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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
81

Enfezamento do brócolis: identificação molecular de fitoplasmas, potenciais insetos vetores e hospedeiros alternativos, e análise epidemiológica da doença / Broccolo stunt: identification of phytoplasmas, potential insect vectors and alternative hosts and epidemiology of the disease

Barbara Eckstein 23 August 2010 (has links)
O brócolis (Brassica oleraceae var. italica) é uma das hortaliças mais importantes do país, cujo volume de comercialização na CEAGESP é de aproximadamente 13 mil toneladas por ano. Recentemente, uma nova doença tem causado perdas relevantes para as culturas instaladas na maior região produtora do Estado de São Paulo. Os sintomas característicos da doença são expressos pelo enfezamento da planta e necrose dos vasos de floema. Devido ao fato destes sintomas indicarem a presença de fitoplasmas nas culturas de repolho e couve-flor, localizadas na mesma região geográfica onde foi observada esta nova doença, levantou-se a suspeita de que estes mesmos agentes patogênicos pudessem estar associados com as plantas doentes de brócolis. Assim, o DNA total de plantas de brócolis sintomáticas foi analisado por PCR com primers específicos para a região 16S rDNA de fitoplasmas. Os resultados revelaram que estes patógenos estavam associados com as plantas doentes. Através das técnicas de RFLP do sequenciamento de nucleotídeos desta mesma região genômica, os fitoplasmas foram identificados como pertencentes aos grupos 16SrI, 16SrIII e 16SrXIII. Através de análise de RFLP, fitoplasmas também foram identificados em diversas espécies de plantas daninhas e em cigarrinhas da família Cicadellidae coletadas em áreas adjacentes a campos de produção de brócolis. Fitoplasmas do grupo 16SrIII foram identificados em plantas daninhas das espécies Agetarum conyzoides (mentrasto), Crotalaria lanceolata (crotalária), Lepidium virginicum (mentruz), Nicandra physalodes (juá-de-capote), Paulicourea marcgravii (erva-de-rato), Ricinus communis (mamona), Sida rhombifolia (guanxuma), Sonchus oleraceae (serralha amarela), Bidens pilosa (picão preto), Erigeron bonariensis (buva), Emilia sonchifolia (falsa serralha), Leonorus sibiricus (rubim), enquanto que fitoplasmas do grupo 16SrVII foram encontrados as últimas quatro espécies citadas. Com relação aos insetos, fitoplasmas foram detectados em indivíduos das subfamílias Deltocephalinae, Agalliinae e Typhlocybinae. Dentro da subfamília Deltocephalinae, a cigarrinha Balclutha hebe portava fitoplasma do grupo 16SrI, enquanto que cigarrinhas das espécies Atanus nitidus, Planicephalus flavicosta e Schapytopius fuliginosus abrigavam fitoplasmas do grupo 16SrIII. Nos tecidos de duas cigarrinhas da subfamília Agalliinae e uma da Typhlocybinae, as quais não foram identificadas quanto a espécie, foram encontrados fitoplasmas do grupo 16SrIII. As análises epidemiológicas revelaram um padrão espacial agregado de plantas doentes e a ocorrência de um maior progresso da doença nos bordos dos campos de cultivo de brócolis, que estão localizados nas proximidades de áreas com a presença de plantas daninhas. / Broccoli (Brassica oleraceae var. italica) is one of the most important vegetables in Brazil, whose trading volume in CEAGESP is approximately 13 000 tons per year. Recently, a new disease has caused significant losses in this crop cultivated in the largest producing region of the São Paulo State. The characteristic symptoms of the disease are expressed by plant stunting and necrosis of phloem vessels. Because these symptoms indicate the presence of phytoplasmas in cabbage and cauliflower crops, grown in the same geographical region, it was suspected that the same pathogens could be associated with the affected broccoli plants. Therefore, the total DNA from symptomatic plants of broccoli was analyzed by PCR with specific primers for the 16S rDNA of phytoplasmas. Through the techniques of RFLP and nucleotide sequencing of the same genomic region, the phytoplasmas were identified as belonging to the groups 16SrI, 16SrIII and 16SrXIII. Through RFLP analysis, phytoplasmas were also identified in several species of weeds and leafhoppers in the family Cicadellidae collected in adjacent areas of broccoli fields. Phytoplasmas belonging of the 16SrIII group were identified in the weeds belonging to the species Agetarum conyzoides, Crotalaria lanceolata, Lepidium virginicum, Nicandra physalodes, Paulicourea marcgravii, Ricinus communis, Sida rhombifolia, Sonchus oleraceae, Bidens pilosa, Erigeron bonariensis, Emilia sonchifolia, Leonorus sibiricus, while phytoplasmas of the 16SrVII group were found in the last four mentioned species. In respect to insects, phytoplasmas were detected in individuals from subfamilies Deltocephalinae, Agalliinae and Typhlocybinae. Within the subfamily Deltocephalinae, the leafhopper Balclutha hebe carried phytoplasmas of the 16SrI group, while that of the species Atanus nitidus, Planicephalus flavicosta e Schapytopius fuliginosus harbored phytoplasmas of the 16SrIII group. In the tissues of two leafhoppers of the subfamily Agalliinae and one of the Typhlocybinae, which were not identified as specie, were found phytoplasmas of the 16SrIII group. The epidemiological analysis revelead an aggregated pattern of the diseased plants and a higher progress of the diseased in the border of the broccoli fields, whitch were located nearby areas where the presence of weeds was abundant.
82

Seleção de estirpe fraca do Zucchini Yellow Mosaic Vírus (ZYMV) e controle dos mosaicos comum (Papaya ringspot vírus) e amarelo (ZYMV) por dupla premunização em abobrinha-de-moita. / Selection of mild strain of Zucchini Yellow Mosaic Virus (ZYMV) and control of Papaya ringspot virus and ZYMV by double cross protection in zucchini squash.

Luiz Cláudio Rabelo 29 May 2002 (has links)
No presente trabalho são apresentados os resultados da seleção de estirpes fracas do vírus do mosaico amarelo da abobrinha (Zucchini yellow mosaic virus – ZYMV) e a sua eficiência para o controle do mosaico amarelo em abobrinha-de-moita (Cucurbita pepo cv. Caserta), através da premunização. Mostram também os resultados da eficiência da dupla premunização, com a estirpe fraca do ZYMV e uma estirpe fraca do Papaya ringspot virus – type Watermelon, denominada PRSV-W-1, no controle dos mosaico amarelo e comum e na produção das plantas de abobrinha-de-moita, em condições de campo. A procura de estirpes fracas do ZYMV foi realizada através das seguintes abordagens: a) a partir de lesões locais em plantas indicadoras mantidas em casa-de-vegetação; b) a partir de lesões locais em plantas indicadoras mantidas a 15 °C e c) a partir de lesões locais em plantas indicadoras inoculadas com suspensão parcialmente purificada do vírus, exposta à luz ultravioleta. Apenas uma estirpe fraca (“Mild”) do vírus, denominada ZYMV-M, foi obtida em abobrinha-de-moita diretamente inoculada com suspensão parcialmente purificada do vírus, exposta à luz ultravioleta, durante 30 minutos. Essa estirpe fraca mostrou-se altamente estável, com base na sintomatologia, após 12 transferências sucessivas em plantas de abobrinha-de-moita, durante 15 meses. Plantas de abobrinha-de-moita premunizadas com a estirpe ZYMV-M e superinoculadas (desafiadas) com estirpes severas originárias de Atibaia, SP (ZYMV-AT), de Iacri, SP (ZYMV-IA) e de Vargem Paulista, SP (ZYMV-VP), não exibiram sintomas severos da doença em testes em casa-de-vegetação. A mesma proteção foi observada em plantas duplamente premunizadas com as estirpes ZYMV-M e PRSV-W-1 e desafiadas com uma mistura de estirpes severas desses dois vírus, em condições de casa-de-vegetação. Teste de proteção em campo, com plantas de abobrinha-de-moita premunizadas apenas com a estirpe ZYMV-M, ou duplamente premunizadas com as estirpes ZYMV-M e PRSV-W-1, também mostraram a eficiência dessa tecnologia para o controle dos mosaicos amarelo e comum, com ganhos significativos na produção de frutos comerciais. As plantas premunizadas apenas com a estirpe ZYMV-M, e duplamente premunizadas, tiveram médias de produções de semelhante, com média de 1,85 kg e 1,70 kg de frutos comercias/planta, respectivamente. Os ganhos de produções dessas plantas, em relação às plantas inoculadas com as estirpes severas desses vírus foram de 101 % e 85 %, respectivamente. Diante desses resultados, tornam-se necessários estudos para avaliar a eficiência da dupla premunização para o controle dos mosaicos amarelo e comum, em outras espécies de cucurbitáceas suscetíveis ao ZYMV e PRSV-W. / Due to the present high incidence of Zucchini yellow mosaic virus (ZYMV) and the damage it causes to cucurbit crops, studies were carried out to select mild strains of the virus and evaluate their efficiency for the control of the disease by cross protection in zucchini squash (Cucurbita pepo L. cv. Caserta). Studies were also done to evaluate the efficiency of double cross protection for the control of ZYMV and Papaya ringspot virus – type W (PRSV-W) in zucchini squash under greenhouse and field conditions. Searching for mild strains was carried out as follows: a) from local lesions caused by ZYMV on indicator hosts maintained under green house conditions; b) from local lesions caused on indicator hosts maintained at 15 °C; and c) from local lesions caused on indicator hosts inoculated with suspension of purified ZYMV, exposed to ultra-violet light. Only one very mild strain of the virus, named ZYMV-M, was obtained in zucchini squash plant directly inoculated with suspension of purified ZYMV exposed to ultra-violet light for 30 minutes. This mild strain remained stable for a period of 15 months, after 12 successive transfers in zucchini squash plants. Experiments carried out under greenhouse showed that zucchini squash plants protected with ZYMV-M, at the cotyledonal stage, did not show severe symptoms of the disease after double challenge inoculation with severe strains of the virus, obtained from three regions of the State of São Paulo. Plants inoculated with the mild strain ZYMV-M and a mild strain of PRSV-W, named PRSV-W-1, were also protected against superinfection with severe strains of both viruses. Field test carried out with zucchini squash protected with ZYMV-M and doubly protected with ZYMV-M and PRSV-W-1, showed that this technology was effective for the control of the mosaic diseases caused by severe strains of these viruses. The yield of marketable fruits from plants protected with ZYMV-M, or doubly protected, were 1.85 kg and 1.70 kg of fruits/plant, respectively. These yields were, respectively, 101 % and 85 % higher than the yield of marketable fruits from plants inoculated with a mixture of severe strains of both viruses. Studies are necessary to evaluate the efficiency of double cross protection for the control of ZYMV and PRSV-W in other cucurbit species susceptible to these viruses.
83

Laurel Wilt Disease: Early Detection through Canine Olfaction and "Omics" Insights into Disease Progression

Mendel, Julian L 08 June 2017 (has links)
Laurel wilt disease is a vascular wilt affecting the xylem and water conductivity in trees belonging to the family Lauraceae. The disease was introduced by an invasive species of ambrosia beetle, Xyleborus glabratus. The beetle, together with its newly described fungal symbiont Raffaelea lauricola (pathogenic to host trees), has lead to the devastation and destruction of over 300 million wild redbay trees in southeastern forests. Ambrosia beetles make up a very unique clade of beetle and share a co-evolved obligatory mutualistic relationship with their partner fungi. Rather than consuming host tree material, the beetles excavate galleries or canals within them. These galleries serve two purposes: reproduction and fungal gardening. The beetles house fungal spores within specialized sacs, mycangia, and essentially inoculate host trees with the pathogenic agent. They actively grow and cultivate gardens of the fungus in galleries to serve as their sole food source. Once the fungus reaches the xylem vessels of the host tree, it thrives and leads to the blockage of water flow, both because of fungal accumulation and to the host response of secreting gels, gums and tyloses to occlude vessels in an attempt to quarantine the fungus. This disease spreads rapidly, and as a result, once symptoms become visible to the naked eye, it is already too late to save the tree, and it has likely already spread to adjacent ones. The present study presents the first documented study involving the early detection of disease from deep within a tree through the use of scent-discriminating canines. In addition, the present study has lead to the development of a novel sample collection device enabling the non-destructive sampling of beetle galleries. Finally, a metabolomics approach revealed key biochemical pathway modifications in the disease state, as well as potential clues to disease development.
84

Heat shock protein 70 and defence responses in plants: salicylic acid and programmed cell death.

Cronje, Marianne Jacqueline 06 May 2008 (has links)
Background: Heat-shock (HS) proteins (HSP) are induced or increasingly expressed to protect against lethal environmental stresses. Hsp70 in particular, provides protection against various stresses including oxidative stress, is implicated in thermotolerance and appears to have an anti-apoptotic function. Anti-inflammatory salicylates potentiate the induction of the 70 kDa HSP (Hsp70) in mammals in response to HS, enhance thermotolerance and induce apoptosis. In plants, salicylic acid (SA) is a natural signalling molecule, mediating resistance in response to avirulent pathogens. The effects of salicylic acid-mediated increases in Hsp70/Hsc70 expression and its relation to events associated with PCD/ apoptosis in plants are unknown. Hypothesis and Objectives: The hypothesis studied in this investigation was that SA influences Hsp70 expression similar to that found in mammalian cells and may influence the choice between survival or death, whether apoptosis or necrosis. In order to verify this hypothesis the effect of SA alone or in combination with HS on Hsp70/Hsc70 accumulation and events associated with apoptosis were investigated through three main objectives: 1) Determine whether SA in plants, as in mammalian cells, can potentiate heat-induced Hsp70/Hsc70 accumulation or induce Hsp70/Hsc70 by itself at elevated levels. This was done by investigating the effect of SA at various concentrations on Hsp70/Hsc70 expression at normal temperatures or following heat. 2) Establish flow cytometry as a rapid and quantitative alternative for the evaluation of Hsp70 accumulation in plant protoplasts to be evaluated in concert with various parameters indicative of cellular integrity. 3) Investigate whether Hsp70/Hsc70 expression modulated by SA influences cell death (apoptosis/necrosis) or associated events such as mitochondrial membrane permeability (MMP) or reactive oxygen species (ROS) in plant protoplasts using flow cytometry. Materials and Methods: The effect of SA alone or in combination with HS on Hsp70/Hsc70 levels in tomato cells was investigated using biometabolic labelling and Western blotting. A flow cytometric assay was developed to determine Hsp70/Hsc70 levels in tobacco protoplasts. MMP and ROS were monitored by the fluorescent probes DiIC1(5) and H2DCFDA respectively, phosphatidylserine externalisation by annexin V binding and DNA fragmentation by the TUNEL assay in protoplasts treated with SA and/or HS. Results: Results obtained in the attainment of the three main objectives were: 1) In plants, as in mammals, low concentrations of SA do not induce Hsp70/Hsc70 but significantly potentiate heat-induced Hsp70/Hsc70 levels while cytotoxic levels significantly induce Hsp70/Hsc70. In cell suspension cultures, this induction was preceded by increased membrane permeability. 2) Flow cytometry can be implemented as a rapid, quantitative alternative to detect intracellular Hsp70/Hsc70 accumulation in protoplasts. 3) In protoplasts exposed to low doses of SA at normal temperatures, PCD/apoptosis is increased as reflected by increased DNA fragmentation and phosphatidylserine externalisation, but not by increased MMP or ROS. High doses of SA were associated with increased levels of necrosis. Exposure of protoplasts to low doses of SA in combination with HS showed suppression of PCD/apoptosis (reflected by decreased DNA fragmentation and phosphatidylserine externalisation), accompanied by decreased levels of ROS and increased MMP. Discussion: These results suggest that SA-mediated increases in Hsp70/Hsc70 accumulation at normal temperatures are associated with cellular damage and protect cells against necrosis. On the other hand, low doses of SA that potentiate heat-induced Hsp70/Hsc70 accumulation abrogated the induction of apoptosis that was induced by low doses of SA at normal temperatures. The anti-apoptotic effects of Hsp70 could therefore influence plant resistance by interfering with the execution of PCD. These results could contribute to our understanding of heat-induced disease susceptibility, and the manipulation of SA-modulated Hsp70/Hsc70 should be carefully considered in the light of its ability to affect cell death, which may be advantageous or deleterious to the plant cell. / Prof. L. Bornman
85

Phosphoprotein changes in Arabidopsis thaliana cells in response to elicitation by lipopolysaccharides.

Roux, Milena 16 May 2008 (has links)
Plants respond to pathogen attack by inducing a coordinated resistance strategy, which results in the expression of defense gene products. When a plant-pathogen interaction results in disease establishment, parasite colonization is caused by a delayed plant defense response, not due the absence of any response. Thus, the speed and intensity of the plant response and intracellular signalling determines the outcome of a plant-pathogen interaction. The acceleration of plant responses by the application of resistance inducers could provide a commercially, biologically and environmentally feasible alternative to existing pathogen control methods. Lipopolysaccharides are amphipathic lipoglycans that are attached to the outer bacterial membrane by a lipidic entity inserted into the bacterial phospholipid monolayer, with the saccharidic part oriented towards the exterior. The general structure of this compound is comprised of an anchor named lipid A associated with a core polysaccharide, which bears an O-antigen domain. LPS has been described as one of the pathogen-associated molecular patterns (PAMPs) capable of eliciting the activation of the plant innate immune system. LPS present in the outer membranes of plant growth-promoting rhizobacteria (PBPR) are major determinants of induced systemic resistance (ISR). In addition, LPS may function as an activator of systemic acquired resistance (SAR), providing non-specific immunization against later infection. Evidence suggests that LPS may advance plant disease resistance using the mechanism of ISR or SAR through its application to plants as a sensitizing agent, priming them to respond more effectively to subsequent pathogen attack. Phosphorylation plays a major role during the plant defense response, exemplified by its phosphorylation of transcription factors, required for the expression of defense-related genes. One of the most extensively documented phosphorylation responses is that of MAP kinase activation by phosphorylation in response to elicitation by race-specific and non-racespecific elicitors in various plant species.Proteins that undergo differential phosphorylation as a result of elicitation could be components of signal transduction pathways which connect pathogen perception with defense responses. Thus the identification of protein kinases, protein phosphatases and their substrates is essential in the elucidation of plant defense responses. The hypothesis behind this dissertation is that LPS elicitation results in alterations in the phosphorylation profile of Arabidopsis thaliana proteins. In this study, LPS was extracted from the cell walls of Burkholderia cepacia, a bacterial endophyte, and characterized by SDS-PAGE. The exposure of Arabidopsis callus culture cells to LPS resulted in distinctive changes in the phosphoprotein profile of the cells. Radioactive phosphorous labelling of proteins provided evidence that phosphorylation occurs in Arabidopsis following LPS perception, as part of a defense response related to LPS elicitation. Further investigation of differential protein phosphorylation via immunoblotting with antiphosphotyrosine antibodies revealed that tyrosine phosphorylation of Arabidopsis proteins occurs in response to LPS. One of the tyrosine-phosphorylated proteins was found to be a 42 kDa kinase, activated in response to LPS elicitation. The identity of the kinase as a mitogen-activated protein (MAP) kinase was confirmed by immunoblotting with anti-active MAP kinase antibodies. In addition, an assay of MAP kinase activity demonstrated the ability of the LPS-responsive MAP kinase to phosphorylate the ERK-MAP kinase substrate Elk1. In terms of the global phosphoproteome of Arabidopsis in response to LPS, phosphopeptides were purified from a crude protein digest by immobilized metal affinity chromatography and analyzed by liquid chromatography-tandem mass spectrometry (LCMS/ MS). While LC indicated both quantitative and qualitative differences resulting from LPS elicitation, no peptides could be positively identified as phosphopeptides by MS analysis. This work can however be repeated with further precautions to prevent the loss of phosphate groups prior to analysis. The results obtained in this study indicate that LPS causes specific alterations in Arabidopsis protein phosphorylation as a post-translational modification in response to the perception of LPS during a plant-pathogen interaction, proving the original hypothesis. / Prof. I.A. Dubery
86

Efficacy and physical mode of action of fungicides against leather rot of strawberry and sensitivity of phytophthora cactorum isolates to azoxystrobin

Rebollar-Alviter, Angel 14 September 2006 (has links)
No description available.
87

Characterization of the soybean genome in regions surrounding two loci for resistance to soybean mosaic virus

Hayes, Alec J. 11 August 1998 (has links)
Soybean mosaic virus (SMV), has been the cause of numerous and often devastating disease epidemics, causing reduction in both the quality and quantity of soybeans worldwide. Two important genes for resistance to SMV are Rsv1 and Rsv4. Alleles at the Rsv1 locus have been shown to control resistance to all but the most virulent strain of SMV. This locus has been mapped previously to the soybean F linkage group. Rsv4 is an SMV resistance locus independent of Rsv1 and confers resistance to all strains of SMV. This locus has not been mapped previously. The purpose of this study is to investigate the two genomic regions that contain these vitally important resistance genes. A population of 281 F2 individuals that had previously been genotyped for reaction to SMV was evaluated in a mapping study which combined bulk segregant analysis with Amplified Fragment Length Polymorphism (AFLP). A Rsv4-linked marker, R4-1, was identified that mapped to soybean linkage group D1b using a reference mapping population. More than 40 markers were mapped in the Rsv4 segregating population including eleven markers surrounding Rsv4. This will provide the necessary framework for the fine mapping of this important genetic locus. Previous work has located Rsv1 to a genomic region containing several important resistance genes including Rps3, Rpg1, and Rpv. An RFLP probe, NBS5, whose sequence closely resembles that of several cloned plant disease resistance genes has been mapped to this chromosomal region. The efficacy of using this sequence to identify potential disease resistance genes was assessed by screening a cDNA library to uncover a candidate disease resistance gene which corresponds to this NBS5 sequence. Two related sequence classes were identified that correspond to NBS5. Interestingly, one class corresponds to a full length gene closely resembling other previously cloned disease resistance genes offering evidence that this NBS5-derived clone is a candidate disease resistance gene. A new marker technique was developed by combining the speed and efficiency of AFLP with DNA sequence information from cloned disease resistance genes. Using this strategy, three new markers tightly linked to Rsv1 were identified. One of these markers, which maps 0.6 cM away from Rsv1, has motifs consistent with other cloned disease resistance genes, providing evidence that this approach is an efficient method for targeting genomic regions where disease resistance genes are located. / Ph. D.
88

Computational Tools for Improved Detection, Identification, and Classification of Plant Pathogens Using Genomics and Metagenomics

Johnson, Marcela Aguilera 13 February 2023 (has links)
Plant pathogens are one of the biggest threats to plant health and food security worldwide. To effectively contain plant disease outbreaks, classification and precise identification of pathogens is crucial to determine treatment and preventive measurements. Conventional methods of detection such as PCR may not be sufficient when the pathogen in question is unknown. Advances in sequencing technology have made it possible to sequence entire genomes and metagenomes in real-time and at a relatively low cost, opening an opportunity for the development of alternative methods for detection of novel and unknown plant pathogens. Within this dissertation, an integrated approach is used to reclassify a high-impact group of plant pathogens. Additionally, the application of metagenomics and nanopore sequencing using the Oxford Nanopore Technologies (ONT) MinION for fungal and bacterial plant pathogen detection and precise identification are demonstrated. To improve the classification of the strains belonging to the Ralstonia solanacearum species complex (RSSC), we performed a meta-analysis using a comparative genomics and a reverse ecology approach to accurately portray and refine the understanding of the diversity and evolution of the RSSC. The groups identified by these approaches were circumscribed and made publicly available through the LINbase web server so future isolates can be properly classified. To develop a culture-free detection method of plant pathogens, we used metagenomes of various plants and long-read nanopore sequencing to precisely identify plant pathogens to the strain-level and performed phylogenetic analysis with SNP resolution. In the first paper, we used tomato plants to demonstrate the detection power of bacterial plant pathogens. We compared bioinformatics tools for detection at the strain-level using reads and assemblies. In the second paper, we used a read-based approach to test the feasibility of the methodology to precisely detect the fungal pathogen causing boxwood blight. Lastly, with the improvement in nanopore sequencing, we used grapevine petioles to investigate whether we can go beyond detection and identification and do a phylogenetic analysis. We assembled a metagenome-assembled genome (MAG) of almost the same quality as the genomes obtained from cultured isolates and did a phylogenetic analysis with SNP resolution. Finally, for the cases where there may be no related genome in the database like the pathogen in question, we used machine learning and metagenomics to develop a reference-free approach to detection of plant diseases. We trained eight different machine learning models with reads from healthy and infected plant metagenomes and compared the classification accuracy of reads as belonging to a healthy or infected plant. From the comparison, random forest was the best model in terms of computational resources needed while maintaining a high accuracy (> 0.90). / Doctor of Philosophy / Microbes are present in every environment on the planet and have been on Earth for billions of years. While some microbes are beneficial, others can cause diseases. To differentiate the ones causing diseases from those who do not, looking into the evolutionary forces making them different is crucial to classify and identify them correctly. Although microorganisms cause diseases in humans and animals, the ones causing diseases in plants are one of the biggest threats to plant health and food security worldwide. In a perfect world, plant diseases would be diagnosed by eye or simple procedures. However, when a plant disease is present, it is not always obvious which organism, if any, is causing the disease making it hard for outbreaks to be detected and contained promptly. With technological advances, it is now possible to obtain all the genetic information of not only one organism but all the organisms living in an environment at a time. This genetic information can then be used to precisely identify what organism is causing a disease in a plant for faster disease diagnosis and, consequently, more efficient disease prevention and control. In this dissertation, we used the bacterial group, called Ralstonia solanacearum species complex, which can cause different diseases in more than 200 crops, to investigate and understand the evolution and diversity of the members of this group. We also used newly developed technologies to obtain the genetic material of all the organisms living in multiple important plants including tomato, grapevine, and the ornamental bush, boxwood. Using this genetic material, we developed a methodology for the detection of bacteria and a fungus causing plant diseases. While this works well when the suspected organism or a similar one is available for comparison, the detection of plant diseases in cases where this information is not available is challenging. Machine learning models, where computers can learn complex patterns from data, have the potential to detect pathogens without the need to compare the sequences to sequences of other pathogens. Here we also used the genetic material to train and compare different machine learning models to classify plants as either being infected or healthy.
89

Potenciais hospedeiros alternativos para o fitoplasma e o espiroplasma, agentes do enfezamento do milho, e alterações bioquímicas em plantas infectadas pelo espiroplasma / Potencial hosts for maize mollicutes, agent of corn stunt, and biochemical changes in plants infected by the spiroplasma

Haas, Isolda Cristina Ruschel 16 April 2010 (has links)
Os enfezamentos vermelho e pálido são importantes doenças do milho, causadas, respectivamente, por um fitoplasma e por um espiroplasma (Spiroplasma kunkelii). As duas formas de enfezamento foram relatadas no Brasil no início da década de 70 e se tornaram economicamente relevantes no início dos anos 80, com a introdução de novas técnicas de cultivo no milho. Apesar de ser um patossistema conhecido e estudado, ainda há certos pontos em relação à doença que permanecem desconhecidos. Um deles é em relação à sobrevivência do vetor (Dalbulus maidis) e do patógeno durante a entressafra. Outro, diz respeito às alterações bioquímicas envolvidas na relação hospedeiro-patógeno. O presente trabalho visou avaliar algumas gramíneas, usadas na formação de pastagens, e ervas-daninhas, que ocorrem nas áreas cultivadas com milho, como possíveis hospedeiros alternativos destes patógenos; ainda, buscouse estudar algumas alterações bioquímicas que ocorrem nas plantas de milho quando infectadas por espiroplasma. Para isto, o trabalho foi desenvolvido em três etapas. Na primeira, onze espécies de capins e ervas daninhas foram experimentalmente inoculadas com o espiroplasma através do vetor. As avaliações foram realizadas com base na observação de sintomas, na detecção molecular do espiroplasma nos tecidos das plantas inoculadas e na contagem de insetos sobreviventes nestas plantas inoculadas. Como resultado, nenhuma das espécies testadas mostrou resultado positivo para presença do patógeno inoculado e não demonstrou capacidade em hospedar o espiroplasma. Em uma segunda etapa, três gramíneas sabidamente infectadas com o fitoplasma do enfezamento vermelho do milho (capim colonião, capim braquiária e capim marmelada) foram testadas quanto à capacidade de servirem como planta-fonte na aquisição do fitoplasma pelo vetor. Após o estabelecimento dos insetos nestas plantas, os mesmos foram transferidos para plantas sadias de milho. As avaliações também foram realizadas com base na observação de sintomas e detecção molecular do fitoplasma nos tecidos das plantas inoculadas. Das três espécies testadas como hospedeiras alternativas, o capim colonião demonstrou ser um hospedeiro alternativo do fitoplasma. Estes resultados trouxeram uma significativa contribuição ao melhor conhecimento da epidemiologia da doença, mostrando a existência de outro hospedeiro do patógeno além do milho. Na última etapa, foram escolhidos um híbrido suscetível e um resistente, os quais foram inoculados com cigarrinhas infectadas pelo espiroplasma e submetidos à análise bioquímica para avaliação de alguns compostos, como proteínas, fenóis, clorofilas, açúcares e as enzimas peroxidase e -1,3-glucanase. Amostras foliares foram coletadas e avaliadas em 6 diferentes períodos: 0, 10, 20, 40, 60 e 80 dias após a inoculação. Os resultados revelaram um aumento na quantidade de todos os compostos avaliados, porém uma redução na clorofila e proteína total para o híbrido suscetível. As análises evidenciaram que as alterações nas atividades enzimáticas parecem fazer parte de uma resposta inespecífica de defesa da planta. / The maize bushy stunt and corn stunt are relevant diseases caused, respectively, by a phytoplasma and a spiroplasma (Spiroplasma kunkelii). Both kinds of stunting were reported in Brazil in the beginning of the 1970´s and became economically important in the beginning of the 1980´s, with the adoption of new techniques for maize cultivation. Although this pathosystem has been well studied, there are still some unknown points related to the diseases. One of them is related to survival of the leafhopper vector (Dalbulus maidis) and pathogens during the maize off-season. The other one is related to biochemical changes involved in the host-pathogen interaction. This research aimed to evaluate some pasture grasses and weeds that occur on areas cultivated with corn as possible alternatives hosts for these pathogens; an additional study was conducted to investigate biochemical alterations in maize plants infected by S. kunkelii. So, the research was carried out on three steps. First, eleven species of grasses and weeds were inoculated with S. kunkelii by using infective leafhoppers. The evaluations were based on symptoms and molecular detection of the pathogen in the inoculated plants, as well as on counting of surviving insects onto these inoculated plants. S. kunkelii was not detected by PCR or symptoms in any of the inoculated plant species, indicating that they are not able to host this pathogen. In the second step, three species of grasses (Panicum maximum, Brachiaria plantaginea and Brachiaria decumbens) infected with the maize bushy stunt phytoplasma (MBSP) were tested as source plants of this pathogen for acquisition by its vector. After insects establishing on these plants, they were transferred to healthy corn plants. Transmission to maize was determined based on symptoms and molecular detection of the phytoplasma in the inoculated plant tissues. Out of the three grass species tested, only P. maximum was shown to serve as an alternative host of the phytoplasma. These results represent a relevant contribution to understanding of the disease epidemiology, indicating a species distinct of maize as a source plant for MBSP. In the last study, a susceptible and a resistant hybrid were inoculated with S. kunkelii by infective leafhoppers. Biochemical analyses were carried out to evaluate changes in proteins, phenols, chlorophylls, total sugars and enzymes peroxidase and -1, 3 glucanase. Leaf samples were harvested at 6 different times: 0, 10, 20, 40, 60 and 80 days after inoculation. Results revealed an increase in all biochemical parameters evaluated, with exception for the chlorophyll content and soluble protein in a susceptible hybrid that decreased. The analysis showed that enzyme activity may be an unspecific response of the plant to the pathogen.
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Indução de resistência em plantas de berinjela e tomate por Lentinula edodes e Agaricus blazei contra bactérias causadoras de murcha (Ralstonia solanacearum) e cancro (Clavibacter michiganensis subsp. michiganensis) / Induced resistance by Lentinula edodes and Agaricus blazei in tomato plant and eggplant against bacterial wilt (Ralstonia solanacearum) solanacearum) and bacterial canker (Clavibacter michiganensis subsp. michiganensis)

Silva, Ricardo Ferrari 20 April 2007 (has links)
Devido ao aumento da preocupação com o impacto dos agrotóxicos no meio ambiente e na saúde humana, busca-se uma agricultura sustentável. É no âmbito dessa questão que a resistência induzida torna-se uma ferramenta fundamental no manejo integrado de doenças e indispensável para uma nova agricultura, mais racional e sustentável. Dentre os diversos agentes bióticos e abióticos, utilizados em trabalhos de indução de resistência de plantas a patógenos, os cogumelos Lentinula edodes e Agaricus blazei vem sendo pesquisados. Desse modo, este trabalho teve como objetivos avaliar o efeito de diferentes isolados de L. edodes e A. blazei e do acibenzolar-S-metil (aSm) in vitro contra as bactérias e o controle de doenças de importância econômica para as culturas do tomate e da berinjela, em casa-de-vegetação. Depois de obtida a proteção, estudar os possíveis mecanismos bioquímicos ativados nas plantas através do uso dos extratos dos cogumelos e buscar a purificação parcial destes extratos, a fim de identificar o(s) princípio(s) ativo(s). No patossistema berinjela/Ralstonia, os extratos aquosos dos cogumelos não exerceram nenhum efeito direto sobre o patógeno, sendo que os isolados Abl-11 e Abl-28 de de A. blazei reduziram significativamente a ocorrência de folhas murchas das plantas em casa-devegetação, em relação aos demais tratamentos. Ocorreu um aumento na atividade da peroxidase, fenilalanina amônia-liase e polifenoloxidase nas folhas tratadas. O preciptado 60-80% obtido pela precipitação com sulfato de amônia e a fração 4 da cromatografia de troca aniônica (CTA) de Abl-28 reduziram a ocorrência de folhas murchas, sendo que a separação eletroforética revelou a presença de uma banda no gel com aproximadamente 29 kDa nesta fração. Em tomate, os extratos aquosos dos isolados dos cogumelos e o acibenzolar-S-metil não exerceram nenhum efeito inibitório in vitro no crescimento de Ralstonia solanacearum e Clavibacter michiganensis subsp. michiganensis. Porém, os isolados Abl-26 de A. blazei, Le-96/17 de L. edodes e aSm foram os que conferiram maior proteção das plantas de tomates contra os patógenos, diminuindo a ocorrência de folhas murchas, proporcionando um aumento na atividade da peroxidase no patossistema tomate/Ralstonia e um aumento na atividade de peroxidase, quitinase, fenilalanina amônia-liase e polifenoloxidase no patossistema tomate/Clavibacter. O preciptado 40-80% de Le-96/17 foi submetido à CTA, obtendo-se seis frações protéicas. As frações 3 e 4, junto com aSm e o extrato aquoso de Le-96/17 reduziram a ocorrência de folhas murchas. A separação eletroforética destas frações da CTA, do preciptado 40-80% e do extrato aquoso de Le-96/17 revelaram a presença de mais de uma banda no gel na fração 3 e 4 da CTA, no preciptado 40-80% e no extrato aquoso bruto de Le-96/17. Com base nos resultados, os cogumelos A. blazei e L. edodes apresentam compostos que induziram resistência em plantas berinjela e tomate, podendo auxiliar no controle de doenças. / Because the increase of the impact of chemical products in the environment and in human health, a search by sustainable agriculture is needed. It is in the scope of this problem that the induced resistance becomes a tool in the integrated management of pests and diseases and indispensable for a new agriculture, more rational and sustainable. Among the biotic and abiotic agents used to induce resistance, the mushrooms Lentinula edodes and Agaricus blazei have being studied. Thus, the objectives of the present work were evaluate the effects of different isolates of L. edodes and A. blazei and of the acibenzolar-S-methyl (aSm) on in vitro bacterial growth and the control of the diseases in tomato and eggplant under greenhouse conditions. The studies also tried to elucidate the mode of action of the extracts from the fruiting bodies and partially purify them. In eggplant plants, the aqueos extracts from the different mushroom isolates did not have any direct effect on the pathogen. The isolates Abl-11 and Abl-28 of A. blazei reduced the wilt in eggplant leaves, under greenhouse conditions, and increased peroxidase, phenylalanine ammonia-lyase and polyphenoloxidase activities in treated leaves. The fraction of aqueous extract of A. blazei (Abl-28) obtained with ammonium sulfhate and fraction 4 from anion exchange chromatography reduced bacterial wilt and a protein fraction exhibiting molecular mass around 29 kDa was obtained. In tomato plants, the aqueos extracts from the different mushrooms and the acibenzolar-S-methyl did not inhibit in vitro growth of Ralstonia solanacearum and Clavibacter michiganensis subsp. michiganensis. However, the isolates Abl-26 of A. blazei, Le-96/17 of L. edodes and aSm protected tomato plants against the bacterial pathogens, reducing the wilt and causing an increase in peroxidase activity in the tomato/Ralstonia interaction and an increase in peroxidase, chitinase, phenylalanine ammonialyase and polyphenoloxidase activities in the tomato/Clavibacter interaction. The ammonium sulphate fraction of Le-96/17 was submitted to anion exchange chromatography, and the proteins from fractions 3 and 4, aSm and the aqueous extract of Le-96/17 reduced the occurrence of wilt in the leaves. A protein fraction exhibiting proteins with molecular mass around 29, 37 and 45 kDA was obtained in fractions 3 and 4. Thus, the results showed that the mushrooms A. blazei and L. edodes edodes have substances that induce resistance in eggplant and tomato plants.

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