Grandes perdas de tecido neural não permitem a reparação por meio de anastomose primária. Nesses casos, a auto-enxertia de nervo é considerado o melhor tratamento. A despeito de um tratamento cirúrgico adequado, déficits funcionais são observados e melhoras quanto à recuperação funcional e diminuição das seqüelas são desejáveis. Várias são as técnicas que almejaram esse propósito. A interposição de condutores tubulares, como ponte entre os cotos proximal e distal do nervo seccionado, apresenta-se como uma técnica alternativa que oferece vantagens teóricas. A veia é um material estudado como possível condutor tubular avaliado experimentalmente e em casos clínicos. Estudos recentes têm dado importância na utilização de transplantes de tecidos armazenados em banco de tecidos. O glicerol é utilizado para preservação de tecidos, tendo sido relatado seu uso em nervos e vasos. Entretanto, não há relatos da utilização de veias preservadas em glicerol como substituto de enxerto de nervo. O objetivo deste trabalho foi comparar, em ratos, o grau de regeneração neural, utilizando análise histológica e análise funcional, obtida com a interposição de enxerto autógeno de nervo, veia autógena, veia autógena preservada em glicerol e veia alógena preservada em glicerol. Com técnica microcirúrgica, foram criados defeitos de 5 mm do nervo fibular de ratos da raça Lewis. Os animais foram divididos em quatro grupos de seis, de acordo com o tratamento empregado para correção do defeito: nos animais do Grupo A (grupo controle), foi realizado o reposicionamento do fragmento de nervo retirado (auto-enxerto); nos animais do Grupo B, foi interposto um segmento de 1 cm de veia jugular externa autógena; nos animais do Grupo C, foi interposto a veia jugular externa autógena preservada em glicerol a 98% a 4ºC por sete dias; no Grupo D os animais doadores foram ratos da raça Sprague-Dawley que tiveram a veia jugular externa preservada em glicerol de forma igual ao Grupo C e utilizadas para reconstrução do defeito neural em ratos da raça Lewis, sendo considerado um enxerto alógeno preservado em glicerol. Os animais foram sacrificados após seis semanas para realização dos estudos histológicos. Para a avaliação da recuperação funcional foram estudados os padrões de deambulação dos ratos (\"walking track analysis\") no pós-operatório imediato, 3 e 6 semanas de pós-operatório. O grupo controle (auto-enxerto) apresentou resultados histológicos semelhantes aos grupos de veias preservadas em glicerol (autógena e alógena), entretanto apresentou uma maior reação tecidual perineural e maior presença de escape axonal se comparada a todos os grupos. A utilização de veia autógena sem preservação demonstrou padrão histológico com maior neoangiogênese e áreas de rarefação axonal com presença de tecido conectivo no estroma neoformado. O padrão histológico foi semelhante nos demais grupos. O grupo que utilizou veia autógena (sem glicerol) apresentou menor recuperação funcional quando comparado com os demais grupos para 3 e 6 semanas. O resultado funcional foi estatisticamente semelhante entre os grupos de veias preservadas (autógena e alógena) e o auto-enxerto. / Great losses of neural tissue cannot be repaired by primary conventional suturing. In such cases, nerve autografting is considered to be the treatment of choice. In spite of adequate surgical treatment, functional deficits occur. Also, improvement in functional recuperation and decrease in sequelae are expected. There are many techniques aiming at this purpose. The interposition of tubular conduits, as a bridge between the ends of a sectioned nerve, among these the vein graft, is an alternative technique which offers theoretical advantages. The vein is a studied material as possible evaluated tubular conductor experimentally and in clinical cases. Recent studies have given importance in the use of tissues transplants stored in banks. Glycerol is used for tissue preservation, having been told to its use in nerves and vessels. However, it does not have studies of the use of glycerol reserved veins in as substitute of nerve graft. The purpose of this study was to compare, in rats, the neural regeneration degree, using histological analysis and functional analysis, obtained after interposition of a nerve graft, autogenous vein, autogenous vein preserved in glycerol and allograft vein preserved in glycerol. A 5 mm neural gap in the fibular nerve of rats (Lewis breed) has been created under microsurgical techinique. Four groups of six animals each have been divided according to the treatment employed: Group A - control group: replacement of the fibular nerve itself (autograft); Group B - a 1omm segment of external jugular vein was interposed; Group C - a preserved external jugular vein in glycerol 98% per 7 days was interposed in the fibular nerve gap; Group D - external jugular vein preserved in glycerol of Sprague-Dawley rats had been used equal form to group C in Lewis rats. The animals had been sacrificed after 6 weeks for accomplishment of the histological studies. The functional walking track analysis was performed after in the pre-op, and in the pos-op (immediately, 3 and 6 weeks). The control group (autograft) presented similar histological results to the groups of glycerol preserved veins (autogenous vein and allograft vein), however it presented a bigger perineural tecidual reaction and bigger presence of escape axonal if compared with all the groups. The use of autogenous vein without preservation demonstrated histological results with greater neoangiogenesis and presence of connective tissue inside the neo-formed stroma. Histological pattern was similar to other studied groups. The group that used autogenous vein (without glycerol) presented little functional recovery for 3 and 6 weeks. No statistical difference was seen between groups A (autograft) and groups C and C(preserved veins) in the degree of functional recovery.

A auto-enxertia de nervo é considerado o melhor tratamento para a restauração de grandes perdas de nervo periférico. Mesmo com o tratamento cirúrgico adequado, déficits funcionais são observados e melhoras quanto à recuperação funcional e diminuição das seqüelas são desejáveis. Várias são as técnicas que almejaram esse propósito. A interposição de condutores tubulares, como ponte entre os cotos proximal e distal do nervo seccionado, apresenta-se como uma técnica alternativa que oferece vantagens teóricas. A veia é um material estudado como possível condutor tubular avaliado experimentalmente e em casos clínicos. Estudos recentes têm dado importância na utilização de transplantes de tecidos armazenados em banco de tecidos. O glicerol é utilizado para preservação de tecidos, tendo sido relatado seu uso em nervos e vasos. Entretanto, não há relatos da utilização de veias preservadas em glicerol como substituto de enxerto de nervo. O objetivo deste trabalho foi comparar, em ratos, o grau de regeneração neural, utilizando análise histológica qualitativa e quantitativa e a recuperação funcional, obtida com a interposição de enxerto autógeno de nervo, veia autógena, veia autógena preservada em glicerol e veia alógena preservada em glicerol. Com técnica microcirúrgica, foram criados defeitos de 5 mm do nervo fibular de ratos da raça Lewis. Os animais foram divididos em quatro grupos de seis, de acordo com o tratamento empregado para correção do defeito: nos animais do Grupo A (grupo controle), foi realizado o reposicionamento do fragmento de nervo retirado (auto- enxerto); nos animais do Grupo B, foi interposto um segmento de 1 cm de veia jugular externa autógena; nos animais do Grupo C, foi interposto a veia jugular externa autógena preservada em glicerol a 98% a 4ºC por sete dias; no Grupo D os animais doadores foram ratos da raça Sprague-Dawley que tiveram a veia jugular externa preservada em glicerol de forma igual ao Grupo C e utilizadas para reconstrução do defeito neural em ratos da raça Lewis, sendo considerado um enxerto alógeno preservado em glicerol. Os animais foram sacrificados após seis semanas para realização dos estudos histológicos. Para a avaliação da recuperação funcional foram estudados os padrões de deambulação dos ratos (walking track analysis)no pós-operatório imediato, 3 e 6 semanas de pós-operatório. O grupo controle (auto-enxerto) apresentou resultados histológicos semelhantes aos grupos de veias preservadas em glicerol (autógena e alógena), entretanto apresentou uma maior reação tecidual perineural e maior presença de escape axonal se comparada a todos os grupos. A utilização de veia autógena sem preservação demonstrou padrão histológico com maior neoangiogênese e áreas de rarefação axonal com presença de tecido conectivo no estroma neoformado. O padrão histológico foi semelhante nos demais grupos. A análise histológica quantitativa demonstrou estatisticamente menor concentração de axônios regenerados no grupo B (veia autógena) do que a dos demais grupos. O grupo que utilizou veia autógena (sem glicerol) apresentou menor recuperação funcional quando comparado com os demais grupos para 3 e 6 semanas. O resultado funcional foi estatisticamente semelhante entre os grupos de veias preservadas (autógena e alógena) e o auto-enxerto / Nerve autografting is considered the best treatment for the restoration of great losses of peripheral nerve. In spite of adequate surgical treatment, functional deficits occur. Also, improvement in functional recuperation and decrease in sequelae are expected. There are many techniques aiming at this purpose. The interposition of tubular conduits, as a bridge between the ends of a sectioned nerve, among these the vein graft, is an alternative technique which offers theoretical advantages. The vein is a studied material as possible evaluated tubular conductor experimentally and in clinical cases. Recent studies have given importance in the use of tissues transplants stored in banks. Glycerol is used for tissue preservation, having been told to its use in nerves and vessels. However, it does not have studies of the use of glycerol reserved veins in as substitute of nerve graft. The purpose of this study was to compare, in rats, the neural regeneration degree, using qualitative and quantitative histological analysis and functional recovery, obtained after interposition of a nerve graft, autogenous vein, autogenous vein preserved in glycerol and allograft vein preserved in glycerol. A 5 mm neural gap in the fibular nerve of rats (Lewis breed) has been created under microsurgical techinique. Four groups of six animals each have been divided according to the treatment employed: Group A Î control group: replacement of the fibular nerve itself (autograft); Group B Î a 1omm segment of external jugular vein was interposed; Group C Î a preserved external jugular vein in glycerol 98% per 7 days was interposed in the fibular nerve gap; Group D - external jugular vein preserved in glycerol of Sprague-Dawley rats had been used equal form to group C in Lewis rats. The animals had been sacrificed after 6 weeks for accomplishment of the histological studies. The functional walking track analysis was performed after in the pre-op, and in the pos-op (immediately, 3 and 6 weeks). The control group (autograft) presented similar histological results to the groups of glycerol preserved veins (autogenous vein and allograft vein), however it presented a bigger perineural tecidual reaction and bigger presence of escape axonal if compared with all the groups. The use of autogenous vein without preservation demonstrated histological results with greater neoangiogenesis and presence of connective tissue inside the neo- formed stroma. Histological pattern was similar to other studied groups. Quantitative histological analysis showed statistically lower concentration of regenerated axons in group B (autogenous vein) than the other groups.The group that used autogenous vein (without glycerol) presented little functional recovery for 3 and 6 weeks. No statistical difference was seen between groups A (autograft) and groups C and C (preserved veins) in the degree of functional recovery

Dans les génomes bactériens, les fréquents transferts horizontaux de gènes (HGT) introduisent des innovations génomiques qui peuvent entraîner la diversification des populations bactériennes. À l'inverse, la recombinaison homologue (RH) au sein des populations homogénéise leurs génotypes, et ainsi renforce leur cohésion. Ces processus d'échange génétique, et la fréquence à laquelle ils interviennent au sein et entre les populations, doivent avoir un grand impact sur la cladogénèse bactérienne. Au-delà de la configuration des échanges qui se sont réellement produits entre les bactéries, les traces de RH et de HGT que nous observons dans leurs génomes reflètent les événements qui ont été fixés tout au long de leur histoire. Ce processus de fixation peut être biaisé en ce qui concerne la nature des gènes ou allèles qui ont été introduits. La sélection naturelle peut notamment conduire à la fixation des gènes transférés qui apportent de nouvelles adaptations écologiques. En outre, des biais mécaniques dans le processus de recombinaison lui-même peuvent conduire à la fixation d'allèles non-adaptatifs. Nous avons cherché à caractériser certains de ces processus adaptatifs et non-adaptatifs qui façonnent les génomes bactériens. À cette fin, plusieurs aspects de l'évolution des génomes, comme les variations de leurs répertoires de gènes, de leur architecture et de leur composition en nucléotides ont été examinés à la lumière de leur histoire de transfert et de recombinaison / In bacterial genomes, the frequent horizontal gene transfers (HGT) introduce genomic novelties that can promote the diversification of bacterial populations. In opposition, homologous recombination (HR) within populations homogenizes their genotypes, enforcing their cohesion. These processes of genetic exchange, and their patterns of occurrence among and within lineages, must have a great impact on bacterial cladogenesis. Beyond the pattern of exchanges actually occurring between bacteria, the traces of HR and HGT we observe in their genomes reflect what events were fixed throughout their history. This fixation process can be biased regarding the nature of genes or alleles that were introduced. Notably, natural selection can drive the fixation of transferred genes that bring new ecological adaptations. In addition, some mechanical biases in the recombination process itself may lead to the fixation of non-adaptive alleles. We aimed to characterize such adaptive and non-adaptive processes that are shaping bacterial genomes. To this end, several aspects of genome evolution, such as variations of their gene repertoires, of their architecture and of their nucleotide composition were examined in the light of their history of transfer and recombination

Les défauts dans la réparation des cassures double-brin de l'ADN (DSBs) peuvent avoir d'importantes conséquences pouvant entrainer une instabilité génomique et conduire à la mort cellulaire ou au développement de cancers. Dans la plupart des cellules mammifères, le mécanisme de Jonction des Extrémités Non Homologues (NHEJ) est le principal mécanisme de réparation des DSBs. L'ADN Ligase IV (LigIV) est une protéine unique dans sa capacité à promouvoir la NHEJ classique. Elle s'associe avec deux autres protéines structuralement similaires, XRCC4 et XLF (ou Cernunnos). LigIV interagit directement avec XRCC4 pour former un complexe stable, tandis que l'interaction entre XLF et ce complexe est médiée par XRCC4. XLF stimule fortement l'activité de ligation du complexe LigIV/XRCC4 par un mécanisme encore indéterminé. Récemment, un rôle structurel non catalytique a été attribué à LigIV (Cottarel et al., 2013). Dans le travail de thèse présenté ici, nous avons reconstitué l'étape de ligation de la NHEJ en utilisant des protéines recombinantes produites dans des bactéries afin d’une part, d'explorer les bases moléculaires du rôle structural de LigIV, d’autre part de comprendre le mécanisme par lequel XLF stimule le complexe de ligation, et enfin de mieux comprendre comment ces trois protéines coopèrent au cours de la NHEJ. Nos analyses biochimiques suggèrent que XLF via son interaction avec XRCC4 lié à LigIV, pourrait induire un changement conformationnel dans la LigIV. Ce réarrangement de la ligase exposerait son interface de liaison à l'ADN ce qui lui permettrait alors de ponter deux molécules indépendantes d'ADN, une capacité indépendante de l'activité catalytique de LigIV. / Failure to repair DNA double-strand breaks (DSBs) may have deleterious consequences inducing genomic instability and even cell death. In most mammalian cells, Non-Homologous End Joining (NHEJ) is a prominent DSB repair pathway. DNA ligase IV (LigIV) is unique in its ability to promote classical NHEJ. It associates with two structurally related proteins called XRCC4 and XLF (aka Cernunnos). LigIV directly interacts with XRCC4 forming a stable complex while the XLF interaction with this complex is mediated by XRCC4. XLF strongly stimulates the ligation activity of the LigIV/XRCC4 complex by an unknown mechanism. Recently, a structural noncatalytic role of LigIV has been uncovered (Cottarel et al., 2013). Here, we have reconstituted the end joining ligation step using recombinant proteins produced in bacteria to explore not only the molecular basis for the structural role of LigIV, but also to understand the mechanism by which XLF stimulates the ligation complex, and how these three proteins work together during NHEJ. Our biochemical analysis suggests that XLF, through interactions with LigIV/XRCC4 complex, could induce a conformational change in LigIV. Rearrangement of the LigIV would expose its DNA binding interface that is able to bridge two independent DNA molecules. This bridging ability is fully independent of LigIV’s catalytic activity. We have mutated this interface in order to attempt to disrupt the newly identified DNA bridging ability. In vitro analysis of this LigIV mutant will be presented as well as a preliminary in vivo analysis.

Grâce au développement des technologies de métagénomique au cours des dix dernières années, il a été constaté que les micro-organismes représentent la plus grande ressource de diversité métabolique et génétique sur Terre. En effet, un gramme de sol contient 109 cellules bactériennes et 103-104 différentes espèces bactériennes. Certaines sont en mesure de réaliser des réactions enzymatiques conduisant à la dégradation complète de certains polluants toxiques pour l’environnement comme les composés organiques tels que la quinoléine. Cependant, l'immense réservoir de molécules et enzymes microbiennes n'a pas encore été exploité, car plus de 99% d'entre elles ne sont, pour l’instant, pas cultivables in vitro. Mon travail s’inscrit dans le cadre d’une collaboration entre l’Université SJTU (Shanghai Jiao Tong Université en Chine) et le groupe de G. M.E (Génomique Microbienne Environmentale) du laboratoire Ampère à l’Ecole Centrale de Lyon. Nos partenaires à l’Université SJTU ont construit un réacteur de dénitrification à l'échelle du laboratoire capable de dégrader la quinoléine en retirant la demande chimique en oxygène. Un nouvel outil appelé "Genefish" a été developpé dans notre laboratoire comme une méthode alternative de la métagénomique pour aider à la découverte de nouveaux gènes d’intérêt industriel ou environnemental. A la suite des premiers travaux réalisés dans notre laboratoire, ma thèse présentée ici comporte deux parties.Dans la première partie de ce travail, nous avons étudié le potentiel de dégradation de la quinoléine présente dans les bactéries d’un sol de référence largement étudié au laboratoire. Pour cela nous avons mis en place des expériences de microcosme qui visent à révéler la diversité potentielle des bactéries responsables de la dégradation de la quinoléine. Des analyses comparatives des profils RISA (Ribosomal Intergenic Spacer analysis) nous ont permis de mettre en évidence des changements dans la structure de la communauté des bactéries du sol incubé en conditions aérobie et anaérobie en présence de quinoléine. La dégradation de la quinoléine a été confirmée par technique de GC/MS (Gas Chromatography-Mass Spectrometry). Les travaux futurs seront de vérifier la communauté de bactéries responsables de la dégradation de quinoléine en utilisant la technique de NGS (Next Generation Sequencing).Le deuxième objectif de ma thèse a été d'utiliser Genefish dont la finalité est de capturer des gènes ciblés (le gène bcr qui serait responsable de la degradation de quinoléine dans le réacteur de nos partenaires) dans l'ADN métagénomique extrait du sol. Genefish consiste à élaborer une souche d’E.coli incluant un plasmide de capture permettant de pêcher les gènes recherchés dans un échantillon d’ADN metagénomique par recombinaison homologue. Le plasmide de capture comprend une cassette de deux gènes toxiques pour la souche qui activés par induction chimique vont permettre la sélection positive directe des clones recombinants, et deux sites multiples de clonage dans lesquels sont insérées les zones de recombinaison qui vont jouer le rôle d’hameçons. Nous avons testé la capacité de Genefish à capturer des produits PCR du gène bcr, l'efficacité de recombinaison reste faible à cause de la persistance de plusieurs copies du plasmide suicide dans la cellule après l’ évenement de recombinaison. Par conséquent, trois stratégies ont été essayées pour améliorer l’efficacité: la co-électroporation, la ségrégation de plasmide et la construction de plasmide suicide en mono-copie. Finalement, la stratégie de la ségrégation plasmidique fonctionne mais l'efficacité de recombinaison est encore trop faible peut-être due à l’incertitude des modèles de recombinaison homologue. Les travaux futurs se concentreront sur l'amélioration des fréquences de recombinaison par transfert de fragments du plasmide de capture dans le chromosome de la souche Genefish. / As the development of metagenomic technologies in the past ten years, it is unquestionned that microorganisms encompass the largest resource of metabolic and genetic diversity in the world. Actually, one gramme of soil contains more than 109 bacteria and 103-104 species. Some of their members are able to carry out enzymatic reactions leading to the complete degradation of pollutants (such as quinoline). So, the biodegradation of some highly toxic or organic compounds by microorganisms will be a general trend for pollutant treatment. However, the huge reservoir of molecules and enzymes from microorganisms still need to be explored because more than 99% of microorganisms cannot be cultivated in vitro.My work was based on collaboration between the University SJTU and Ecole Centrale de Lyon. Our partners at the University SJTU have built a laboratory scale denitrification reactor which was capable of degrading quinoline by removing the chemical oxygen demand. A new tool called "Genefish" has been developed in our laboratory as an alternative method for metagenomics which aims to discover novel industrial or environmental genes of interest. Following the early work in our laboratory, my thesis is presented here in two parts.In the first part, we set up a quinoline microcosm experiment both under aerobic and anaerobic condition using reference soil extensively studied in the laboratory at Ecole Centrale de LYON. This work aimed to reveal the potential bacterial diversity and even genes responsible for quinoline degradation. We used RISA(Ribosomal intergenic Spacer analysis) to analyze the bacteria community structure changes and GC/MS (Gas Chromatography-Mass Spectrometry) was also used to detect the quinoline degradation and reveal potential quinoline metabolic pathways under aerobic and anaerobic condition. Results showed great bacteria community structure changes and high quinoline degradation activity after the quinoline addition under aerobic condition. The future work is to investigate the bacteria community which may be responsible for quinoline degradation using the technique of NGS (Next Generation Sequencing).The second object of my thesis was to use the Genefish tool to capture targeted genes (the bcr gene responsible for the quinoline degradation in the wastewater treatment bioreactor) from the soil metagenome. The aim was to construct an E.coli strain containing a capture plasmid and Red system for capturing targeted genes from metagenomic DNA by homologous recombination. The capture plasmid includes a toxic cassette consisting of two suicide genes which can be activated by chemical induction, finally support the positive recombinants selection. It also contains two multiply cloning sites in which highly conserved sequences were inserted and works as the bait during recombination. We have tested the capacity of Genefish to capture the PCR products of bcr gene; the efficiency was low because of the persistence of several copies of the capture plasmid into the Genefish strain after recombination events. So, three strategies were tried to improve the recombination efficiency: co-electroporation, plasmid segregation and mono-copy capture plasmid construction. Finally, the strategy of plasmid segregation works but the recombination efficiency was still low maybe caused by the uncertain model of homologous recombination. The further research will focus on the transfer of the toxic cassette and homologous arms into the host strain chromosome, this new strategy will exclude the bad effect of low copy number capture plasmid, uncertain model of λ Red induced homologous recombination and the homologous arms site in the capture plasmid which are the most important factors influencing the homologous recombination efficiency in Genefish.

Macromolecular assemblies such as the ribosome, spliceosome, polymerases are imperative for cellular functions. The current understanding of these important machineries and many other assemblies at the molecular level is poor. The lack of structural data for many macromolecular assemblies further causes a bottleneck in understanding the cellular processes and the various disease manifestations. Hence, it is essential to characterize the structures and molecular architectures of these macromolecular assemblies. Though the number of 3-D structures for individual proteins structures or domains in the Protein Data Bank (PDB) is growing, the number of structures deposited for macromolecular assemblies is relatively poor. Hence, apart from the use of experimental techniques for characterizing macromolecular assembly structures, the use of computational techniques would help in supplementing the growth of macromolecular assembly structures. This thesis deals with the use of integrative approaches where computational methods are combined with experimental data to model and understand the mechanistic features of macromolecular assemblies with a special focus on a sub-complex of the spliceosome machinery. Chapter 1 of this thesis provides an introduction to protein-protein interactions and macromolecular assemblies. Further, the modelling of macromolecular assemblies using integrative methods are discussed, with a subsequent introduction to the spliceosome machinery. In chapter 2, modelling studies were performed on the proteins involved in the general amino acid control mechanism, which is triggered in yeast under amino acid starvation conditions. The proteins involved in the study were Gcn1, a ribosome binding protein and the RWD-domain containing proteins Gcn2, Yih1, Gir2 and Mtc5. From laboratory experiments it is known that in order for Gcn2 activation, an eIF2α kinase, its RWD-domain has to bind to Gcn1 and the residue Arg-2259 is important for this interaction. As the 3-D structure for the Gcn1 region containing Arg-2259 is not currently available, its 3-D structure was inferred using fold recognition and comparative modelling techniques. Further, in order to understand the Gcn2 RWD domain-Gcn1 molecular interaction, a complex structure was inferred by using a restrained protein-protein docking procedure. As the proteins, Yih1 and Gir2 are known to bind to Gcn1 using their RWD-domains, first the structures of the RWD-domain containing proteins including Mtc5 were inferred using a Gcn2 RWD domain NMR structure. Additionally, the Gcn1-Gcn2 complex was used to build a set of complexes to explain the binding of other RWD domain containing proteins Yih1, Gir2 and Mtc5. The important molecular interactions were obtained on analysing the interacting residues in these complexes. Thus, the Gcn1-Gcn2 interaction at the molecular level has been proposed for the first time. Future experiments guided by the protein-protein complex models and the proposed set of mutations should provide an understanding about the critical molecular interactions involved in the general amino acid control mechanism. Chapter 3 describes an integrative approach that was used to decipher a pseudo-atomic model of the closed form of human SF3b complex. SF3b is a multi-protein complex containing seven components – p14, SF3b49, SF3b155, SF3b145, SF3b130, SF3b14b and SF3b10. It recognizes the branch point adenosine in the pre-mRNA as part of U2 snRNP or U11/U12 di-snRNP in the spliceosome. Although, the cryo-EM map for human SF3b complex has been available for more than a decade, the structure and relative spatial arrangement of all components in the complex are not yet known. The integrative modelling approach used here involved utilizing structural data in the form of available X-ray and NMR structures, fold recognition and comparative modelling as well as currently available experimental datasets, along with the available cryo-EM density map to provide a model with high structural coverage. Hence, the molecular architecture of closed form human SF3b complex was derived that can now provide insights into the functioning of SF3b in splicing. This might also help the future high resolution structure determination efforts of the entire human spliceosome machinery In chapter 4, the molecular architecture of the closed form of SF3b complex obtained from the use of integrative modelling approach (Chapter 3) is extensively discussed. The structure-function relationships for some of the SF3b components based on the pseudo-atomic model has also been provided. In addition, the extreme flexibility associated with some of the SF3b components based on dynamics analysis has also been examined. Further, using an existing U11/U12 di-snRNP cryo-EM map and the closed form SF3b complex pseudo-atomic model, an open form of the SF3b complex was modelled and the component structures were fit into it. Hence, it was found that the transition between closed and open forms is primarily caused by a flap containing the HEAT repeat protein, SF3b155. This Protein is also known to harbour cancer causing mutations and has the potential to affect the Closed to open transition as well as SF3b complex structure and stability. Thus, this provides a framework for the future understanding of the closed to open transition in SF3b functioning within the spliceosome. Chapter 5 builds upon the integrative modelling approach (Chapter 3) that proposed the molecular architecture of the closed form of human SF3b complex and an open form of SF3b that was derived due to a flap opening of the closed form and which might help in accommodating RNA and other trans-acting factors within the U11/U12 di-snRNP (Chapter 4). In the current chapter, the SF3b open form and its interaction with the RNA elements is studied. The 5' end of U12 snRNA and its interaction with pre-mRNA in branch point duplex was modelled guided by the open form of SF3b that provided the necessary structural constraints and the RNA model is topologically consistent with the existing biochemical data. Further, utilizing the SF3b opens form-RNA model and the existing experimental knowledge, an extensive discussion has been provided on how the architecture of SF3b acts as a scaffold for U12 snRNA: pre-mRNA branch point duplex formation as well as its potential implications for branch point adenosine recognition fidelity. Moreover, the reasons for SF3b to be defined as a “fuzzy” complex - a complex with highly flexible folded regions along with intrinsically disordered regions is also discussed. Hence, the current work adds to the excellent developments made previously and deepens the understanding of the structure-function relationship of the human SF3b complex in the context of the spliceosome machinery. In chapter 6, a methodology has been proposed for the use of evolutionary conservation of protein-protein interfacial residues in multiple protein cryo-EM density based fitting of the protein components in the low-resolution density maps of multi-protein assemblies. First, the methodology was tested on a dataset of simulated density maps generated at four different resolutions -10, 15, 20 and 25 Å. On utilizing the evolutionary conservation scores obtained from multiple sequence alignments to score the fitted complexes, it was found that there was a decrease in the conservation scores when compared to that of the crystal structures, which were used to generate the simulated density maps. Further, the assessment of the multiple protein density fitting technique to align the actual protein-protein interface residues correctly using a performance metric called F-measure showed there was a decrease in performance as the resolutions became poorer. Hence, based on evolutionary conservations scores as well as F-measure the decrease in conservation scores or performance was found to be mainly due to the errors associated with the fitting process. Subsequently, a refinement methodology was designed involving the use of conservation scores, which improved the accuracy of the fitted models and the same, was observed in an experimental cryo-EM density test case of RyR1-FKBP12 complex. Hence, the conservation information acts as an effective filter to distinguish the incorrectly fitted structures and improves the accuracy of the fitting of the protein structures in the density maps. Thus, one can incorporate the conserved surface residues information in the current density fitting tools to reduce ambiguity and improve the accuracy of the macromolecular assembly structures determined using cryo-EM. In the concluding chapter 7, the learnings on the structural and mechanistic features of protein assemblies obtained from the use of computational techniques and integration of experimental datasets is discussed. In chapter 2, the modelling of a binary macromolecular complex such as the Gcn1-Gcn2 complex was performed using computational structure prediction strategies to understand the molecular basis of its interaction. Due to the potential inaccuracies which can exist in computational modelling, the chapters 3 to 5 dealt with the use of integrative approaches, primarily guided by the cryo-EM map, in order to decipher the molecular architecture of the human SF3b complex in the closed and open forms as well as its contribution for branch point adenosine recognition. Based on the extensive experience gained in modelling of assemblies using cryo-EM data in the previous chapters, a new method has been proposed on the use of evolutionary conservation information to improve the accuracy of cryo-EM density based fitting. Hence, these studies have provided strategies for modelling macromolecular assemblies as well as a deeper understanding of its mechanistic features.

Maintenance of genomic integrity with high fidelity is of prime importance to any organism. An insult which may result in compromised genome integrity is prevented or its consequences are monitored by advanced cellular networks, collectively called the DNA damage response (DDR). Various DNA repair pathways, which are part of DDR, constantly correct the genome in the event of any undesirable change in the genetic material and prevent the transmission of any impairment to daughter cells. Non homologous DNA end joining (NHEJ) is the predominant DNA repair pathway associated with DDR in higher eukaryotes, correcting double-strand breaks (DSBs). Microhomology mediated end joining (MMEJ), an alternate mechanism to NHEJ also exists in cells, which is associated with erroneous joining of broken DNA, leading to mutagenesis. DDR is of paramount importance in cellular viability and therefore, any defects in DDR or the imbalance of repair pathways contribute to mutations, cellular transformations and various neurodegenerative and congenital abnormalities. Here, we investigate the DDR via NHEJ and MMEJ pathways during embryonic development in mice as well as in presence of an environmental pollutant, Endosulfan, in order to understand how physiological and exogenous factors condition the balance of repair pathways. Among various classes of pesticides known to cause side effects, organochlorine pesticides (OCPs) lead the list, possessing high transport potential, and a variety of toxic and untoward health effects. Endosulfan is a widely used organochlorine pesticide and is speculated to be detrimental to human health. However, very little is known about mechanism of its genotoxicity. Using in vivo and ex vivo model systems, we showed that exposure to Endosulfan induced reactive oxygen species (ROS) in a concentration dependent manner. Using an array of assays and equivalents of sub-lethal concentrations comparable to the detected level of Endosulfan in humans living in active areas of exposure, we demonstrated that ROS production by Endosulfan resulted in DNA double-strand breaks in mice, rats and human cells. In mice, the DNA damage was predominantly detected in type II pneumocytes of lung tissue; spermatogonial mother cells and primary spermatids of testes. Importantly, Endosulfan-induced DNA damage evoked DDR, which further resulted in elevated levels of classical NHEJ. However, sequence analyses of NHEJ junctions revealed that Endosulfan treatment resulted in extensive processing of broken DNA, culminating in increased and long junctional deletions, thereby favouring erroneous repair. We also find that exposure to Endosulfan led to significantly increased levels of MMEJ, which is a LIGASE III dependent, alternative, non classical repair pathway, encompassing long deletions and processing of DNA. Further, we show that the differential expression of proteins following exposure to Endosulfan correlated with activation of alternative DNA repair. At the physiological level, using mouse model system, we showed that exposure to Endosulfan affected physiology and cellular architecture of organs and tissues. Among all organs, damage to testes was extensive and it resulted in death of different testicular cell populations. We also found that the damage in testes resulted in qualitative and quantitative defects during spermatogenesis in a time dependent manner, increasing epididymal ROS levels and affecting sperm chromatin integrity. This further culminated in reduced number of epididymal sperms and actively motile sperms, which finally resulted in reduced fertility in male but not in female mice. Repair of DSBs is important for maintaining genomic integrity during the successful development of a fertilized egg into a whole organism. To date, the mechanism of DSB repair in post implantation embryos has been largely unknown except for the differential requirement of DNA repair genes in the course of development. These studies relied on null mutation analysis of animal phenotypes and therefore a quantitative understanding of repair pathways was absent. In the present study, using a cell free repair system derived from different embryonic stages of mice, we found that canonical NHEJ is predominant at 14.5 day of embryonic development. Interestingly, all types of DSBs tested were repaired by LIGASE IV/XRCC4 and Ku-dependent classical NHEJ. Characterization of end-joined junctions and expression studies further showed evidence for C-NHEJ. Strikingly, we observed non canonical end joining accompanied by DSB resection, dependent on microhomology and LIGASE III in 18.5-day embryos. Further we observed an elevated expression of CtIP, MRE11, and NBS1 at this stage, suggesting that it could act as a switch between classical and microhomology-mediated end joining at later stages of embryonic development. Keeping these observations in mind, we wondered if Endosulfan affected the differential regulation of DDR during development, similar to mice tissues. Upon analysing the effect of endosulfan on NHEJ/MMEJ at above mentioned stages of mouse embryonic development, we found that C-NHEJ efficiency remained low or unaltered while the efficiency of MMEJ was upregulated significantly, perturbing the repair balance during embryo development and hence facilitating mutagenic repair. Thus, our results establish the existence of both classical and non classical NHEJ pathways during the post implantation stages of mammalian embryonic development. Our studies also provide deeper insights into physiological and molecular events leading to male infertility upon Endosulfan exposure and its impact on impairing the differential regulation of DNA repair during embryonic development. Our findings suggest the plasticity of DNA repair pathways in physiological and pathological conditions and provide insights into mechanism of genome instability due to DNA repair imbalance, when exposed to environmental mutagens.

Cette recherche clinique vise à explorer le retentissement de l'hypofertilité masculine et de la fécondation in vitro (FIV) sur le fonctionnement psychique des épouses dans le premier centre de consultation FIV en Egypte (1986), en contexte culturel égyptien. Près de 60% des couples qui consultent au Centre FIV présentent le diagnostic d'infertilité d'origine masculine. Nous nous intéressons à comprendre ce qui constitue la spécificité du fonctionnement psychique de ces femmes dans ce contexte culturel où l'infertilité masculine est une pathologie taboue, suscitant la honte familiale, et où seule la FIV homologue- utilisant les gamètes d'un couple marié- est autorisée par la loi. La première hypothèse renvoie à l'existence d'une souffrance psychique chez l'épouse liée au maintien du secret de l'hypofertilité masculine. La seconde hypothèse suppose que le diagnostic et les traitements médicaux sont accompagnés chez l'épouse d'une idéalisation oedipienne de ses propres parents. Notre échantillon est composé de dix femmes âgées de 20 à 40 ans inscrites dans un protocole FIV. Sur le plan méthodologique, nous nous sommes basés sur des entretiens de recherche semi-directifs et sur l'inventaire abrégé de dépression de Beck BDI-13. L'analyse des résultats met en évidence la présence chez les épouses d'un discours de plainte adressé envers leurs conjoints, en même temps que l'expression d'une idéalisation de leurs propres parents. La présence de symptômes de dépression variables est relevée dans l'échantillon. Enfin, la manière dont les femmes s'approprient subjectivement l'expérience de la FIV est un indicateur pertinent de leur équilibre psychique. Pour conclure, cette étude se veut être une recherche-action visant à mettre en place un dispositif clinique au service des femmes et des couples dans une institution médicale, et qui soit adapté à ce contexte culturel particulier. / This study aims at exploring the impact of male subfertility and In Vitro Fertilization (IVF) on the psychological functioning of a group of female spouses, in the first Egyptian IVF center in Egypt (1986), within the Egyptian cultural context. Approximately 60% of couples consulting at the Egyptian Center for IVF carry the diagnosis of male factor infertility. We are interested in understanding what constitutes the specificity of the psychological functioning of these women within this cultural context, where male infertility is a taboo pathology provoking family shame, and where only homologous IVF -using a married couple's gametes- is allowed by the law. The first hypothesis states that there is a specific female suffering related to the maintenance of the secret of male subfertility. The second hypothesis assumes that for the wife, the diagnosis disclosure and medical treatments are followed by an oedipal idealization of the her parents. Our sample is composed of ten women aged between 20 and 40 years old, and undergoing an IVF protocol. On the methodological aspect, we have used semi-structured interviews and the 13-Item Beck Depression Inventory. Results indicate the existence of a complain discourse among the wives, addressed towards their husbands, and at the same time an idealization of their own parents. Variable depression symptoms have been observed in our sample. Finally, the way women integrate psychologically the IVF experience is a relevant indicator of their psychological balance. As a conclusion, this study aims at being a research-action, which objective is to elaborate a clinical intervention at the service of women and couples, and suitable to this particular cultural context.

Costimulation blockade protocols are promising alternatives to the use of chronic immunosuppression for promoting long-term allograft survival. However, the efficacy of costimulation blockade-based protocols is decreased by environmental insults such as viral infections. For example, lymphocytic choriomeningitis virus (LCMV) infection at the time of costimulation blockade treatment abrogates skin allograft survival in mice. In this dissertation, we test the hypothesis that viruses shorten allograft survival by activating the innate immune system through pattern-recognition receptors (PRRs), such as toll-like receptors (TLRs). To investigate the role of innate immunity in shortening allograft survival, costimulation blockade-treated mice were co-injected with TLR2 (Pam3Cys), TLR3 (polyinosinic:polycytidylic acid, poly(I:C)), TLR4 (lipopolysaccharide, LPS), or TLR9 (CpG DNA) agonists, followed by transplantation with skin allografts 7 days later. Costimulation blockade prolonged skin allograft survival that was shortened in mice coinjected with TLR agonists. To investigate the underlying mechanisms of this observation, we used synchimeric mice, which circulate trace populations of anti-H2b transgenic alloreactive CD8+ T cells. In synchimeric mice treated with costimulation blockade, co-administration of all four TLR agonists prevented deletion of alloreactive CD8+ T cells. These alloreactive CD8+ T cells 1) expressed the proliferation marker Ki-67, 2) upregulated CD44, and 3) failed to undergo apoptosis. We also demonstrate that costimulation blockade-treated CD8α-deficient mice exhibit prolonged allograft survival when co-injected with LPS. These data suggest that TLR agonists shorten allograft survival by impairing the apoptosis of alloreactive CD8+T cells. We further delineate the mechanism by which TLR agonists shorten allograft survival by demonstrating that LPS and poly(I:C) fail to shorten allograft survival in IFNRI- deficient mice. Interestingly, the ability of poly(I:C) to more potently induce IFN-α/β than LPS correlates with its superior abilities to shorten islet allograft survival and induce allo-specific CTL activity as measured by an in vivo cytotoxicity assay. The ability to shorten allograft survival and induce IFN-α/β is a TLR-dependent process for LPS, but is a TLR-independent process for poly(I:C). Strikingly, the injection of IFN-β impairs alloreactive CD8+T cell deletion and shortens allograft survival, similar to LPS and poly(I:C). These data suggest that LPS and poly(I:C) shorten allograft survival by inducing IFN-α/β through two different mechanisms. Finally, we present data showing that viruses (LCMV, Pichinde virus, murine cytomegalovirus and vaccinia virus) impair alloreactive CD8+T cell deletion and shorten allograft survival, in a manner comparable to LPS and poly(I:C). Similar to LPS, LCMV and MCMV exhibit an impaired ability to shorten allograft survival in MyD88-deficient mice. These data suggest that the MyD88 pathway is required for certain viruses and TLR-agonists to shorten allograft survival. In this dissertation, we present data supporting an important role for TLRs and IFN- α/β in shortening allograft induced by costimulation blockade. Our findings suggest that targeting these pathways during the peri-transplant period may enhance the efficacy of costimulation blockade protocols in the clinic.

Cette recherche clinique vise à explorer le retentissement de l'hypofertilité masculine et de la fécondation in vitro (FIV) sur le fonctionnement psychique des épouses dans le premier centre de consultation FIV en Egypte (1986), en contexte culturel égyptien. Près de 60% des couples qui consultent au Centre FIV présentent le diagnostic d'infertilité d'origine masculine. Nous nous intéressons à comprendre ce qui constitue la spécificité du fonctionnement psychique de ces femmes dans ce contexte culturel où l'infertilité masculine est une pathologie taboue, suscitant la honte familiale, et où seule la FIV homologue- utilisant les gamètes d'un couple marié- est autorisée par la loi. La première hypothèse renvoie à l'existence d'une souffrance psychique chez l'épouse liée au maintien du secret de l'hypofertilité masculine. La seconde hypothèse suppose que le diagnostic et les traitements médicaux sont accompagnés chez l'épouse d'une idéalisation oedipienne de ses propres parents. Notre échantillon est composé de dix femmes âgées de 20 à 40 ans inscrites dans un protocole FIV. Sur le plan méthodologique, nous nous sommes basés sur des entretiens de recherche semi-directifs et sur l'inventaire abrégé de dépression de Beck BDI-13. L'analyse des résultats met en évidence la présence chez les épouses d'un discours de plainte adressé envers leurs conjoints, en même temps que l'expression d'une idéalisation de leurs propres parents. La présence de symptômes de dépression variables est relevée dans l'échantillon. Enfin, la manière dont les femmes s'approprient subjectivement l'expérience de la FIV est un indicateur pertinent de leur équilibre psychique. Pour conclure, cette étude se veut être une recherche-action visant à mettre en place un dispositif clinique au service des femmes et des couples dans une institution médicale, et qui soit adapté à ce contexte culturel particulier. / This study aims at exploring the impact of male subfertility and In Vitro Fertilization (IVF) on the psychological functioning of a group of female spouses, in the first Egyptian IVF center in Egypt (1986), within the Egyptian cultural context. Approximately 60% of couples consulting at the Egyptian Center for IVF carry the diagnosis of male factor infertility. We are interested in understanding what constitutes the specificity of the psychological functioning of these women within this cultural context, where male infertility is a taboo pathology provoking family shame, and where only homologous IVF -using a married couple's gametes- is allowed by the law. The first hypothesis states that there is a specific female suffering related to the maintenance of the secret of male subfertility. The second hypothesis assumes that for the wife, the diagnosis disclosure and medical treatments are followed by an oedipal idealization of the her parents. Our sample is composed of ten women aged between 20 and 40 years old, and undergoing an IVF protocol. On the methodological aspect, we have used semi-structured interviews and the 13-Item Beck Depression Inventory. Results indicate the existence of a complain discourse among the wives, addressed towards their husbands, and at the same time an idealization of their own parents. Variable depression symptoms have been observed in our sample. Finally, the way women integrate psychologically the IVF experience is a relevant indicator of their psychological balance. As a conclusion, this study aims at being a research-action, which objective is to elaborate a clinical intervention at the service of women and couples, and suitable to this particular cultural context.