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Characterizing Protein-Protein Interactions of B0238.11, a Previously Uncharacterized Caenorhabditis elegans Intergenic Spacer Binding ProteinOmar, Syed A. A. 11 May 2012 (has links)
A protein, B0238.11, was identified in a yeast one-hybrid screen to bind to the ribosomal intergenic spacer region (IGS) of Caenorhabditis elegans. Proteins interacting with this region of the DNA have been implicated in ribosome biogenesis in other model organisms, so it is also possible that B0238.11 plays a role in RNA transcription by interacting with RNA polymerase I or other transcription machinery. Thus, the goal of this study was to further characterize the structure and function of B0238.11. I used yeast two-hybrid experiments to identify proteins that interact with B0238.11 within the nucleus. RPS-0, K04G2.2, DPY-4, EFT-3, PAL-1, and B0238.11, itself, were found to bind to B0238.11. Additionally, I analysed the amino acid sequence of B0238.11 using in silico bioinformatics methods to determine its structure and putative function and also to identify and characterize the other interacting proteins. I found that B0238.11 contains a high-mobility group box domain, which is also found in HMO1P in yeast and UBF in vertebrates. These other proteins also bind to the IGS, are known to form homodimers and have been implicated in the initiation of ribosomal RNA transcription. Here I scrutinize the validity of the interaction between each protein and B0238.11. I conclude that B0238.11 is likely to be a C. elegans homolog of UBF and present an updated interactome map for B0238.11. / Synopsis: I carried out yeast two-hybrid assay to find proteins interacting with B0238.11 (O16487_CAEEL). I found that this protein's DNA-binding profile and protein interaction profile mimic other HMG-box containing proteins UBF and HMO1P which are involved in ribosomal RNA transcription initiation. Acknowledgements: I would like to thank my supervisor, Dr. Teresa J. Crease, for not only giving me the opportunity to investigate an interesting topic in Molecular Biology, but also for her patient guidance, encouragement and sound advice. I feel extremely lucky to have a supervisor who cared so much about my work, who responded to my questions and queries so promptly, and was always available to discuss project and career related matters. I would also like to thank Dr. Todd Gillis and Dr. Terry Van Raay for their careful consideration of this project and timely constructive criticisms that helped shape my project. I would like to thank all the members of my committee for helping me see things from different perspectives and helping me develop and critical and mature understanding of the scientific process.
I must also express my gratitude to Dr. Robin Floyd for allowing me to build upon his work and Dr. Marian Walhout, at the University of Massachusetts, for providing the Caenorhabditis elegans complimentary DNA library. A large part of this project would not have been possible without the people at the genomics facility in the Department of Integrative Biology, I commend their professionalism and punctuality in delivering results. Completing this work would have been all the more difficult were it not for the support and friendship provided by my peers Shannon Eagle, Tyler Elliott, Nick Jeffery, Joao Lima, Sabina Stanescu, Fatima Mitterboeck and Paola Pierossi. And finally, I would like to thank my parents and siblings Sara Omar and Ali Omar for their continued support through good times and bad, and letting me use their laptops when mine broke down.
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Impact des changements climatiques et de la variabilité génétique sur le développement et la virulence du nématode à kyste du soya (Heterodera glycines)Gendron St-Marseille, Anne-Frédérique 05 1900 (has links)
Les invasions biologiques dans les agroécosystèmes engendrent de lourdes pertes économiques. Parmi les nombreuses espèces en cause, on retrouve les nématodes phytoparasites, vers microscopiques s’attaquant principalement aux racines. Présent dans tous les principaux pays producteurs de soya, le nématode à kyste du soya (NKS), Heterodera glycines, serait à lui seul responsable annuellement de plusieurs milliards de dollars de pertes. La rotation avec des cultivars résistants est le moyen le plus efficace de contrôler les populations de NKS, mais la surutilisation des mêmes lignées a conduit à la sélection d’individus virulents et mené à leur inefficacité. À ce jour, les mécanismes ainsi que les gènes de virulence associés au contournement de la résistance continuent de mystifier les scientifiques. Dans cette thèse, les effets des changements climatiques sur la reproduction et l’établissement du NKS ainsi que sur la phénologie de son hôte, le soya, ont été étudiés. Le premier modèle bioclimatique simulant le cycle de vie du NKS et du soya a été développé. Il a démontré que le nématode peut déjà se reproduire dans toutes les régions du Québec et que la hausse attendue des températures dans le futur proche (2041-2070) permettrait au NKS de pratiquement doubler le nombre de générations produites par saison de croissance dans toutes les régions. De plus, la production de soya issu du groupe de maturité I pourrait s’étendre à toutes les régions du Québec d’ici 2070. Une étude sur la distribution de la variabilité génétique entre 64 populations américaines et ontariennes et les gènes associés à diverses composantes bioclimatiques et leur rôle dans l’adaptation a également été réalisée. Celle-ci a révélé que la diversité génétique était très élevée entre les populations et qu’un flux de gène continu aurait facilité l’adaptation du NKS à diverses conditions bioclimatiques et son établissement dans toutes les régions nord-américaines où l’on produit du soya. Finalement, cette thèse présente l’analyse des génotypes du NKS et des gènes différentiellement exprimés sur des plants de soya résistant (Peking et PI88788) et sensible (Essex). En plus d’identifier plusieurs protéines liées à la virulence, cette étude a permis de mettre en évidence une région génomique sous forte pression évolutive. Cet îlot génique contient plusieurs répétitions en tandem qui ont divergé et dont certaines sont maintenant utilisées de façon sélective pour le contournement de différents types de résistance. / Biological invasions in agroecosystems are a major cause of economic losses. Plant parasitic nematodes are among the many species causing significant crop damages. The soybean cyst nematode (SCN) is causing billions of dollars of losses in all areas where soybean is produced. Rotation with resistant cultivars is the most effective mean of controlling SCN populations, but the overuse of the same lines has led to the selection of virulent individuals and the ineffectiveness of resistance. To this day, the virulence genes and mecanisms associated with the circumvention of resistance continue to mystify scientists. In this thesis, I explored the effects of climate change on the reproduction and establishment of SCN as well as on the phenology of its host, soybean. I have demonstrated that the nematode can already reproduce in all regions of Québec and that the expected rise in temperatures in the near future (2041-2070) will allow the development of more generations per growing season in all regions. In addition, I have demonstrated that the area suitable for the production of soybean from maturity group I will expand toward the north by 2070, further facilitating the expansion of SCN. I have also explored the genetic variability among more than 64 SCN populations from North America and analyzed the genes associated with various bioclimatic components and their role in adaptation. These analyses revealed that the genetic diversity was very high among SCN populations. This diversity associated with a continuous gene flow between populations has facilitated the adaptation of SCN to various bioclimatic conditions and its establishment in all US and Canadian soybean producing regions. Finaly, this thesis presents an analysis of the SCN genotypes and the differentially expressed genes associated with virulence in two resistant soybean lines (Peking and PI88788) and susceptible Essex. This work has identified several proteins associated with virulence and allowed the discovery of a genomic region under strong evolutionary pressure. This island contains several genes in tandem duplications that have diverged and are now used selectively for overcoming different sources of resistance.
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MICROFLUIDIC DEVICES FOR NEMATODE-BASED BEHAVIOURAL ASSAYS USING ELECTROTAXISRezai, Pouya 04 1900 (has links)
<p>Small nematode model organisms such as <em>Caenorhabditis elegans</em> are widely used in the fields of neurobiology, toxicology, drug discovery, etc. They are advantageous due to their fully characterized genomic and cellular system. Traditional screening methods involve the exposure of animals to chemicals/drugs inside multiwell-plates while its effects on growth, movement and other cellular/sub-cellular processes are monitored by visual inspection. Yet, these methods are time-consuming, low-throughput, expensive, tedious, difficult to control, hard to modulate instantaneously, prone to subjectivity and not suitable for movement-based behavioural assays. Hence, a method to induce and to quantify movement on-demand in a rapid, sensitive, precise and reversible manner would greatly facilitate biological studies. In this thesis, microfluidic engineering approaches have been utilized in nematode-based assays due to their potential to obtain high precision measurements in a low-cost, rapid and automated manner. Movement response of worms to a diverse range of electric signals has been quantitatively characterized. DC and pulse-DC electric fields have been shown to stimulate worms’ swimming towards the negative electrode inside a microchannel (electrotaxis). AC electric fields were used to inhibit movement on-demand. Animals’ movement has been characterized in terms of speed and range of motion, body-bend frequency and turning time. Electrotaxis was shown to be mediated by neuronal activities and correlations between animal’s behaviour and neuronal signalling has also been demonstrated. Using this basic understanding, multiple microfluidic components such as position sensors and electric immobilizers have been developed. Electrotaxis has then been applied as a technique to sort worms in accordance to their size/age and phenotype as well as to perform drug screening at a single-animal level. Integration of the techniques and components developed during this research is expected to have a significant impact on the development of an integrated microfluidic platform for high throughput automated behavioural screening of nematodes with applications in drug discovery, toxicology, neurobiology and genetics.</p> / Doctor of Philosophy (PhD)
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Early events leading to the host protective Th2 immune response to an intestinal nematode parasite /Pesce, John Thomas. January 2005 (has links) (PDF)
Thesis (Ph. D.)--Uniformed Services University of the Health Sciences, 2005. / Typescript (photocopy).
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La fumigation biologique comme alternative au bromure de méthyle pour le contrôle du nématode Méloïdogyne incognita dans la production de concombre dans les serres / The use of biofumigation crops as an alternative to Methyl Bromide for the management of the root-knot nematode in greenhouse cucumber productionHaroutunian, Garabed 25 March 2013 (has links)
Les nématodes à galles demeurent l'un des problèmes les plus graves des agriculteurs de serres du Liban et du Moyen-Orient. Dans le passé, la fumigation du sol au bromure de méthyle a été considérée comme la meilleure mesure de contrôle contre ces nématodes. Toutefois, à la lumière de l'élimination globale du bromure de méthyle, l'accès aux alternatives efficaces et durables est devenu une nécessité essentielle.L'objectif de cette étude est d'évaluer l'efficacité des deux engrais verts, le radis huileux (Raphanus sativus oleifera) et à la roquette (Eruca vesicaria sativa) appliquées avec ou sans bâche en plastique, séparément et en combinaison avec Oxamyl, dans la gestion des nématodes à galles en cultures de concombres de serre. En outre, cette étude vise à évaluer la faisabilité financière de la technique de biofumigation avec les deux cultures utilisées et de la rentabilité finale de ces engrais verts en termes de taux coût-profit par rapport au bromure de méthyle.A cette fin, trois expériences sur le terrain ont été menées dans des serres commerciales, situées sur la zone côtière du Liban.Dans les deux expériences A et B, des résultats cohérents ont été enregistrés en termes de production de rendements significativement plus élevés et de la réduction des populations de nématodes avec les engrais verts utilisés avec ou sans bâche en plastique, par rapport au témoin non traité.Quant aux résultats obtenus par les engrais verts par rapport au bromure de méthyle, dans l'expérience A, le rendement produit par le bromure de méthyle était significativement plus élevé que celui du radis huileux avec bâche en plastique. Cependant, la différence n'était pas significative entre la réduction de la population de nématodes résultant du bromure de méthyle et celle du radis huileux avec bâche en plastique. Les différences du rendement ainsi que la réduction des nématodes étaient significatives entre le bromure de méthyle et le radis huileux sans bâche en plastique.Dans l'expérience B, aucune différence significative n'a été observée dans le rendement ni la réduction de la population de nématodes entre aucun des deux engrais verts utilisés avec bâche en plastique et le bromure de méthyle. Ces différences étaient significativement en faveur du bromure de méthyle uniquement lorsque le radis huileux a été utilisé sans bâche en plastique.Dans l'expérience C, où Vydate (Oxamyl) a été appliqué à la dose de 1 litre par 1,000 m2 à tous les traitements, il n'y avait pas de différence significative dans le rendement ni la réduction de la population de nématodes entre chacun des deux engrais verts utilisés avec ou sans bâche en plastique et le bromure de méthyle.L'analyse coût-profit menée sur tous les traitements appliqués dans les 3 expériences a montré que dans tous les cas, tous les traitements appliqués, qu'ils soient chimiques, non-chimique (avec ou sans bâche en plastique) ou en association ont produit des bénéfices nets supérieurs au bromure de méthyle, même lorsque le rendement produit par le bromure de méthyle était significativement plus élevée.L'utilisation du plastique pour couvrir les radis huileux a généralement produit de meilleurs résultats en termes de production de rendements plus élevés, une meilleure réduction des populations de nématodes à galles dans le sol, ainsi conduisant à des augmentations raisonnables des profits nets.A la base de ces résultats et à la lumière de l'élimination globale du bromure de méthyle, on peut conclure que l'utilisation du radis huileux et la roquette comme engrais verts avec bâche en plastique peut être considéré comme un outil alternatif pour la gestion des nématodes à galles dans la production de concombres de serre dans les conditions libanaises. / Root-knot nematodes remain one of the most serious problems faced by greenhouse farmers of Lebanon and the Middle East region. In the past, soil fumigation with methyl bromide has been considered as the best control measure against root-knot nematodes. However, in the light of the global phase out of methyl bromide, finding efficient and viable alternatives is an essential necessity.The objective of this study is to evaluate the efficacy of the two biofumigation crops Oil Radish (Raphanus sativus oleifera) and Arugula (Eruca vesicaria sativa) applied with and without plastic tarp, separately and in combination with Oxamyl in the management of the root-knot nematodes in greenhouse cucumber crops. Additionally, this study aimed at assessing the financial feasibility of the biofumigation technique with the two cops used and the final profitability of these green manure crops in terms of cost to benefit ratio as compared to methyl bromide.For this purpose, three field experiments were carried out in commercial greenhouses situated on the coastal zone of Lebanon.In both experiments A & B consistent results were recorded in terms of production of significantly higher yields and reduction of nematode population with the biofumigation crops used whether with or without plastic cover, as compared to untreated fallow.As to the results achieved by the biofumigation crops with respect to methyl bromide, in experiment A yield produced by methyl bromide was significantly higher than oil radish with plastic cover. However, no significant difference was found between reduction of nematode population resulting from methyl bromide and oil radish with plastic cover. Difference was significant between methyl bromide and oil radish without plastic cover in both yield and reduction of nematodes.In experiment B no significant difference was observed in neither yield nor reduction of nematode population between any of the two biofumigation crops used with plastic cover and methyl bromide. These differences were significantly in favor of methyl bromide only when oil radish was used without plastic cover.In experiment C where Vydate (Oxamyl) was incorporated at the rate of 1 liter per 1,000 m2 to all treatments, there was no significant difference in neither yield nor reduction of nematode population between any of the two biofumigation crops used with or without plastic cover.Cost-benefit analysis made on all treatments applied in the 3 experiments showed that in all cases, all treatments applied, whether chemical, non-chemical (with or without plastic cover) or in combination have produced higher net profits than methyl bromide, even when yield produced by methyl bromide was significantly higher.Use of plastic for covering oil radish has generally produced better results in terms of production of higher yields, better reduction of soil populations of root-knot nematodes and leading to reasonable increases of net profits.Based on these findings and in the light of global phase out of methyl bromide, it can be concluded that the use of oil radish and arugula as biofumigation crops with plastic cover can be considered as an alternative management tool for the root-knot nematode in greenhouse cucumber production under Lebanese conditions.
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Thousand Cankers Disease of Eastern Black Walnut: Ecological Interactions in the Holobiont of a Bark Beetle-Fungal DiseaseGeoffrey M Williams (11186766) 27 July 2021 (has links)
<p>Eastern black walnut (<i>Juglans
nigra</i> L.) ranks among the most highly valued timber species in the central
hardwood forest and across the world. This valuable tree fills a critical role
in native ecosystems as a mast bearing pioneer on mesic sites. Along with other
<i>Juglans</i> spp. (Juglandaceae), <i>J. nigra</i> is threatened by thousand
cankers disease (TCD), an insect-vectored disease first described in 2009. TCD
is caused by the bark beetle <i>Pityophthorus
juglandis</i> Blackman (Corthylini) and the phytopathogenic fungus <i>Geosmithia morbida</i> Kol. Free. Ut. &
Tiss. (Bionectriaceae). Together, the <i>P.
juglandis</i>-<i>G. morbida</i> complex has
expanded from its historical range in southwest North America throughout the
western United States (U.S.) and Europe. This range expansion has led to
widespread mortality among naïve hosts <i>J.
nigra</i> and <i>J. regia</i> planted
outside their native distributions.</p>
<p> The severity
of TCD was previously observed to be highest in urban and plantation
environments and outside of the host native range. Therefore, the objective of
this work was to provide information on biotic and abiotic environmental
factors that influence the severity and impact of TCD across the native and
non-native range of <i>J. nigra</i> and
across different climatic and management regimes. This knowledge would enable a
better assessment of the risk posed by TCD and a basis for developing
management activities that impart resilience to natural systems. Through a
series of greenhouse-, laboratory- and field-based experiments, environmental
factors that affect the pathogenicity and/or survival of <i>G. morbida</i> in <i>J. nigra</i>
were identified, with a focus on the microbiome, climate, and opportunistic
pathogens. A number of potentially important interactions among host, vector,
pathogen and the rest of the holobiont of TCD were characterized. The <i>holobiont</i> is defined as the whole
multitrophic community of organisms—including <i>J. nigra</i>, microinvertebrates, fungi and bacteria—that interact with
one another and with the host.</p>
<p>Our findings indicate that
interactions among host, vector, pathogen, secondary pathogens, novel microbial
communities, and novel abiotic environments modulate the severity of TCD in
native, non-native, and managed and unmanaged contexts. Prevailing climatic
conditions favor reproduction and spread of <i>G.
morbida</i> in the western United States due to the effect of wood moisture
content on fungal competition. The microbiome of soils, roots, and stems of
trees and seedlings grown outside the host native range harbor distinct,
lower-diversity communities of bacteria and fungi compared to the native range,
including different communities of beneficial or pathogenic functional groups
of fungi. The pathogen <i>G. morbida</i> was
also associated with a distinct community of microbes in stems compared to <i>G. morbida</i>-negative trees. The soil
microbiome from intensively-managed plantations facilitated positive feedback
between <i>G. morbida</i> and a
disease-promomting endophytic <i>Fusarium
solani</i> species complex sp. in roots of <i>J.
nigra</i> seedlings. Finally, the nematode species <i>Bursaphelenchus juglandis</i> associated with <i>P. juglandis</i> synergizes with <i>G.
morbida</i> to cause foliar symptoms in seedlings in a shadehouse; conversely,
experiments and observations indicated that the nematode species <i>Panagrolaimus</i> sp. and cf. <i>Ektaphelenchus</i> sp. could suppress WTB
populations and/or TCD outbreaks.</p>
<p>In conclusion, the composition,
function, and interactions within the <i>P.
juglandis</i> and <i>J. nigra</i> holobiont play
important roles in the TCD pathosystem. Managers and conservationists should be
aware that novel associations outside the host native range, or in monocultures,
intensive nursery production, and urban and low-humidity environments may favor
progression of the disease through the effects of associated phytobiomes,
nematodes, and climatic conditions on disease etiology. Trees in higher
diversity, less intensively managed growing environments within their native
range may be more resilient to disease. Moreover, expatriated, susceptible host
species (<i>i.e.</i>, <i>J. nigra</i>) growing in environments that are favorable to novel pests
or pest complexes (<i>i.e.</i>, the western
U.S.) may provide connectivity between emergent forest health threats (<i>i.e.</i>, TCD) and native host populations (<i>i.e.</i>, <i>J. nigra</i> in its native range).</p>
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