Au cours du cycle réplicatif des rétrovirus, l'ADN viral rétro-transcrit est intégré dans l'ADN de la cellule hôte par l'intégrase virale (IN). L'IN possède un rôle clé dans le cycle rétroviral et représente une cible thérapeutique majeure pour le traitement des infections par le virus de l'immunodéficience humaine (VIH). L'IN est constituée de trois domaines (N-terminal, central et C-terminal) connectés par des boucles flexibles, qui la rendent difficilement cristallisable. Le Dr. C. Ronfort (Equipe Rétrovirus et Intégration Rétrovirale) et le Pr. P. Gouet (Laboratoire de BioCristallographie) collaborent depuis 2002 sur l'IN du Rous Associated Virus type 1 (RAV-1). Mes travaux de thèse s'inscrivent dans le cadre de cette collaboration. Il s'agissait de mener une étude cristallographique et moléculaire du domaine central de l'IN du RAV-1 pour pouvoir, ensuite, modéliser des mutants d'intérêt identifiés par l'équipe du Dr. C. Ronfort. Pour ce faire, le fragment protéique a été surproduit et purifié. Sa structure cristallographique a été résolue à une résolution de 1,8 Å. L'examen de cette structure révèle que le dimère de l'IN du RAV-1 peut s'assembler suivant une nouvelle interface moléculaire stabilisée par trois paires d'hélices α. Cet assemblage se caractérise également par la présence d'un étroit sillon basique à sa surface. Par des expériences in vitro de biochimie et in silico de docking, nous avons montré que ce sillon était susceptible de fixer un brin d'ARN. D'autre part, nos données expérimentales permettent d'expliquer comment les conditions de cristallisation, ainsi que la substitution d'un acide aminé de surface, favorisent la formation soit de ce nouvel arrangement dimérique, soit de l'arrangement dimérique classique. Ainsi, l'ensemble des données obtenues au cours de cette thèse suggère que l'intégrase possède des propriétés structurales modulables, lui permettant d'intervenir dans plusieurs étapes du cycle rétroviral en présence d'ADNdb (intégration) ou d'ARNsb (rétro-transcription et/ou encapsidation du génome ARN viral)

Brown-headed cowbird (Molothrus ater) parasitism on the endangered black-capped vireo (Vireo atricapilla) is a management concern. Management for black-capped vireos in east-central Texas has focused on habitat restoration through vegetation modification. Loss of productivity due to parasitism, however, may limit the potential habitat restoration in restoring black-capped vireo populations. I investigated the relationships between frequency of parasitism on black-capped and white-eyed (V. griseus) vireos and characteristics of the neighboring avian assemblage to identify avian characteristics useful for predicting expected frequency of parasitism. I located and monitored vireo nests in March–July 2006 to determine frequency of cowbird parasitism on the 2 vireo species on 6 study sites on private land in east-central Texas. I conducted 100-m-radius circular-plot point count surveys on study sites from 1 April– 31 June 2006 to identify neighboring avian assemblages. All black-capped vireo nests (n = 20) and 81% of white-eyed vireo nests (n = 27) were parasitized. Species richness, species evenness, cumulative bird abundance, and cowbird host abundance did not differ significantly among study sites. Parasitism frequency was positively correlated with the number of cowbirds detected (r2 = 0.673, P= 0.045). Parasitism frequency was negatively correlated with abundance (r2 = 0.687, P = 0.042) and proportion of (r2 = 0.692, P = 0.040) of black-and-white warblers (Mniotilta varia), known cowbird hosts. I did not find a relationship between parasitism frequency and abundance of other cowbird hosts. The relationship between black-andwhite warbler abundance and parasitism frequency may reflect an interaction between parasitism and the vegetation characteristics associated with black-and-white warblers, suggesting the need for future study of the relationships between parasitism frequency and vegetation characteristics in the study region. The frequency of parasitism I observed suggests that cowbird control may be an important management tool if management objectives in the study region continue to include recovery of black-capped vireo populations. Number of cowbirds may be a reasonable predictor of expected parasitism frequency in an area, which may be useful to land managers in selecting areas for implementation of cowbird control.

Although wild birds are natural hosts of avian influenza viruses (AIVs), these viruses can be highly contagious to poultry and a zoonotic threat to humans. The propensity of AIV for genetic variation through genetic shift and drift allows virus to evade vaccine mediated humoral immunity. An alternative approach to current vaccine development is induction of CD8+ T cells which responds to more conserved epitopes than humoral immunity and targets a broader spectrum of viruses. Since the memory CD8+ T lymphocyte responses in chickens to individual AIV proteins have not been defined, the modulation of responses of the memory CD8+ T lymphocytes to H5N9 AIV hemagglutinin (HA) and nucleocapsid (NP) proteins over a time course were evaluated. CD8+ T lymphocyte responses induced by intramuscular inoculation of chickens with AIV HA and NP expressing cDNA plasmids or a non-replicating human adenovirus vector were identified through ex vivo stimulation with virus infected, major histocompatibility complex (MHC) matched antigen presenting cells (APCs). The IFN? production by activated lymphocytes was evaluated by macrophage production of nitric oxide and ELISA. MHC-I restricted memory T lymphocyte responses were determined at 10 days and 3, 5, 7 and 9 weeks post-inoculation (p.i). The use of non-professional APCs and APC driven proliferation of cells with CD8+ phenotype correlated with the activation of CD8+ T lymphocytes. The responses specific to nucleocapsid protein (NP) were consistently greater than those to the hemagglutinin (HA) at 5 weeks when the CD8+ T cell responses were maximum. By 8 to 9 weeks p.i., responses to either protein were undetectable. The T lymphocytes also responded to stimulation with a heterologous H7N2 AIV infected APCs. Administration of booster dose induced secondary effector cell mediated immune responses which had greater magnitudes than primary effector responses at 10 days p.i. Flow cytometric analysis (FACS) of the T lymphocytes demonstrated that memory CD8+ T lymphocytes of chickens can be distinguished from naive lymphocytes by their higher expression of CD44 and CD45 surface antigens. CD45 expression of memory lymphocytes further increases upon ex vivo stimulation with APCs expressing AIV. This is the first characterization of avian memory responses following both primary and secondary expression of any individual viral protein.

ABSTRACT AVIAN COMMUNITY PATTERNS IN THE LESSER CAUCASUS (NORTHEASTERN TURKEY) ATKIN GEN&Ccedil / OgLU, G&uuml / lden M. Sc., Department of Biological Sciences Supervisor: Assoc. Prof. Dr. C. Can Bilgin December 2007, 78 pages Species composition, diversity and species-habitat relations are widely used to describe communities. This study aimed to document diversity, composition and habitat relations of avian communities of the Turkish Lesser Caucasus by using point counts and multivariate analyses. 2845 individuals of 101 bird species were observed at 215 stations located in the study area. Point counts were revealed to be a useful method for terrestrial birds, especially passerines. Species richness and diversity changed significantly within parts of the study area and one particular sub-region was found to be considerably more diverse than the other three. Division of the Lesser Caucasus region into sub-ecoregions may not be justified using bird assemblages since habitat parameters, especially the presence of woody vegetation, seemed to be a better predictor of species composition than geographical proximity. Documented bird and habitat associations provide valuable information on the factors which affect bird occurrence or abundance. Baseline data provided by this study will help detect and understand changes in bird populations in the future. Keywords: avian community, species composition, species diversity, point count method, bird-habitat relationship

Today, infectious animal diseases and the propagation speeds of these diseaseshave been threatening the human health. Threats from animal disease outbreakssuch as Avian Influenza have increased in both number and complexity. So, it is extremely important to determine the animal diseases at first appearances and totake precautions according to propagation speeds of the diseases. Geographic Information Systems (GIS) have become an important tool inveterinary epidemiology, surveillance and monitoring of animal diseases. Such approaches can be used for public health planning and predicting disease risks. This study aims to build a GIS web-based animal health surveillance system in Turkey in order to monitor and analyse disease outbreaks. Different sources of data / geographical data, animal holding locations, disease outbreak recordings, reporting information and special GIS functions have been incorporated in the application. It enables to determine the first, second and third degree risk zones of a disease, query the animals, holdings and disease events, create thematic maps and show the results of explored landscape features associated with Avian Influenza outbreak of 2006 and present graphically illustrated reports. This study will make the management of the disease outbreak situation easier, enhance the response mechanism of the decision makers, help to make better decisions, control the disease as quickly as possible, protect both the animals and humans against diseases, also provide a tool to evaluate different strategies to prevent the spread of infectious diseases. So, in an infectious disease case, emergency precautions can be taken and control strategies can be planned.

Embryonic epiboly has become an important developmental model for studying the mechanisms underlying collective movements of epithelial cells. In the last couple of decades, most studies of epiboly have utilized Xenopus or zebrafish as genetically tractable model organisms, while the avian epiboly model has received virtually no attention. Here, we re-visit epiboly in quail embryos and characterize several molecular markers of epithelial-to-mesenchymal transition (EMT) in the inner zone of the extraembryonic Area Opaca and at the blastoderm edge. Our results show that the intermediate filament vimentin, a widely-used marker of the mesenchymal phenotype, is strongly expressed in the edge cells compared to the cells in the inner zone, and that epiboly is inhibited when embryos are treated with Withaferin-A, a vimentin-targeting drug. Laminin, an extracellular matrix protein that is a major structural and adhesive component of the epiblast basement membrane, is notably absent from the blastoderm edge, and shows three distinct morphological regions approaching the leading edge. While these expression profiles are consistent with a mesenchymal phenotype, several other epithelial markers, including cytokeratin, β-catenin, and E-cadherin, were present in the blastoderm edge cells. Moreover, the results of a BrDU proliferation assay suggest that expansion of the edge cell population is primarily due to recruitment of cells from the inner zone, and not proliferation. Taken together, our data suggest that the edge cells of the avian blastoderm have characteristics of both epithelial and mesenchymal cells, and could serve as an in-vivo model for cancer and wound healing studies.

The full geographic distribution and habitat use of the Florida Burrowing Owl, a state "Species of Special Concern," is not well-understood, particularly in remote, non-urban areas. This thesis aimed to expand and improve knowledge about non-urban burrowing owls. We first compiled databases of historic sighting observations. Fieldwork verified and updated existing breeding observation point records and also yielded new breeding locations. Using a GIS, we characterized observed land use, landcover, relevant soil attributes, projected future land use and managed area status for selected points. We quantified landcover within biologically-determined buffer distances around burrows from our own field-verified records. Using standard resource selection methods, we compared observed and available proportions, calculated selection indices, and determined selection/avoidance for each landcover class. These empirical results were used in combination with expert opinion and literature review to finalize criteria for and map "suitable" landcover. Suitability of relevant soil attributes were also empirically-determined and used to further reduce the overall "suitable" area. The final suitable habitat maps appear to relate well to the overall distribution of known non-urban burrowing owl records and demonstrate that a great deal of potentially-suitable breeding habitat exists throughout Florida's central interior. Improved pasture, the most prevalent landcover class, also appears to be the most strongly selected in this study and may be of high importance to non-urban, breeding burrowing owls. Our results could be useful to wildlife officials managing this species. Recommendations include improving surveys and conservation efforts in non-urban areas and enhancing cooperation with landowners, particularly ranchers, as success on private lands seems critical to the long-term persistence of this species.

published_or_final_version / Public Administration / Master / Master of Public Administration

From fighting microbial infections to preparing for pandemics, Brett Finlay is discovering how the body's own defenses could boost our chances in the battle against infectious diseases.

Computational evolutionary analyses, particularly phylogenetics and ancestral reconstruction, have been extensively exploited under different algorithms and evolutionary models to better understand genome evolution from both small- and large-scale perspectives in order to assign genotypes based on assortment, resolve species relationships and gene annotation issues, further understand gene gain/loss within individual gene families, measure functional divergence among homologs, and infer ancestral character states. These evolutionary studies provide us with insights into biologically relevant issues including paleoenvironments inferred from resurrected proteins, developmental physiology associated with functional divergence of duplicated genes, viral epidemics and modes of transmission in attempt to better prepare, prevent and control diseases, evolution of lineage-specific pathogenicity, and attempts to create a synthetic ancient organism that would benefit the field of synthetic biology. Our work also provides us with greater insights into the accuracies and limitations of ancestral sequence reconstruction methods. In total, our work highlights the diverse questions that evolutionary studies attempt to address and the different biological levels that can be studied to answer these questions.