La gale bactérienne des Solanées à graines est une maladie répandue dans la plupart des aires de production de tomate et des Capsicum spp. (piment, poivron) du monde. Elle est très sévère dans les régions tropicales et subtropicales et sa présence est récurrente dans la région Sud-Ouest de l'océan Indien. Cette maladie est complexe car cinq taxons sont actuellement reconnus comme agents causaux, X. vesicatoria , X. perforans , X. gardneri , X. euvesicatoria et X. campestris pv. raphani . Néanmoins certaines études récentes suggèrent des synonymies de certaines de ces espèces entre elles et également avec d'autres Xanthomonas. Les objectifs principaux de la thèse étaient (1) l'analyse de la diversité sur une collection mondiale à l'aide des deux techniques moléculaires à haut débit, AFLP et MLSA, avec un accent particulier sur la diversité génétique et pathologique régionale (2) la description des relations phylogénétiques entre ces taxons et les autres Xanthomonas (3) la mise au point d'un outil d'identification rapide qui tienne compte de la diversité de l'agent pathogène et basé sur des marqueurs SCAR identifiés par AFLP. Une absence de congruence entre les topologies d'arbres dérivées des séquences de 4 gènes de ménage étudiés a été mise en évidence, de même que plusieurs évènements de recombinaison sur trois d'entre eux. Un inventaire des espèces trouvées dans les îles SWIO a pu être dressé, mettant à jour une grande diversité dans cette région. Nos données ont confirmé de fortes similarités génétiques entre X. alfalfae , X. euvesicatoria et X. perforans d'une part et de X. cynarae et X. gardneri d'autre part, qui ont probablement le statut d'espèces-synonyme.

Hypertrophic scarring is a common occurrence for severe burn victims leading to major functional, physiological, and aesthetic effects to the patients. Limiting the hypertrophic scarring of the patients alleviates the functional, physiological, and aesthetic effects. Silicone gels, over the past decade, have been widely used to remediate and limit hypertrophic scarring but the mechanism of action is yet to be determined. One explanation has been that hydration of the outermost area of the burn is induced by the silicone gel . However, non-silicone polymers which increase hydration could not mimic the effect. An alternative interpretation is that there may be silicone species that migrate from the silicone gel into the viable tissue to mediate reactions in the extra-cellular matrix that result in a decreased deposition of excessive amounts of collagen - a central feature of the hypertrophic scar. A novel and informative technique to study these species is MALDI-TOF/MS (Matrix Assisted Laser Desorption Ionisation-Time of Flight Mass Spectrometry) in conjunction with gel permeation chromatography. MALDI-TOF/MS, which has allowed the detection of intact molecular species that were not possible with more established mass spectrometric techniques. The mobile species that may migrate from polydimethylsiloxane medical gel sheeting into skin have been identified by MALDI-MS. The bulk gel contains predominantly cyclic oligomers with a mass distribution peaking at n = 19 (number of repeating siloxane units), but in an aqueous environment the species at the surface of the silicone medical gel are predominantly methyl/methylol-terminated linear siloxanes. By using a gelatine matrix as a model substrate, the distribution of silicon after application of the silicone gel for 16 weeks was determined by Energy-dispersive X-Ray mapping of the sectioned gelatine. The association of the linear and cyclic oligomers with proteins relevant in hypertrophic scarring are considered. The mobility of silicone species across stratum corneum was confirmed by Attenuated Total Reflectance Fourier Transform Infrared spectroscopy (ATR-FT/IR). This method confirms our hypothesis that not only are the low molecular weight silicone species mobile, but also that they do traverse the natural barrier, the stratum corneum, to levels that are detectable by ATR after a continuous application over approximately 11 days. Invitro studies of the effects of LMWS on primary line fibroblast cells indicate a response that down regulates the proliferation of fibroblast cells and protein production. Preliminary results indicate that a family of pendant functional LMWS are effective in down regulating hypertrophic-derived fibroblast primary cells. Studies on hypertrophic scar tissue treated with silicone medical gel indicate that LMWS permeate across the stratum corneum into viable scar tissue. In some areas, the LMWS tend to pool as detected by SEM/EDX elemental silicon analysis. These areas of LMWS pooling tend to be composed of highly disorganised collagen nodules.

Doctor of Philosophy (PhD) / BACKGROUND: The accumulation of abnormal extracellular deposits beneath the retinal pigment epithelium characterises the pathology of early age-related macular degeneration. However, the histopathological threshold at which age-related changes become early AMD is not defined, and the effect of each of the deposits (basal laminar deposit and membranous debris) on disease progression is poorly understood. Evidence suggests that macrophages play a key role in the development of AMD lesions, but the influence of basal laminar deposit (BLamD) and membranous debris on the recruitment and programming of local macrophages has not been explored. Although evidence also suggests that inflammation and innate immunity are involved in AMD, the significance of anti-retinal autoantibodies to disesase pathogenesis is not known. AIMS: (i) To determine the histopathological threshold that distinguishes normal ageing from early AMD; (ii) to determine the influence of BLamD and membranous debris on disease progression; (iii) to examine whether distinct early AMD phenotypes exist based on clinicopathological evidence; (iv) to determine the histopathological context in which Bruch’s membrane macrophages first found; (v) to examine the relationship between Bruch’s membrane macrophages and subclinical neovascularisation; (vi) to determine if the progressive accumulation of BLamD and membranous debris alters the immunophenotype of Bruch’s membrane macrophages and/or resident choroidal macrophages; (vii) to determine if the anti-retinal autoantibody profile differs significantly between normal individuals and those with early AMD, neovascular AMD or geographic atrophy; (viii) to examine whether baseline anti-retinal autoantibodies can predict progression to advanced AMD in individuals with early AMD; and (ix) to examine whether baseline anti-retinal autoantibodies can predict vision loss in individuals with neovascular AMD. METHODS:Clinicopathological studies were performed to correlate progressive accumulation of BLamD and membranous debris to fundus characteristics and visual acuity, as well as to sub-macular Bruch’s membrane macrophage count. Immunohistochemical studies were perfomed to determine whether the presence of BLamD and membranous debris altered the programming of Bruch’s membrane or resident choroidal macrophages. The presence of serum anti-retinal autoantibodies was determined by western blotting, and the association with disease progression examined in early and neovascular AMD. RESULTS: The presence of both basal linear deposit (BLinD) and a continuous layer of BLamD represents threshold early AMD histopathologically, which was seen clinically as a normal fundus in the majority of cases. Membranous debris accumulation appeared to influence the pathway of progression from early AMD to advanced AMD. Bruch’s membrane macrophages were first noted when a continuous layer of BLamD and clinical evidence of early AMD were present, and increased with the amount of membranous debris in eyes with thin BLamD. Eyes with subclinical CNV had high macrophage counts and there was some evidence of altered resident choroidal macrophage programming in the presence of BLamD and membranous debris. Serum anti-retinal autoantibodies were found in a higher proportion of early AMD participants compared with both controls and participants with neovascular AMD, and in a higher proportion of individuals with atrophic AMD compared to those with neovascular AMD. The presence of baseline anti-retinal autoantibodies in participants with early AMD was not associated with progression to advanced AMD. Participants with neovascular AMD lost more vision over 24 months if they had IgG autoantibodies at baseline compared to autoantibody negative participants. CONCLUSIONS: The finding that eyes with threshold early AMD appear clinically normal underscores the need to utilise more sophisticated tests to enable earlier disease detection. Clinicopathological evidence suggests two distinct early AMD phenotypes, which follow two pathways of AMD progression. Macrophage recruitment and programming may be altered by the presence of BLamD and membranous debris, highlighting the need to further characterise the biology of human resident choroidal macropahges. Anti-retinal autoantibodies can be found in both control and AMD sera, and future approaches that allow the examination of subtle changes in complex repertoires will determine whether they are involved in AMD disease pathogenesis.

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No. of bitstreams: 1 danielgustavomesquitadasilva.pdf: 3042917 bytes, checksum: 06395c899324e2d8dfd65fdbf105d471 (MD5) Previous issue date: 2018-06-19 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Valores precisos de Secção de Choque Total (SCT) para o espalhamento de elétrons por álcoois primários, como metanol, etanol, 1-propanol e 1- butanol, são muito importantes em muitas áreas aplicadas, uma vez que refletem a reatividade do alvo molecular no processo de colisão, como função da energia dos elétrons. Esses valores são muito úteis, por exemplo, quando se quer modelar a combustão do álcool no processo de ignição por centelha dentro de um motor de combustão interna. Através dessa modelagem, podemos melhorar o desempenho de veículos motorizados e de todas as tecnologias que utilizam atualmente combustíveis fósseis. Medidas de SCT absoluta para espalhamento de elétrons por moléculas do 1-propanol foram realizadas neste trabalho, para energias de impacto de 40 a 500 eV. Esses dados foram obtidos utilizando um novo aparelho desenvolvido neste trabalho, baseado na atenuação de um feixe de elétrons colimado através de uma célula gasosa que contém as moléculas a serem estudadas, a uma pressão e temperatura conhecidas. Este aparelho é constituído de um canhão de elétrons, uma célula gasosa, um analisador de energia de elétrons composto de um sistema de lentes eletrostáticas desaceleradoras seguido por um analisador cilíndrico dispersivo 127° (ACD 127°) e um coletor de Faraday. O aparelho está instalado dentro de uma câmara de vácuo coberta por 5 camadas de mu-metal, para blindagem de campos magnéticos espúrios, sendo diferencialmente bombeada através de duas bombas turbomoleculares; uma com velocidade de bombeamento de 80 l/s, para bombear a câmara do canhão de elétrons, a fim de evitar mudanças nas características de emissão do filamento quando o gás é introduzido na câmara; e a outra, com uma velocidade de bombeamento de 600 l/s, para bombear a célula de espalhamento e a região do analisador. O aparelho desenvolvido mostrou excelente desempenho, quando os dados de SCT por ele produzidos foram comparados com dados da literatura para os gases Ar, He, N2. Nossos dados experimentais de SCT para o 1-propanol, pelo melhor de nosso conhecimento, são os primeiros da literatura. Eles foram comparados com os resultados teóricos produzidos pelo Modelo do Átomo Independente Regra da Aditividade Revisada mais contribuições de interferências (MAIRAR+I), sendo verificada uma boa concordância. / Precise values of the Total Cross Section (TCS) for electron scattering by primary alcohols such as methanol, ethanol, 1-propanol and 1-butanol, are very important in many applied areas, given that the TCS reflects the reactivity of a molecular target in the collision processes as a function of the electron energy. These values are very useful, for instance, when modeling alcohol combustion through a spark ignition process within an internal combustion engines. Through this modeling we can improve the performance of motor vehicles, and all technologies currently utilizing fossil fuels. Absolute Total Cross Section (ATCS) measurements for electron scattering from 1-propanol molecules were obtained in this work, for impact energies from 40 to 500 eV. These data were obtained using a new apparatus developed in this work, which is based on the measurement of the attenuation of a collimated electron beam through a gas cell containing the molecules to be studied at a given pressure and temperature. This new apparatus consists of an electron gun, a gas cell, an electron energy analyzer composed of an array of decelerating electrostatic lenses, a cylindrical dispersive 127° analyzer (CDA 127°), and a Faraday cup. The apparatus is housed inside a vacuum chamber covered by 5 layers of mu-metal, for shielding against spurious magnetic fields, and differentially pumped through two turbomolecular pumps; one with a pumping speed of 80 l/s, for pumping the electron gun chamber in order to avoid changes in the electron emitting filament characteristics when gas is introduced into the chamber; and the other, with 600 l/s pumping speed, for pumping the scattering cell and analyzer region. The developed apparatus showed excellent performance when comparing our TCS data produced with it, with data from literature for the gases Ar, He, N2. Our TCS measurements for 1-propanol, to the best of our knowledge, are the first in the literature. These experimental measurements were compared with calculated TCS using the Independent-Atom Model with Screening Corrected Additivity Rule and Interference (IAM-SCAR+I) approach with the level of agreement between them being typically found to be very good.

La transparence et les propriétés optiques du greffon cornéen sont des qualités essentielles pour le résultat post opératoire après la kératoplastie perforante et la kératoplastie lamellaire antérieure qui sont les 2 greffes les plus utilisées au monde. Pourtant, la transparence est difficile à mesurer avec précision avec les techniques d’eye banking actuelles et les propriétés optiques ne le sont pas du tout car lors de la conservation cornéenne à 4°C et plus encore en organoculture, la cornée séparée du globe est moins transparente que sur le sujet vivant et comporte des plis. Nous avons développé un outil de conservation, un bioréacteur, permettant de simuler les conditions physiologiques de la cornée pendant la conservation, permettant ainsi la caractérisation optique du greffon. L’objectif de cette thèse a été la conception et la réalisation des instruments de caractérisation des propriétés optiques et tissulaires des greffons conservés en BR. Ces propriétés sont la densité cellulaire endothéliale, la transparence, la puissance, l’épaisseur et la détection d’interfaces cicatricielles / The optical properties of a corneal graft, namely its transparency, are pivotal to the post-operative result of penetrating keratoplasty and deep anterior lamellar keratoplasty, which are today the world’s two most performed grafts. However, transparency is difficult to accurately measure with modern eye banking techniques, and other optical properties are not measurable at all, as with both hypothermic storage and organ culture the enucleated cornea is less transparent than in a living eye, and presents endothelial folds. We developed a corneal storage device, a bioreactor, to simulate the eye’s physiological conditions during storage, thus allowing the measurement of the graft’s optical properties. The goal of this thesis was to create a set of instruments to be used in eye banking for the optical characterization of corneal grafts. The parameters to be measured are endothelial cell density, transparency, dioptric power, thickness and the presence of scar tissue

MSc (Botany) / Department of Botany / See the attached abstract below

Using flake dimensions and attributes commonly agreed are associated with site use, occupation age, and occupation duration, it was argued that relative estimations of site function and occupation age could be determined using debitage. This is particularly beneficial for assemblages that have little to no diagnostics that could provide a general cultural period for one or more occupations at a site. The results of this study suggest that, although certain attributes are generally associated with lithic production stage, relative age, and duration indicators, they were not all applicable within this study. The methods employed were relatively successful; however, reducing the number of classes, removing of a dimension, and more sites that meet the definition of lithic scatter is needed. Furthermore, testing occupation duration using the number of breaks on a flake is not possible unless it is proven a single occupation site.

No description available.

No description available.

La fusariose vasculaire du cyclamen est une maladie causée par le champignon tellurique Fusarium oxysporum f. sp. cyclaminis. Elle est considérée comme l’une des maladies les plus graves du cyclamen et se traduit par des pertes atteignant jusqu’à 50 % de la production. Actuellement, les moyens de lutte ne permettent pas de contrôler la maladie. Dans ce contexte, une collaboration s’est engagée entre l’institut technique de l’horticulture, Astredhor, représentant les producteurs, l’INRA de Dijon pour son expertise sur F. oxysporum et la société Agrene pour son expertise en lutte biologique. Les objectifs de cette collaboration étaient doubles : i) identifier un marqueur spécifique de la forme spéciale cyclaminis et développer un outil de détection de l’agent pathogène permettant de mettre en place des méthodes de lutte appropriées ; ii) identifier un agent de lutte biologique efficace contre le pathogène. Le travail s’est donc structuré autour de ces deux objectifs.Une collection de souches représentatives de la diversité des populations de F. oxysporum f. sp. cyclaminis a été constituée. Elle regroupe des souches provenant de collections internationales et des isolats obtenus de cyclamens symptomatiques ou non. L’analyse moléculaire de cette collection a permis de caractériser son importante diversité génétique et a mis en exergue la difficulté d’identifier un marqueur moléculaire spécifique. Néanmoins, un fragment d’ADN spécifique de l’agent pathogène a pu être mis en évidence par amplification aléatoire d’ADN polymorphe. A partir de ce fragment, un couple d’amorces spécifiques a été dessiné et un outil moléculaire a été développé. Ce dernier permet une détection du champignon in planta en PCR conventionnelle et en PCR en temps réel.Parallèlement, une étude bibliographique approfondie relative aux méthodes de lutte biologique contre les fusarioses induites par F. oxysporum sur les plantes ornementales a été effectuée. Cette revue a souligné la possibilité d’utiliser des ressources d’origine microbienne et d’origine végétale pour contrôler F. oxysporum, mais cette stratégie impliquant une étape de sélection nous est apparue lourde et laborieuse. Nous avons opté pour une autre démarche visant à identifier, parmi des produits déjà sur le marché, ceux susceptibles de réduire significativement la gravité de la maladie. Des bioessais ont été conduits en serre, dans des conditions proches de celles de la production pour tester sept produits reposant sur la formulation de bactéries, de champignons ou de combinaisons de ces microorganismes. Les produits les moins performants ont été éliminés à l’issue d’un premier essai. Des bioessais ont été conduits à nouveau avec trois produits. Un seul de ces produits donne satisfaction mais son efficacité devra être validée en conditions de production réelles.En conclusion, l’outil de détection spécifique permettra aux producteurs de s’assurer de la qualité sanitaire de la culture et des supports de culture. L’agent de lutte biologique retenu à l’issue de nos essais permettra dans un premier temps aux producteurs de prévenir le risque d’activité infectieuse de F. oxysporum f. sp. cyclaminis. Cependant, un travail de recherche d’un agent de lutte plus performant s’avère nécessaire. Des pistes sont proposées. / Fusarium wilt of cyclamen is one of the most damaging diseases of cyclamen. The causal agent, Fusarium oxysporum f. sp. cyclaminis, is a soil-borne fungus. Losses can reach more than 50 % of the production. Several methods of control are available, but none of them offer an efficient and environmentally friendly solution. In this context, a project was developed in collaboration with the French institute of horticulture, Astredhor, which represents the producers, the INRA of Dijon, for its expertise on F. oxysporum and the company Agrene for its expertise in biological control. The project has two goals: i) design a molecular marker specific of Fusarium oxysporum f. sp. cyclaminis allowing a better management of the disease, ii) identify one or several efficient biological control agents.A collection of strains representative of the diversity of F. oxysporum f. sp. cyclaminis populations was made up with strains from international collections and isolates collected from symptomatic and asymptomatic cyclamens. A molecular study of the collection demonstrated the high genetic diversity of the forma specialis, which makes the identification of a specific molecular marker more complicated. However, a specific DNA fragment was identified by random amplified polymorphic DNA. A primer pairs was designed and a specific tool of detection was developed. Thanks to this tool, it is now possible to detect the fungus in planta by conventional and real-time PCR.Simultaneously, a broad literature analysis on the biocontrol of ornamental plant diseases caused by F. oxysporum was performed. The review emphasized that biocontrol of F. oxysporum encompassed both microbial biocontrol agents and botanicals. To avoid the laborious and time-consuming screening step, we decided to assess the antagonistic activity of seven commercial products containing bacteria, fungi or a combination of both microorganisms. Greenhouse trials were performed under conditions similar to those of the production. First trial led to the exclusion of the less efficient products. Other trials were conducted with the three remaining products. Disease reduction was obtained with one of these products although it must be validated in production.Finally, the molecular tool of detection will allow producers to insure the health status of the culture. In addition, the efficient biocontrol agent identified will prevent the disease progress for a while but more investigations are needed to obtain reliable, efficient and sustainable biocontrol agents. Proposals to improve Fusarium wilt control are discussed.