titratable acidity and pH, nine replicates for each treatment. The imposition of water deficit from the phenological phase of 'closed lock' in grapevine ‘Syrah’ results in the plant cycle with greater efficiency in water use and savings on water resources. The rootstock ‘1103 Paulsen’ demonstrates tolerance and / or resistance to water deficit and scion ‘Syrah’, anisohydric behavior. The greater water availability in the full irrigation promotes the highest rates of assimilation, transpiration and stomatal conductance at 73 and 87 days after pruning. It also provides the highest activity of nitrate reductase at... (Complete abstract click electronic access below)

GVB é um patógeno agrícola composto por RNA de fita simples de senso positivo, com extremidades 3’ poliadeniladas e tem seu diagnóstico feito por testes biológicos, imunológicos e moleculares. Juntamente com outros vírus, causa a síndrome do “complexo rugoso”, que impede a pega da enxertia, destruindo o floema e matando a planta precocemente. A produção de anticorpos contra uma proteína do capsídeo e o desenvolvimento de teste imunológico são os objetivos deste trabalho. A clonagem da região codificante da proteína do capsídeo do Grapevine Virus B foi obtida por PCR, utilizando primers específicos para região codificante e com sítios de restrição para endonucleases BamHI e NdeI, obtendo-se um amplicon de 594 pb. Este fragmento foi clonado no vetor de expressão pET19b e transformado em Escherichia coli BL21 Codon Plus (DE3) RP (Stratagene). Para a expressão da proteína rGVB1a (24 kDa com cauda de histidina), estabeleceu-se uma indução de 1 mM de IPTG (isopropyl-beta-Dthiogalactopyranoside), mantida sob agitação a 250C por 18 horas. A expressão foi analisada por SDS-PAGE 13% e a presença da rGVB1a foi confirmada por Western blot, usando anticorpo monoclonal anti-histidina. A rGVB1a expressada foi purificada por cromatografia de afinidade a cauda de histidina em resina sepharose-Ni2+. A proteína purificada foi utilizada para imunizar um coelho e sete lotes de três camundongos para obtenção de soro policlonal e monoclonal contra a proteína recombinante. A fusão de células de linfócitos B com mielomas SP2/0 foi realizada, obtendo-se um hibridoma produtor de anticorpo IgG2a que em testes de ELISA e Western blot reconhecem a proteína recombinante. Adicionalmente, testes de Western blot utilizando extrato total de plantas sintomáticas e assintomáticas foram realizados para verificar se estes soros reconheciam a proteína nativa. / GVB is an agricultural pathogen composed by a single-stranded positive sense RNA with poliadenilated 3’ end and its diagnosis is based on biological, immunological and molecular tests. Together with another virus, it causes the rugose wood complex disease which prevents grafting, destroying the phloem and killing the plant early. The objectives of this work are the production of antibodies against the coat protein and the development of an immunological test. Cloning of a coat protein coding gene from Grapevine Virus B was performed by PCR, using specific primers for the coding region with restriction sites for BamHl and Ndel endonucleases, obtaining an amplicon of 594 bp. This fragment was cloned into the pET19b expression vector and transformed with Escherichia coli BL21 Codon Plus (DE3) RP (Stratagene). For expression of rGVB1a protein (24 kDa with histidine tail) a protocol with 1 mM IPTG (isopropyl-beta-D-thiogalactopyranoside), and shaking for 18 hours at 25ºC was established. The expression was analyzed by SDS-PAGE 13% and the presence of rGVB1a was confirmed by Western-blot, using an anti-histidine monoclonal antibody.rGVB1a expressed was purified by histidine tail Ni2+ Sepharose affinity chromatography. Purified protein was used to immunize a rabbit and seven lots of mice to obtain policlonal serum and monoclonal antibody against the recombinant protein. Cell fusions of lymphocyte B and SP2/0 were performed and a hybridoma producer of IgG2a antibody was obtained. This hybridoma recognized the recombinant protein in ELISA and Western blot tests. Additionally, Western blot using the extract of symptomatic and assymptomatic plants were developed to investigate if these serum recognize the native protein.

Orientador: João Domingos Rodrigues / Coorientador : Bárbara França Dantas / Banca: Elizabeth Orika Ono / Banca: Valtemir Gonçalves Ribeiro / Banca: Teresinha Costa Silveira de Albuquerque / Banca: Giuseppina Pace Pereira Lima / Resumo: A vitivinicultura é uma atividade econômica, relativamente, recente no Brasil e a região semiárida do Submédio do Vale do São Francisco, utilizando-se de irrigação localizada, tem atraído muitos investidores internacionais para a produção de uvas e vinhos. O presente trabalho teve o objetivo de avaliar a fisiologia e o metabolismo da videira 'Syrah', sob três estratégias de irrigação (Irrigação com Défice Controlado-IDC, Irrigação Deficitária-ID e Irrigação Plena-IP,) no Submédio do Vale do São Francisco. A pesquisa foi desenvolvida na Embrapa Semiárido, especificamente, no Campo Experimental de Bebedouro, localizado no município de Petrolina-PE. O delineamento experimental foi em blocos casualizados, em três esquemas fatoriais: 3 x 5, três estratégias de irrigação e cinco avaliações para potencial hídrico foliar de base (Ψb), teor SPAD da clorofila e atividade da enzima nitrato redutase (NR); 3 x 6, três estratégias de irrigação e seis avaliações para trocas gasosas, açúcares solúveis totais, açúcares redutores, proteína solúvel total e atividade das invertases e 3 x 3, três estratégias de irrigação e três avaliações para as análises químicas de sólidos solúveis, acidez titulável, relação sólidos solúveis/acidez titulável e pH, sendo nove repetições para cada tratamento. A imposição da deficiência hídrica controlada a partir da fase fenológica de 'cacho fechado' em videira cv. Syrah resultou em plantas ao longo do ciclo com maior eficiência no uso da água e economia no recurso hídrico. O porta-enxerto 'Paulsen 1103' demonstra tolerância e/ou resistência ao défice hídrico e a cultivar copa Syrah, comportamento anisohídrico. A maior disponibilidade hídrica na irrigação plena promoveu as maiores... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Viticulture is a relatively recent economic activity in Brazil and the semiarid region of the Submedium of the San Francisco Valley, using drip irrigation, has attracted many international investors to grapes and wine production. The study aimed to evaluate the physiology and metabolism of grapevine 'Syrah' under three irrigation strategies (Regulated Deficit Irrigation-RDI, Deficit Irrigation-DI and Full Irrigation-FI,) in the Submedium of the San Francisco Valley. The research was conducted at Embrapa Semiarid, specifically in the Bebedouro Experimental Field, located in Petrolina, Pernambuco-Brazil. The statistical design was in randomized blocks, factorial in three regimens: 3 x 5, three irrigation strategies and five evaluations of leaf water potential (Ψb), SPAD chlorophyll content and activity of the nitrate reductase enzyme (NR); 3 x 6, three irrigation strategies and six evaluations for gas exchange, soluble sugars, reducing sugars, total soluble protein and invertase activity, and 3 x 3, three irrigation strategies and three evaluations for the chemical variables: soluble solids, titratable acidity, soluble solids / titratable acidity and pH, nine replicates for each treatment. The imposition of water deficit from the phenological phase of 'closed lock' in grapevine 'Syrah' results in the plant cycle with greater efficiency in water use and savings on water resources. The rootstock '1103 Paulsen' demonstrates tolerance and / or resistance to water deficit and scion 'Syrah', anisohydric behavior. The greater water availability in the full irrigation promotes the highest rates of assimilation, transpiration and stomatal conductance at 73 and 87 days after pruning. It also provides the highest activity of nitrate reductase at... (Complete abstract click electronic access below) / Doutor

Le travail effectué au cours de cette thèse a permis une avancée importante dans la connaissance de l’élicitation des cellules de vigne. Nous avons étudié les effets de deux éliciteurs, le méthyljasmonate et la méthyl-β-cyclodextrine, employés seuls et en élicitation croisée sur des suspensions de cellules de vigne (porte-greffe 41B et Vitis labrusca), pour la production de stilbènes (resvératrol et viniférines). Ceci a permis d’atteindre des concentrations de resvératrol très élevées pour un métabolite secondaire et les relations entre la concentration d’éliciteur, la biomasse à l’inoculum et la durée de l’élicitation ont été étudiées. D’autre part, le travail a également porté sur le changement d’échelle quant à la culture cellulaire et son élicitation et sur le suivi de plusieurs phénomènes et paramètres (croissance cellulaire, consommation des sucres, production du resvératrol, suivi du taux d’oxygène dissous et du pH). Des essais en bioréacteur clos de 5L ont ainsi abouti à une production significative de resvératrol à cette échelle et ont permis l’élaboration de modèles cinétiques rendant compte de la croissance de la biomasse et de la production du resvératrol. Un autre aspect de l’étude s’est intéressé à la localisation intracellulaire de la synthèse du resvératrol. Les résultats obtenus par microscopie confocale ont confirmé que le resvératrol s’accumulait majoritairement dans la paroi de la cellule et dans des vésicules cytoplasmiques (organites sphériques présents à proximité de la paroi), avant d’être excrété dans le milieu de culture. Enfin, une démarche a été initiée en vue de la production d’autres métabolites à partir du resvératrol notamment l’ε-viniférine. / The work presented here addressed two main subjects, namely that of grapevine cells elicitation for the production of stilbenes (resveratrol and viniferins) and the scale up of such culture in bioreactors. Shake-flask cultures of grapevine (rootstock 41B and Vitis labrusca) were elicited with methyl jasmonate or methyl-β-cyclodextrin, alone or in combination. This resulted in a significant accumulation of resveratrol in the medium. The relationship between the production of resveratrol and factors such as the elicitor concentration, inoculation rate and the duration of elicitation phase were studied. The second part of this work was concerned with scale up of the culture from shake-flask to 5 L bioreactor. Several parameters were monitored such as cell growth, sugars consumption, resveratrol production, dissolved oxygen concentration and pH. Kinetic models explaining growth and resveratrol production were developed using the results from three bioreactor batches. Preliminary work was performed to initiate the study of metabolites related to resveratrol such as ε-viniferin. The study also completed previous work that looked at the localisation of resveratrol synthesis within the cells using confocal microscopy. The results confirmed that resveratrol was accumulated mainly in the cell wall and in the cytoplasmic vesicles before being excreted/secreted into the culture medium.

GVB é um patógeno agrícola composto por RNA de fita simples de senso positivo, com extremidades 3’ poliadeniladas e tem seu diagnóstico feito por testes biológicos, imunológicos e moleculares. Juntamente com outros vírus, causa a síndrome do “complexo rugoso”, que impede a pega da enxertia, destruindo o floema e matando a planta precocemente. A produção de anticorpos contra uma proteína do capsídeo e o desenvolvimento de teste imunológico são os objetivos deste trabalho. A clonagem da região codificante da proteína do capsídeo do Grapevine Virus B foi obtida por PCR, utilizando primers específicos para região codificante e com sítios de restrição para endonucleases BamHI e NdeI, obtendo-se um amplicon de 594 pb. Este fragmento foi clonado no vetor de expressão pET19b e transformado em Escherichia coli BL21 Codon Plus (DE3) RP (Stratagene). Para a expressão da proteína rGVB1a (24 kDa com cauda de histidina), estabeleceu-se uma indução de 1 mM de IPTG (isopropyl-beta-Dthiogalactopyranoside), mantida sob agitação a 250C por 18 horas. A expressão foi analisada por SDS-PAGE 13% e a presença da rGVB1a foi confirmada por Western blot, usando anticorpo monoclonal anti-histidina. A rGVB1a expressada foi purificada por cromatografia de afinidade a cauda de histidina em resina sepharose-Ni2+. A proteína purificada foi utilizada para imunizar um coelho e sete lotes de três camundongos para obtenção de soro policlonal e monoclonal contra a proteína recombinante. A fusão de células de linfócitos B com mielomas SP2/0 foi realizada, obtendo-se um hibridoma produtor de anticorpo IgG2a que em testes de ELISA e Western blot reconhecem a proteína recombinante. Adicionalmente, testes de Western blot utilizando extrato total de plantas sintomáticas e assintomáticas foram realizados para verificar se estes soros reconheciam a proteína nativa. / GVB is an agricultural pathogen composed by a single-stranded positive sense RNA with poliadenilated 3’ end and its diagnosis is based on biological, immunological and molecular tests. Together with another virus, it causes the rugose wood complex disease which prevents grafting, destroying the phloem and killing the plant early. The objectives of this work are the production of antibodies against the coat protein and the development of an immunological test. Cloning of a coat protein coding gene from Grapevine Virus B was performed by PCR, using specific primers for the coding region with restriction sites for BamHl and Ndel endonucleases, obtaining an amplicon of 594 bp. This fragment was cloned into the pET19b expression vector and transformed with Escherichia coli BL21 Codon Plus (DE3) RP (Stratagene). For expression of rGVB1a protein (24 kDa with histidine tail) a protocol with 1 mM IPTG (isopropyl-beta-D-thiogalactopyranoside), and shaking for 18 hours at 25ºC was established. The expression was analyzed by SDS-PAGE 13% and the presence of rGVB1a was confirmed by Western-blot, using an anti-histidine monoclonal antibody.rGVB1a expressed was purified by histidine tail Ni2+ Sepharose affinity chromatography. Purified protein was used to immunize a rabbit and seven lots of mice to obtain policlonal serum and monoclonal antibody against the recombinant protein. Cell fusions of lymphocyte B and SP2/0 were performed and a hybridoma producer of IgG2a antibody was obtained. This hybridoma recognized the recombinant protein in ELISA and Western blot tests. Additionally, Western blot using the extract of symptomatic and assymptomatic plants were developed to investigate if these serum recognize the native protein.

Grapevine leafroll-associated virus type 3 (GLRaV-3) is the major causative agent of grapevine leafroll disease. The disease has a major negative impact on grape production for wineries, and can cause up to 62.8% loss in production. Despite the negative impact of GLRaV-3 on the grapevine industry worldwide, knowledge on the variability of the virus, which is essential for developing effective control measure of the virus in vineyards, is surprisingly scarce. To test this, six primers sets used in a one tube, one step polymerase chain reaction (PCR) protocol, together with ELISA were used to detect GLRaV-3 virus in 135 plant samples collected from a single vineyard. As expected the more sensitive PCR detected more infected samples than ELISA. However, some samples yielded positive results with the ELISA, but negative results using PCR. This might suggest that strain variants exist. Amongst PCR results of the different primer sets, anomalous results occurred, as often a plant will yield an amplicon with one primer set, but not with another primer set. Using the entire set of 7 PCR results per sample, each plant was assigned a PCR ‘fingerprint’. This yielded 24 different fingerprints in the vineyard. Mapping the spatial distribution of given fingerprints supported the possibility that strain variants exist. However, sequencing areas incorporating the primer binding sites showed no nucleotide sequence differences, indicating that the anomalous PCR results were not due to variants, but rather to protocol error. The PCR protocol used initially was adapted to obtain more optimal detection of virus. Different extraction methods and PCR protocols were tested. It was found that using the two step RT-PCR and using a less dilute plant macerate in ELISA extraction buffer (1:5), yielded amplicon of the expected size from all known infected plant samples. The protocol was further optimized with regards the RT step and subsequent PCR. Since the modified protocol did detect all known infected plant samples it can be concluded that in the 135 plant samples tested no significant sequence variation in strains at the primer binding sites occurred and that the anomalous PCR results initially obtained were due to a sub-optimal extraction method. / Dissertation (MSc (Microbiology))--University of Pretoria, 2008. / Microbiology and Plant Pathology / unrestricted

Grapevine Leafroll disease (GLD), one of the most destructive diseases of grapevines, has been found in every country where grapevines are grown. Grapevine Leafroll associated virus type 3 (GLRaV-3), one of several viruses associated with GLD globally, is the most prevalent virus in South African grapevines and therefore control of GLRaV-3 takes high priority in any strategy aimed at control of GLD. GLD can be controlled through the use of an integrated strategy which includes using certified plant material, controlling insect vectors through use of systemic insecticides and the removal of infected vines by roguing. Infected individuals are identified each autumn, using either symptom display (in red cultivars, where infected individuals display interveinal reddening and downward rolling of leaves) or ELISA (in symptomless white cultivars). ELISA is laborious, time consuming and relatively insensitivity compared to molecular techniques and a simpler, more rapid and more sensitive means of indentifying GLRaV-3 infected vines is required. A simple RNA extraction procedure combined with a single-tube reverse transcriptase loop-mediated amplification (RT-LAMP) has been developed which allows for the rapid, simple detection of GLRaV-3. Using RT-LAMP, a viral target can be amplified in 2 hours under isothermal conditions. This GLRaV-3 specific RTLAMP uses hydroxy napthol blue (HNB), a colourimetric indicator that changes from violet to sky blue only where a positive RT-LAMP reaction has occurred, making results quick and easy to interpret. The sensitivity of this technique was compared to ELISA and nested PCR by pooling samples at varying ratios of healthy to infected plants. Using nested PCR and RT-LAMP 1 infected sample could be detected amongst 50 healthy individuals while ELISA could only detect 1 amongst 30 infected making RT-LAMP more sensitive than ELISA. Further RT-LAMP could be performed in 2 hours compared to nested PCR and ELISA’s 8 and 48 hours respectively. Based on these results, RT-LAMP is viable alternative for ELISA for the detection of GLRaV-3 in the field. RT-LAMP was also tested for its ability to detect GLRaV-3 in grapevine rootstocks where, due to low viral titres and erratic distribution, it is notoriously difficult to detect. The rootstocks which were used for testing of GLRaV-3 had been tested in a previous study and it was found that only 28% of samples tested positive after 33 months (post inoculation). Using RT-LAMP, 78% of samples tested positive for GLRaV-3. Although further testing must be done, RT-LAMP may also be a viable alternative for testing grapevine rootstocks for GLRaV-3 infection. / Dissertation (MSc)--University of Pretoria, 2013. / gm2014 / Microbiology and Plant Pathology / unrestricted