Le virus de la fièvre catarrhale ovine (Bluetongue virus, BTV) est l’agent étiologique de la maladie du même nom, une arbovirose non contagieuse transmise aux ruminants domestiques et sauvages par l’intermédiaire de morsures de moucherons hématophages du genre Culicoides. Il existe actuellement 27 sérotypes décrits de BTV à travers le monde qui se distinguent par les pathologies qu’ils induisent et leur capacité à infecter et se propager chez leur(s) hôte(s) mammifère(s). Le premier objectif de mon projet de thèse visait à identifier les interactions cellulaires spécifiques des sérotypes 8 et 27 pour identifier des facteurs de pathogénicité/virulence et/ou de franchissement de barrière d’espèces. Pour atteindre cet objectif, l’ensemble des protéines virales du BTV a été criblé par la méthode du double-hybride en levure contre deux banques d’ADN complémentaires, l’une d’origine bovine et l’autre d’origine culicoïde. A l’issue de 70 cribles, une centaine de nouvelles interactions virus-hôtes a été mise en évidence et révèle un enrichissement pour quatre processus cellulaires : l’épissage des ARNm, les ribosomes, la SUMOylation et l’apoptose. Cette étude nous a ainsi permis de réaliser le premier interactome pour le BTV qui se poursuit au travers de multiples validations biochimiques et fonctionnelles des interactions identifiées. En parallèle de ce travail de protéomique, le second objectif de mon projet de thèse a été de déterminer l’impact du BTV sur la voie MAPK/ERK, une voie cellulaire essentielle à la prolifération et différenciation cellulaire et classiquement modulée lors d’infections virales. En plus de son rôle antagoniste sur la voie des interférons de type I, nous avons démontré la capacité de la protéine NS3 de BTV à activer la voie MAPK/ERK. En effet, nous avons démontré que NS3 a la capacité d’augmenter le niveau de phosphorylation des protéines kinases ERK1/2 mais également du facteur de traduction eIF4E. Cette fonction, qui semble être spécifique au BTV par rapport aux autres orbivirus, implique l’interaction de NS3 avec la protéine cellulaire BRAF, une protéine MAP3 kinase jouant un rôle majeur dans l’activation de la voie MAPK/ERK. L’activation cette voie par NS3 pourrait être un mécanisme de détournement de la traduction cellulaire au profit de celle du virus mais aussi constituer un élément de réponse pour expliquer l’hyper-inflammation observée dans le cas d’une infection par ce virus / Bluetongue virus (BTV) is the etiological agent of the bluetongue (BT) disease, a non-contagious arbovirus that affects a wide range of wild and domestic ruminants. It is transmitted by blood-feeding midges of the genus Culicoides. There are currently 27 serotypes described of BTV in the world that are distinguished by their differences in term of pathology/virulence and their capacity to infect and disseminate in their mammalian host(s). The first objective of my thesis project was to identify specific cellular interactions of serotype 8 and 27 to reveal new factors of pathogenicity/virulence and/or cross species barrier. To reach this goal, all the proteins encoded by BTV were used as baits to screen, by a high-throughput yeast two-hybrid (Y2H) approach, two complementary DNA libraries originating from hosts naturally infected by BTV : Culicoides and cattle. Therefore, 70 screens were performed to identify a hundred of new virus-host interactions and reveal an enrichment for four cellular processes : mRNA splicing, ribosomes, SUMOylation and apoptosis. This study allowed us to build the first interactome of BTV which continues through multiple biochemical and functional validations of the identified interactions. In parallel to this proteomics work, my second objective was to determine the impact of BTV on the MAPK/ERK pathway, a cellular pathway essential for cell proliferation and differentiation usually modulated during viral infections. In addition to its antagonist role on the type I interferon pathway, we have demonstrated the ability of BTV-NS3 to activate the MAPK/ERK pathway. Indeed, we have demonstrated that NS3 has the ability to increase the level of phosphorylation of ERK1/2 protein and the eIF4E translation factor. This function, which seems to be specific to BTV compared to other orbiviruses, involves the interaction of NS3 with BRAF cellular protein, a MAP3 kinase protein that plays a major role in the regulation of the MAPK/ERK pathway. These results could provide a better understanding of the molecular basis underlying the hijacking of the translation machinery to support virus replication but also constitute a hypothesis to explain the hyperinflammation observed in the BTV infection context

Orientador: Paula Rahal / Banca: Hamilton Cabral / Banca: Nelson José Freitas da Silveira / Banca: Maria Tercília Vilela de Azeredo Oliveira / Banca: José Osmar Gaspar / Resumo: A proteína NS3 apresenta dois domínios e é bifuncional. Apresenta três funções enzimáticas que são; 1) atividade de protease; 2) NTPase e 3) helicase. A função protease relaciona-se a tradução da proteína precursora e as funções NTPase e helicase tem grande participação na replicação do material genético viral. Trata-se de uma molécula essencial para o processamento da poliproteína precursora e também para a replicação viral e portanto, um dos principais alvos para o desenvolvimento de drogas antivirais. No domínio Protease foram evidenciadas substituições na tríade catalítica e na região de ligação ao íon zinco nos pacientes avaliados. Estas substituições, quando somadas podem explicar a resposta ao tratamento. Também foram visualizadas alterações na porção Helicase da NS3. As substituições ocorreram nos sítios de ligação ao ATP e ao RNA. Outros resíduos da Helicase relevantes para o desenvolvimento de inibidores, como R2133 e F258 e F264 não apresentaram substituições, evidenciando tratarem-se de aminoácidos conservados nessa região. Os resultados obtidos nesse trabalho fornecem informações sobre o perfil genético do vírus HCV do genótipo 3 especificamente da região codificadora da proteína NS3, permitindo o conhecimento do genoma viral e a identificação de regiões para ligação de possíveis inibidores. Este projeto certifica que a modelagem é uma ferramenta útil para a biologia estrutural e funcional, e que os modelos obtidos aqui contribuem para o desenho de novas drogas anti-virais específicas para o genótipo 3 do vírus HCV / Abstract: The NS3 protein has two domains and is bifuntional. It presents three functions: 1) protease activity, 2) NTPase and 3) helicase. The protease function is related to the translation of the poliprotein precursor and functions NTPase and helicase has great participation in the replication of the viral genetic material. So. The NS3 is considered the major target for the development of antiviral drugs. In the Protease portion substitutions were evidenced in catalytic triad and the zinc ion binding sites, in the patients evaluated. These substitutions, when added up can explain the response to treatment. Also were observed changes in Helicase portion of NS3. The substitutions took place on ATP and RNA binding sites. Other residues of Helicase relevant to the development of inhibitors, as R2133 and F258 and F264, showed no substitutions, highlighting the great conservation of amino acids in this region. The results obtained in this work provide information on the genetic profile of the HCV virus genotype 3, specifically the region of NS3 protein, allowing the knowledge of the viral genome and the identification of regions for possible connection of inhibitors. This project certifies that the modeling is a useful tool for structural biology and functional, and that the models obtained here contribute to the design of new anti-viral drugs specific to the genotype 3 of HCV virus / Doutor

La nanocommunication est un nouveau paradigme qui permet de communiquer à l'échelle nanométrique, via des mécanismes moléculaires, électromagnétiques, acoustiques, ou nano-mécaniques. Le cadre général de cette thèse concerne les réseaux de nanocapteurs sans fil et les nanoréseaux sur puce. Plus précisément, il s'agit des architectures d'interconnexion et des protocoles de communication dans la bande de fréquence des Térahertz. En effet, les architectures réseaux et les protocoles de communication existants doivent être repensés en tenant compte des mécanismes de communication à l'échelle nanométrique.En premier lieu, nous nous sommes focalisés sur la nécessité de développer des approches de diffusion efficaces dans le contexte des réseaux de nanocapteurs sans fil. Une approche de diffusion efficace, issue d'une adaptation d'un protocole de la famille des protocoles d'inondation probabilistes, est présenté et son efficacité et validée par simulations à l'aide de Nano-Sim et NS3.En second lieu, une étude approfondie de l'impact des portées de transmission sur les performances du mécanisme de diffusion basé sur les ondes électromagnétiques à l'échelle nanométrique a été effectuée. Les résultats des simulations montrent que l'adaptation des portées des nano-noeuds permet de contrôler le mécanisme d'inondation et de réduire les redondances des paquets tout en augmentant les débits. Une approche adaptative de sélection de portées de transmission contrôlée au niveau des nano-noeuds est proposée. En dernier lieu, nous nous sommes attaqués à un troisième défi en examinant ce nouveau paradigme de nanocommunication dans le contexte de la conception des nanoréseaux sur puce (Network on Chip, NoC). / Nanocommunication is a new paradigm that enables connectivity at the nanoscale through molecular, electromagnetic, acoustic, or nanomechanical mechanisms. The general context of this thesis concerns wireless nanosensor networks and nanonetworks on chips. More precisely, the thesis deals with interconnection architectures and communication protocols in the terahertz band. The existing network architectures and communication protocols should be revisited taking into account the communication mechanisms at the nanoscale.First, dissemination approaches in the context of wireless nanosensor networks are addressed. An efficient broadcasting approach is presented and the simulation performance results with Nano-Sim and NS3 show that the proposed scheme is superior to flooding, especially in the cases of excessive broadcasts.Second, we investigated the impact of transmission ranges on the performance of broadcast mechanisms based on electromagnetic waves at the nanoscale. Adaptive transmission range of electromagnetic-based communication approaches are proposed. Simulations are conducted with fixed and adaptive transmission ranges to show the efficiency of the proposed approaches in terms of throughput and latency according to the network density.The third part addresses the hypothesis of using EM-based nanonetwok as an on-chip interconnect for SoCs.

No description available.

L'infection chronique par le virus de l'hépatite C (VHC) peut s'associer chez les patients à des manifestations extrahépatiques auto-immunes. La question se pose de l'origine de cette auto-réactivité et de ses cibles. Le stress induit par l'infection chronique par le VHC induit la surexpression d'HSP70 dans les tissus hépatiques et dans le sang, phénomène s'accompagnant de l'apparition d'anticorps anti-HSP uniquement chez les patients ayant une dysimmunité associée au VHC. Grâce à un modèle cellulaire exprimant de façon stable une partie de la polyprotéine virale, nous montrons qu'à l'échelon cellulaire, ce stress viral se traduit non seulement par une augmentation du taux d'HSP, mais aussi par la présence de complexes HSP-peptides inhabituels, doués d'antigénicité. Ce stress cellulaire semble être en partie lié à l'activité protéolytique de la protéase NS3. C'est la première fois qu'est mis en évidence le rôle direct d'une protéase virale dans le développement du stress cellulaire secondaire à une infection virale. NS3 semble exercer une activité protéolytique vis-à-vis de plusieurs protéines cellulaires substrats dont le cytochrome P450 2D6, dont des épitopes sont impliqués dans l'hépatite auto-immune associée au VHC. NS3 est donc susceptible de favoriser, par son activité protéase, l'émergence d'épitopes nouveaux. L'interaction de NS3 avec C1Inh suggère un possible contrôle cellulaire de la protéase, qui serait favorisé par l'IFN, cytokine connue pour augmenter la synthèse de C1Inh.

<p>This thesis describes the design, synthesis and structure-activity relationships analysis of potential inhibitors targeting the hepatitis C virus (HCV) NS3 protease. Also discussed is the disease caused by HCV infection and the class of enzymes known as proteases. Furthermore are explained why such enzymes can be considered to be suitable targets for developing drugs to combat diseases in general and in particular HCV, focusing on the NS3 protease. Moreover, some strategies used to design protease inhibitors and the desired properties of potential drug candidates are briefly examined. Synthesis of linear and macrocyclic NS3 protease inhibitors comprising a designed trisubstituted cyclopentane moiety as an <em>N</em>-acyl-(4<em>R</em>)-hydroxyproline bioisostere is also addressed, and several very potent and promising compounds are evaluated.</p> / Report code: LIU-TEK-LIC-2006:46.

Hepatitis C is a blood-borne disease affecting 130-170 million people worldwide. The causative agent, hepatitis C virus (HCV), infects the liver and is the major reason for chronic liver disease worldwide. The HCV NS3 protease, a key enzyme in the virus replication cycle, has been confirmed to be an important target for drug development. With the recent release of two HCV NS3 protease inhibitors onto the market and an arsenal of inhibitors in clinical trials, there are now hopes of finally combating the disease. However, the success of treatment relies heavily on the ability to overcome the emergence of drug-resistant forms of the protease. The main focus of this thesis was on designing and synthesizing novel inhibitors of the NS3 protease with a unique resistance profile. Efforts were also made to decrease the peptide character of the compounds, with the long-term goal of making them into more drug-like compounds. Special attention was devoted to developing inhibitors based on a phenylglycine in the P2 position, instead of the highly optimized and commonly used P2 proline. Around ninety acyclic and macrocyclic inhibitors have been synthesized and biochemically evaluated. P2 pyrimidinyloxy phenylglycine was successfully combined with an aromatic P1 moiety and alkenylic P1´ elongations, yielding a distinct class of HCV NS3 protease inhibitors. Macrocyclization was performed in several directions of the inhibitors via ring-closing metathesis. Only the macrocyclization between the P3-P1´ residues was successful in terms of inhibitory potency, which suggests that the elongated P1-P1´ residue is oriented towards the P3 side chain. The metathesis reaction was found to be significantly more dependent on the substrate than on the reaction conditions. It was also found that the P3 truncated inhibitors were able to retain good inhibitory potency, which initiated the synthesis and evaluation of a series of P2-P1´ inhibitors. The potential of the P3-P1´cyclized inhibitor and the smaller, acyclic P2-P1´ as new potential drug leads remains to be determined through pharmacokinetic profiling. Gratifyingly, all the inhibitors evaluated on A156T and D168V substituted enzyme variants were able to retain inhibitory potency towards these as compared to wild-type inhibition.

This thesis describes the design, synthesis and structure-activity relationships analysis of potential inhibitors targeting the hepatitis C virus (HCV) NS3 protease. Also discussed is the disease caused by HCV infection and the class of enzymes known as proteases. Furthermore are explained why such enzymes can be considered to be suitable targets for developing drugs to combat diseases in general and in particular HCV, focusing on the NS3 protease. Moreover, some strategies used to design protease inhibitors and the desired properties of potential drug candidates are briefly examined. Synthesis of linear and macrocyclic NS3 protease inhibitors comprising a designed trisubstituted cyclopentane moiety as an N-acyl-(4R)-hydroxyproline bioisostere is also addressed, and several very potent and promising compounds are evaluated. / Report code: LIU-TEK-LIC-2006:46.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2007. / Härtill 4 uppsatser.

This thesis focuses on the description of nanocommunication networks, models for wireless communication networks and the description of motion in nanocommunication networks. The practical part describes the settings of the simulation scenarios for the definition of Brownian motion. Description is made for the simulation software NS-3 and N3Sim. In this thesis, the measured results of the simulations are summarized in tables and graphs. From the measured results the regression analysis is prepared. General summary of the results is provided at the end of thise thesis.