Chez les mammifères, la réparation des CDBs par la voie NHEJ (Non Homologous End Joining) implique plusieurs complexes multi-protéines : (i) de reconnaissance (ADN-Ku70/Ku80), (ii) de maturation et (iii) de ligation comprenant XRCC4, XLF et ligase IV. Si les protéines impliquées dans le NHEJ sont connues, leurs propriétés structurales et fonctionnelles le sont moins. Au cours de ma thèse, j’ai combiné des approches biochimiques, de Microscopies Electronique et à Force Atomique, pour caractériser les propriétés de XRCC4, de XLF et leurs interactions avec le complexe de reconnaissance en particulier Ku. J’ai montré que la protéine complète XRCC4 est capable de polymériser et former des filaments alors qu’elle ne peut pas en faire en absence de la région C-terminale. Par Microscopies Electronique et à Force Atomique; nous avons montré que le filament XRCC4 forme une structure hélicoidale de chiralité gauche. XLF seule ne forme pas de filament mais peut être incorporé dans le filament XRCC4, ce que nous avons montré par immunomarquage. L’analyse d’images réalisé en collaboration et avec l’algorithme d’Edward Egelman (Université de Virginie-USA) a permis d’obtenir une reconstruction 3 D du filament XRCC4. Il est composé de 2 filaments enroulés l’un autour de l'autre avec un pas de 54 nm. Des Etudes sont en cours afin d’obtenir une structure 3D en CryoEM à haute résolution. L’étude des propriétés physicochimiques de l’assemblage du filament en fonction de la concentration, la température et le temps d’incubation a permis de montrer la dynamique du filament avec une stabilisation à basse température, et une concentration située entre 50 et 250 nM. L’ADN avec ou sans extrémités interagit avec les filaments. Cette interaction stabilise et promeut l’extension du filament. L’incorporation de XLF stabilise aussi le filament XRCC4. L’analyse des complexes formés entre l’ADN et XRCC4 ou XLF à l’état oligomérique montre des événements de pontage intra ou intermoléculaires. Parallèlement, nous avons étudié les propriétés de reconnaissance de l’ADN par l’hétérodimère Ku70/Ku80 et avons montré que le domaine KBM de XLF interagit avec Ku80 au sein de l’hétérodimère. En conclusion, nous montrons que le filament XRCC4 pourrait jouer un rôle d’architecture en maintenant les extrémités physiquement proches. Le recrutement de XLF dans le filament XRCC4 permettrait d’assembler le complexe de ligation avec le complexe de reconnaissance grâce aux interactions entre Ku et XLF. / In mammals, DSBs repair by the Non Homologous End Joining (NHEJ) pathway involves several multi-protein complexes : (i) the recognition complex (the Ku70 / Ku80 heterodimer), (ii) the maturation complex and (iii) the ligation complex comprising XRCC4, XLF, PAXX and ligase IV. If the proteins involved in NHEJ are identified and characterized, their structural and functional properties are often poorly understood. During my thesis I combined biochemical approaches, and molecular microscopies (Electron Microscopy and Atomic Force Microscopy), to characterize the properties of XRCC4, XLF and their interactions with the recognition complex (Ku-DNA). I have shown that the full length XRCC4 forms oligomers in solution (dimers and tetramers) and it polymerize into filaments whereas it can’t do it when the C-terminal region is absent. We initially characterized the structure of this filament in Electron Microscopy and Atomic Force Microscopy. XRCC4 filament forms a helicoidal structure of left chirality. XLF alone does not forms a filament but can be incorporated into the XRCC4 filament, which we have shown by immunostaining with gold beads. In collaboration with Edward Egelman (University of Virginia-USA), the image analysis performed using his algorithm allowed us to obtain a 3D reconstruction of the XRCC4 filament. It consists of 2 filaments wound around each other in a helical manner with a pitch of 54 nm. Studies in CryoEM are in progress to obtain a 3D high resolution structure. The study of the physicochemical properties of the filament assembly as a function of the concentration, the temperature and the incubation time allowed to show the dynamics of the filament with stabilization at low temperature, and a concentration between 50 and 250 nM. DNA with or without ends interacts with the filaments. This interaction stabilizes and promotes the extension of the filament. Similarly, incorporation of XLF stabilizes the Xrcc4 filament. Analysis of complexes formed between DNA and XRCC4 or XLF in the oligomeric state shows intra- or intermolecular bridging events. In parallel, we have studied the DNA recognition properties of the Ku70/Ku80 heterodimer and we have shown that KBM domain of XLF interacts with Ku80 within the heterodimer. In conclusion, we show that the XRCC4 filament could play an architectural role favoring repair events by keeping the ends physically close. The recruitment of XLF into XRCC4 filaments ans its interaction with Ku allow the link between ligation and recognition complexes.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第18879号 / 医博第3990号 / 新制||医||1008(附属図書館) / 31830 / 京都大学大学院医学研究科医学専攻 / (主査)教授 髙田 穣, 教授 平岡 眞寛, 教授 小松 賢志 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19555号 / 医博第4062号 / 新制||医||1012(附属図書館) / 32591 / 京都大学大学院医学研究科医学専攻 / (主査)教授 高田 穣, 教授 戸井 雅和, 教授 鈴木 実 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

No description available.

付記する学位プログラム名: 充実した健康長寿社会を築く総合医療開発リーダー育成プログラム / 京都大学 / 新制・課程博士 / 博士(医学) / 甲第24521号 / 医博第4963号 / 新制||医||1065(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 斎藤 通紀, 教授 萩原 正敏, 教授 戸井 雅和 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

No description available.

Résumé : Il est généralement admis que les cassures double-brin (CDB) de l’ADN sont parmi les lésions les plus toxiques induites par les radiations ionisantes (RI). Les CDBs non ou mal réparées peuvent conduire à une instabilité génomique et à la mort cellulaire. La chimioradiothérapie concomitante est l’une des modalités la plus efficace pour le traitement de certains cancers surtout en stade avancé. Le rendement des CDBs a augmenté quand l’ADN a été irradié en présence de cisplatine avec des électrons de basse énergie (EBEs). Notre étude a pour objectif de réévaluer la contribution des CDBs et d’autres lésions induites par les RI dans la létalité cellulaire. L'effet des RI sur la fonctionnalité de l’ADN plasmidique modifié ou non de façon covalente par le cisplatine a été étudié par mesure de l'efficacité de transformation du plasmide dans E. coli. Les complexes cisplatine-ADN ont été préparés de telle sorte qu’il y avait en moyenne deux adduits de cisplatine par plasmide tel que mesuré par ICP-MS. Nos échantillons ont été irradiés en solution avec des doses croissantes de rayonnements gamma (137Cs). La présence de cisplatine a augmenté la formation des CDBs par un facteur de 2.6 par comparaison avec l'ADN non modifié. Malgré cette augmentation, le rendement des CDBs reste très faible et ne peut pas expliquer la perte de fonctionnalité observée. Alors que, les dommages multiples localisés (LMDS) (non-DSB cluster damage) donnant naissance à des CDBs sous l’action des enzymes de réparation la formamidopyrimidine [fapy]-DNA glycosylase (Fpg) et l’endonuclease III (Nth) où leur rendement a été augmenté d’un facteur de 2.1 lorsque l’ADN a été irradié en présence de cisplatine, ont pu expliquer la perte de fonctionnalité observée. Ces résultats suggèrent que le cisplatine peut agir, non seulement comme un agent chimiothérapeutique, mais aussi comme un radiosensibilisateur efficace par addition d’autres lésions à l’ADN. Aussi, pour la première fois nous avons pu évaluer l’effet des EBEs sur la létalité cellulaire. Des films d'ADN ont été préparés en utilisant la méthode d’adsorption douce sur un substrat de graphite pyrolytique, en présence de 1,3- diaminopropane (Dap[indice supérieur]2+) et ont été irradiées avec des EBEs 10 eV. Nous avons pu conclure, qu’en plus des CSBs, CDBs et des dommages de base, les EBEs sont capables aussi d’induire des LMDS (non-DSB cluster damage) et induire la perte de fonctionnalité de l’ADN. Le rendement des CDBs est très faible d’où ils n’ont pas pu expliquer la perte de fonctionnalité de plasmide observée, après irradiation avec les EBEs. Le rendement très faible des LMDS (non-DSB cluster damage) ne peut pas expliquer la perte de fonctionnalité de l’ADN. Il semble que les EBEs sont capables d’induire des dommages très proches les uns des autres et qui ne peuvent pas être révélés par les enzymes de réparation Fpg et Nth. Plus les dommages sont proches les uns des autres, plus leur réparation est difficile, car une de ces lésions peut inhiber la réparation de l’autre la plus proche. // Abstract : It is generally accepted that DNA double-strand breaks (DSB) are among the most toxic lesions induced by ionizing radiation (IR). Unrepaired or misrepaired DSB can lead to genomic instability and cell death. It is known that concomitant chemoradiation therapy is one of the most preferred methods for the treatment of certain cancers especially in advanced stage. The yield of DSBs was increased when DNA was irradiated with low energy electron (LEEs). The aims of our study was to reassess the contribution of DSBs and other lesions induced by indirect and direct effect of IR in cell lethality. The effect of IR on the DNA functionality of the plasmid modified covalently with cisplatin was studied by measuring the transformation efficiency of the plasmid in E. coli. Cisplatin-DNA complexes were prepared such that there was an average of two cisplatin adducts per plasmid as measured by ICP-MS. Aqueous solutions of the samples were irradiated with 137Cs [gamma]-rays at various doses. Gel electrophoresis analysis shows that cisplatin enhances, by a factor of 2.6, the formation of DSB by [gamma]-rays relative to those in unmodified DNA. Despite this increase, the yield of DSBs is very low and cannot explain the loss of functionality observed after transformation with plasmids modified with cisplatin. While locally multiple damaged sites (LMDS) revealed by repair enzymes Fpg (Formamidopyrimidine [fapy]-DNA glycosylase) and Nth (Endonuclease III) as DSB (nonDSB cluster damage), where their yield was increased by a factor of 2.1 when DNA was irradiated in the presence of cisplatin were able to explain the observed loss of DNA functionality. These results suggest that cisplatin may act not only as a chemotherapeutic agent, but also as an effective radiosensitizer by addition of other DNA lesions. For the first time, we could also evaluate the effect of low energy electrons (LEEs) on DNA functionality. Highly ordered DNA films were prepared on pyrolytic graphite by molecular self-assembly using 1,3-diaminopropane ions (Dap[superscript]2+) to bind together the plasmids and irradiated with LEE (10 eV). We concluded that in addition to CSBs, DSBs and base damage, LEEs induced the formation of non-DSB cluster damage and also induced the loss of DNA functionality under LEE irradiation. The yields of DSBs and of non-DSB cluster damage are too low and so one unable to explain the loss of DNA functionality. It seems that LEEs are able to induce a high complex damage that cannot be revealed by repair enzymes Fpg and Nth. The high complex damage is difficult to repair possibly because the repair of one lesion, may inhibit the repair of another.

Made available in DSpace on 2014-07-29T14:52:11Z (GMT). No. of bitstreams: 1 Tese_ADILSON santos.pdf: 8026419 bytes, checksum: d59ad1a2514d62fabb78f8c2501b3bfc (MD5) Previous issue date: 2010-03-29 / Recombination is one of the most important factors in the evolution of genome organization. It provides the links between homologous chromosomes that ensure their proper segregation during the first meiotic division. It is responsible for the creation of novel allele combinations and yields genetic diversity on which evolutionary selection can act. Double-strand DNA breaks (DSB) initiate meiotic recombination and when the 3 terminus of one of the broken strands invades the unbroken DNA molecule and primes DNA synthesis a double Holliday junction must be resolved through some alternative pathways. When homologous chromosomes exchange genetic material with each other, an event of recombination or a crossover takes place, which may be seen through chiasma. Citological, genetics, and molecular studies in many organisms have demonstrated that crossovers have a non homogeneous distribution across chromosomes, and rather concentrated in relative small DNA fragments usually called recombination hotspots. In searching for genomic features associated with recombination hotspots a model fitted to human genome data explained 42% of recombination rate variation in a 5 mega base pairs scale. Despite the fact that genomes of some plant species have been already sequenced, up to this moment, no research has been published concerning a high resolution characterization of recombination rate variation across a plant s genome. This study used OH- radical cleavage intensity estimates and sequence data of chromosome 4 of A. thaliana and population genetic data from a public set of 250 thousand SNP genotypes obtained for 362 A. thaliana accessions to: i) characterize the recombination rate and linkage disequilibrium (LD) distributions across the chromosome 4 in different scales; ii) search for recombination hotspots; iii) evaluate probable associations between sequence motifs and genomic features with recombination hotspots. The results have shown that the distribution of recombination events across chromosome 4 of A. thaliana is very concentrated: 50% to 60% of all recombination events spans in only 13% to 20% of the total length of the chromosome. Genomic features as G+C percent (G+C%) and OHradical cleavage intensity showed important associations with LD estimates in several scales. The mean OH- radical cleavage intensity and G+C% showed redundancy in correlation analysis with LD and recombination rates. Artificial strong and statistically significant correlations arose from the usage of sliding windows. DNA fragments considered as hotspots lay preferentially in the middle third of the chromosome, while those characterized for having long range LD decay are most localized in the two distal thirds of the chromosome. / A recombinação é um processo chave na evolução da organização dos genomas das espécies, importante para garantir a segregação adequada dos cromossomos homólogos durante a meiose I e criar novas combinações de alelos, gerando variabilidade genética para a ação da seleção natural. Do ponto de vista molecular, a recombinação é iniciada por uma lesão na fita dupla de DNA, denominada Double-Strand Break (DSB), seguida da formação de uma junção dupla de Holliday (dHJ), a qual é resolvida por vias alternativas. Quando há troca de material genético entre os cromossomos homólogos caracteriza-se a ocorrência de um evento de recombinação, crossover, visualizado citogeneticamente por meio de um quiasma. Estudos citológicos, genéticos e moleculares realizados em vários organismos demonstraram que a distribuição de crossover ao longo dos cromossomos não é regular, mas concentrada em fragmentos relativamente pequenos de DNA, denominados hotspots de recombinação. Na busca por correlações entre a distribuição de elementos genômicos e a de ocorrência de hotspots um modelo ajustado com dados do genoma humano se mostrou capaz de explicar até 42% da variação na taxa de recombinação, numa escala de 5 mega pares de bases. Em plantas, apesar da existência de vários genomas já sequenciados nenhum trabalho nesse sentido ainda foi realizado, pelo menos na ordem de resolução proporcionada pela recente disponibilidade de dados genéticos obtidos com o uso de chips de alta densidade de marcas SNP. Usando dados genéticos de populações, obtidos por genotipagem de 362 acessos de A. thaliana com 250 mil marcas SNP, estimativas da intensidade de clivagem por radical OH- e dados da sequência de nucleotídeos do cromossomo 4 de A. thaliana o presente trabalho propõe-se a: i) caracterizar a distribuição de taxas de recombinação e de desequilíbrio de ligação ao longo do cromossomo 4, em várias escalas; ii) identificar fragmentos hotspots de recombinação; e iii) identificar elementos genômicos com provável associação à ocorrência desses hotspots. Os resultados obtidos mostraram que a distribuição das taxas de recombinação ao longo do cromossomo 4 de A. thaliana é bastante concentrada, pois proporções entre 50% e 60% dos eventos de recombinação ocorrem em apenas 13% a 20% da sequência de DNA. Variáveis genômicas como a porcentagem da soma das bases G e C (G+C%) e a intensidade de clivagem por radical OH- apresentam correlações significativas com as estimativas do desequilíbrio de ligação em várias escalas. A média da intensidade de clivagem por radical OH- proporciona informação redundante com a variável G+C%. O uso de janelas deslizantes sobrepostas gera distroções que provocam o surgimento artificial de correlações fortes e significativas. Os fragmentos hotspots de recombinação têm uma distribuição concentrada no terço médio do cromossomo, enquanto os fragmentos caracterizados por longo alcance do desequilíbrio de ligação estão localizados, predominantemente, nos terços distais.

Ce travail de thèse, réalisé dans le cadre des projets de recherche ROSIRIS (IRSN) et Geant4-DNA, porte sur la construction d’une simulation multi-échelle dédiée au calcul des dommages radio-induits précoces à l’ADN qui peuvent apparaître suite à l’irradiation d’un noyau cellulaire. L’outil développé s’appuie sur une version modifiée du code de Monte Carlo Geant4-DNA et est capable de simuler dans le détail le transport et les interactions physiques entre l’irradiation ionisante et la matière biologique (étape physique), la création d’espèces chimiques (étape physico-chimique) et les réactions et processus de diffusion de ces dernières (étape chimique). Durant la simulation de ces trois étapes, un modèle géométrique de l’ADN, décrivant l’ensemble du génome humain avec une précision moléculaire, est généré avec un nouveau logiciel développé dans le cadre de cette thèse : DnaFabric. Les premiers résultats obtenus pour des irradiations avec des protons et des ions alpha sont détaillés et comparés à des données de la littérature. Un bon accord est observés avec ces dernières illustrant ainsi la cohérence de l’ensemble de la simulation. L’influence très significative du critère de sélection utilisé pour identifier les dommages à l’ADN est également démontrée. / This work was performed in the frame of the ROSIRIS (IRSN) and Geant4-DNA research projects and describes the development of a simulation tool to compute radioinduced early DNA damages in a cell nucleus. The modeling tool is based on a modified version of the Monte Carlo code Geant4-DNA and is able to simulate the physical interactions between ionizing particles and the biological target (physical stage), the creation of chemical species within the cell nucleus (physico-chemical stage) as well as the reactions and diffusion processes of these chemical species (chemical stage). During all the simulation, a geometrical model that describes the DNA content of a human diploid cell nucleus is taken into account. This model was generated with a new software (DnaFabric) developed in the frame of this work and has a molecular level of detail.The first results (in term of DNA strand breaks) obtained with this tool are detailed and compared with experimental data from the literature. The good agreement between the simulation results and those data shows the coherence of our modeling. The significant influence of the selection criteria used to identify the DNA damages is also demonstrated.

The World Trade Organization ("WTO") and its dispute resolution systém is unique in the international economic law, reasons are following: (i) enforcement, (ii) two-level proceding, (iii) exclusive jurisdiction of the Dispute Settlement Body ("DSU"). DSU continues to follow the case law based on GATT 1947 however develops more complex rule of law. How successful DSB is in this task is subject of examination of the thesis. Thesis is divided into two parts: theoritecal and practical. First chapter explains aim of the DSU, comparison of procedural rules with GATT 1947. Following, the second chapter explains the hard law and procedural rules, function and aim of WTO, followed by ideas for improvement of the dispute settlement. Last chapter of this parts is dedicated to methods of interpretation. The second part, practical, analyses the case law of DSU from its establishment in 1995 until now. It analyses possible conflicts between agreements of WTO or conflicts that arise during acting based on the agreements. Among the first cases belong the discrepancies between main 3 agreements - GATT 1994, GATS and TRIPS and cases such as Canada - Periodicals or Argentina- Textiles and Apparel, Indonesia - Auto; another group of cases represents isme of conflict between WTO agreement and other agreement of public...