Les régions alpines sont particulièrement sensibles aux changements climatiques en cours. Ainsi, l’ouest des Alpes s’est réchauffé deux fois plus vite que l’hémisphère Nord au cours du XXème siècle. Les rythmes saisonniers des arbres, comme beaucoup d’autres organismes, sont fortement modifiés par le réchauffement climatique. La phénologie et les variations temporelles fines du climat apparaissent comme des composantes incontournables à prendre en compte pour prédire la répartition des espèces. L’objectif principal de ce travail de thèse a été de comprendre la réponse de la phénologie des espèces arborées au réchauffement climatique dans les Alpes et de développer des outils pour évaluer cette réponse dans le futur. Pour atteindre cet objectif nous avons utilisé des données phénologiques (débourrement, floraison, senescence foliaire,) pour le noisetier, le frêne, le bouleau, le mélèze et l’épicéa, issues du programme de sciences participatives Phénoclim.Nos résultats montrent que le réchauffement de l’hiver retarde la levée de la dormance des bourgeons et par conséquent les dates de débourrement et de floraison le long du gradient d’altitude. Cet effet est plus important à basse altitude. La robustesse des projections des modèles de répartition basés sur les processus dépend fortement de la robustesse des modèles phénologiques qu’ils utilisent. En comparant des modèles phénologiques présentant différents niveaux de complexité nous avons montré que les modèles basés sur les processus étaient les plus robustes particulièrement lorsque l’estimation de leurs paramètres reposait sur une estimation directe à l'aide de mesures expérimentales. Les modèles prévoient une réduction des écarts entre les dates de débourrement le long du gradient d'altitude pour toutes les espèces d'ici la fin du 21e siècle. Ceci est dû d’une part à un avancement des dates de débourrement à haute altitude et d’autre part à un retard des dates de débourrement à basse altitude. Nous avons également testé de nouvelles hypothèses sur le déterminisme environnemental de la croissance cellulaire dans les bourgeons, mais aucune des hypothèses testées n’a significativement amélioré les performances des modèles. Nous avons ensuite intégré les modèles phénologiques les plus performants que nous ayons obtenus au modèle d’aire de répartition basé sur les processus PHENOFIT. Nous avons réalisé pour la première fois avec ce modèle des simulations à haute résolution spatiale. Les projections du modèle montrent que les espèces arborées devraient se déplacer vers le haut du gradient d’altitude. Cependant, des phénomènes d’extinction locale pourraient avoir lieu dans les fonds des vallées liés à des dates de floraison trop tardives qui diminuerait le succès reproducteur des individus. Selon les espèces, la limite altitudinale supérieure serait contrôlée par le risque d'exposition au gel tardif des fleurs ou par la longueur de la saison de croissance qui détermine le temps disponible pour la maturation des fruits.L’ensemble de ces résultats nous a permis d’apporter des éléments de réponse sur la dynamique future des écosystèmes forestiers altitudes face au réchauffement climatique. Ils nous ont également permis de montrer que les données du programme Phénoclim étaient de qualité suffisante pour être utilisées dans des travaux de recherche scientifique. / Mountainous regions are particularly exposed to the ongoing climate change. Indeed, in the Western Alps the temperature increased twice faster than in the northern hemisphere during the 20th century. Trees’ annual cycle, as in many other organisms, is largely affected by climate change. Phenology and the fine temporal variations of climate appear key to predict species distribution. The main objective of this PhD thesis work was to understand the response of tree phenology to climate change in the Alps and to develop tools to evaluate this response in future conditions. It has been carried out using the phenological observations (budburst, flowering, leaf senescence) of five tree species (hazel, ash, birch, larch and spruce) of the citizen science program Phenoclim.Our results show that warmer winters slow down bud dormancy break, and consequently the budburst and flowering dates along the elevation gradient. This effect is stronger at low elevation. The robustness of process-based species distribution models depends strongly on the robustness of their process-based phenology sub-model. By comparing different phenology models differing in their level of complexity and we showed that process-based models were the most robust especially when their parameter estimates relied on forward estimation using experimental data. Models project a reduction in the phenological cline along the elevation gradient by the end of the 21th century. This is due, on one hand, to an advancement of the budburst dates at high elevation and on the other hand, to a delay of the budburst dates at low elevation. We also tested several hypotheses on the environmental determinism of bud cell growth. However, none of the hypotheses improved significantly the models’ performance. We then implemented the best phenology models we obtained in the process-based species distribution model PHENOFIT. We carried out for the first time simulations at high spatial resolution. Projections showed that species are expected to move up along the elevation gradient in response to climate change. However, local extinction events may occur in the bottom of the valleys due to late flowering dates that would decrease the reproductive success. Depending on the species, the upper altitudinal limit would be controlled by the risk of flowers’ exposure to late spring frost or to the length of growing season, which determine fruit maturation success.All of these results, allowed us to provide some answers on the future dynamics of high altitude ecosystems in the face of global climate change. They also allowed us to show that the Phenoclim data were of sufficient quality to be used to address important scientific questions.

<p> The biosynthesis of lycopodine was studied by feeding radioactive acetate, acetoacetato, lysine and pelletierine to Lycopodium tristachyum. Partial degration of the radioactive lycopodine recovered from these experiments revealed specific incorporation of these precursors. The labeling pattern obtained is discussed in the light of the two major blogenetic hypothesis advanced for the Lycopodium alkaloids. </p> <p> The results obtained disproved Conroy's polyacetate hypothesis. They are consistent with the hypothesis that regards these alkaloids derived from lysine and acetate. </p> / Thesis / Doctor of Philosophy (PhD)

Les voies de signalisation exercent à l’échelle moléculaire un contrôle spatiotemporel précis sur de nombreux processus cellulaires. Par exemple, à l’échelle d’un organisme en développement, ces réseaux complexes d’interaction opèrent entre différents groupes cellulaires et établissent une régulation fine, dynamique et intégrée de multiples processus tels la spécification, la différentiation, la prolifération et la migration cellulaire. Comprendre ces phénomènes requiert d’étudier la fonction précise de ces molécules et de ces réseaux de signalisation. Il est donc nécessaire de concevoir des outils adaptés contrôlant localement l’activité de molécules de signalisation pour étudier leur implication dans la régulation de processus cellulaires fondamentaux. Afin de développer des outils innovants pour l’étude de systèmes biologiques, nous proposons d’implémenter la technique de la relaxation chimique au sein de microsystèmes. Cette approche repose sur la conception de micro-dispositifs dédiés qui génèrent une modulation spatio-temporelle précise de la concentration de molécules de signalisation. Une telle perturbation génère une réponse spécifique du système biologique qui livre des informations décisives quant à la dynamique des réactions et quant à l’organisation des réseaux moléculaires à l’œuvre. Cette stratégie d’ingénierie pour l’étude de systèmes biologiques est générique et intrinsèquement multidisciplinaire. Au cours de ce travail, elle a été mise en œuvre pour deux projets collaboratifs, d’une part BioModulator à l’échelle cellulaire, et d’autre part Electromice à l’échelle d’un organisme complet. Nous avons mis nos compétences de physiciens spécialistes de micro/nanofabrication au service de l’équipe du Dr. Zoher Gueroui de l’Ecole Normale Supérieure ainsi que de l’équipe du Dr. Aitana Perea-Gomez de l’Institut Jacques Monod, ces deux équipes étudiant respectivement les processus impliqués dans l’auto-assemblage des microtubules et le développement de l’embryon précoce de souris. Plus précisément, le projet BioModulator repose sur la génération de gradients localisés de protéines présumées régulatrices du fuseau mitotique alors que le projet Electromice propose l’électroporation localisée d’acides nucléiques au sein d’embryons de souris pour modifier spatio-temporellement l’expression des gènes qui régissent le devenir des cellules visées et ainsi étudier les interactions contrôlant la croissance, la migration et la spécification de différents types cellulaires. Au cours de cette thèse, nous avons donc développé des méthodologies expérimentales ainsi que des protocoles adaptés à l’utilisation d’une instrumentation miniaturisée dédiée à l’étude de systèmes biologiques multi-échelles. Enfin, nous avons pu démontrer l’efficacité ainsi que la validité d’approches collaboratives et multidisciplinaires. En effet, elles permettent à la fois l’émergence de stratégies innovantes et ambitieuses et aussi de répondre à d’importantes questions en sciences de la vie et ce, pour le plus grand profit de toutes les communautés scientifiques participant à ce type de projet. / Cell-fate decisions and cellular functions are dictated by the spatiotemporal dynamics of molecular signaling networks. Moreover, at the scale of an entire organism, especially during its development, complex interactions between cell groups enable the fine, dynamic, and integrated regulation of tissue specification. Understanding these phenomena necessitates new dedicated tools. In this doctoral research, we propose to implement relaxation techniques in microfluidic systems. Our goal is to be able to precisely modulate in space and time the concentration of signaling molecules and to deduce, from the response of the biological system, information on the dynamics of the scrutinized reaction networks. More exactly, microsystems are used to perturbate living systems and associated models accounting for the recorded response are validated thanks to computer simulations. We have implemented this strategy both at the cellular level and at the organism scale during two collaborative projects. On one hand, we focused on the control by magnetic fields of microtubules regulators conjugated to magnetic particles, in order to decipher the basic molecular mechanisms responsible for the assembly and regulation of the mitotic spindle. On the other hand, we proposed a device for localized electroporation of DNA constructs into mouse embryos, in order to be able to study the dynamic cellular interactions that control the growth, migration and specification of the visceral endoderm between 5 and 7 days of development. A distinctive feature of this work lies in the proposed interdisciplinary approach. Combining several states of the art techniques from Chemistry, Physics, and Biophysics, our ambition has been to demonstrate that micro/nanotechnologies can open new perspectives in Biology.

<p>Availability of genome sequences for numerous bacterial species comprising of different bacterial strains allows elucidation of species and strain specific adaptations that facilitate their survival in widely fluctuating micro-environments and enhance their pathogenic potential. Different bacterial species use different strategies in their pathogenesis and the pathogenic potential of a bacterial species is dependent on its genomic complement of virulence factors. A bacterial virulence factor, within the context of this study, is defined as any endogenous protein product encoded by a gene that aids in the adhesion, invasion, colonization, persistence and pathogenesis of a bacterium within a host. Anecdotal evidence suggests that bacterial virulence genes are undergoing diversifying evolution to counteract the rapid adaptability of its host&rsquo / s immune defences. Genome sequences of pathogenic bacterial species and strains provide unique opportunities to study the action of diversifying selection operating on different classes of bacterial genes.</p>

<p>Availability of genome sequences for numerous bacterial species comprising of different bacterial strains allows elucidation of species and strain specific adaptations that facilitate their survival in widely fluctuating micro-environments and enhance their pathogenic potential. Different bacterial species use different strategies in their pathogenesis and the pathogenic potential of a bacterial species is dependent on its genomic complement of virulence factors. A bacterial virulence factor, within the context of this study, is defined as any endogenous protein product encoded by a gene that aids in the adhesion, invasion, colonization, persistence and pathogenesis of a bacterium within a host. Anecdotal evidence suggests that bacterial virulence genes are undergoing diversifying evolution to counteract the rapid adaptability of its host&rsquo / s immune defences. Genome sequences of pathogenic bacterial species and strains provide unique opportunities to study the action of diversifying selection operating on different classes of bacterial genes.</p>

Philosophiae Doctor - PhD (Biotechnology) / Availability of genome sequences for numerous bacterial species comprising of different bacterial strains allows elucidation of species and strain specific adaptations that facilitate their survival in widely fluctuating micro-environments and enhance their pathogenic potential. Different bacterial species use different strategies in their pathogenesis and the pathogenic potential of a bacterial species is dependent on its genomic complement of virulence factors. A bacterial virulence factor, within the context of this study, is defined as any endogenous protein product encoded by a gene that aids in the adhesion, invasion, colonization, persistence and pathogenesis of a bacterium within a host. Anecdotal evidence suggests that bacterial virulence genes are undergoing diversifying evolution to counteract the rapid adaptability of its host&rsquo;s immune defences. Genome sequences of pathogenic bacterial species and strains provide unique opportunities to study the action of diversifying selection operating on different classes of bacterial genes. / South Africa

A pesquisa visa a estudar as inter-relações1 entre os processos de projeto da arquitetura contemporânea, mediados por tecnologia computacional, e os processos da biologia, com o olhar sob os conceitos da ecologia, apoiados na teoria dos sistemas e na cibernética. As análises pretendem relacionar questões de âmbitos teórico e prático, dentro da observação dos processos de projeto, por meio das seguintes etapas: 1. Introdução e compreensão das atuais mudanças de paradigma nas áreas da biologia, ecologia e ciência da computação, que influenciam diretamente os modos de produção de informação nos processos de projeto digital em arquitetura; 2. Reflexões sobre a teoria da cibernética e sistemas complexos como costuradores dos processos biológicos aos processos de projeto de arquitetura, com implicações em emergência e inovação em arquitetura e 3. Análises práticas da integração de processos de projeto e produção digitais recorrentes das interrelações da arquitetura com a biologia. / The research aims to study the interrelationship between the contemporary architecture design processes, mediated by computer technology and the biology processes, with a view under the concepts of ecology, supported on system theory and cybernetics. The analyzes aim to relate issues on the spheres of theory and practice, within the observation of design processes, through the following steps: 1. Introduction and understanding of the current paradigm shifts in biology, ecology and computer science, which directly holds the modes of producing information in architecture digital design processes; 2. Thoughts on cybernetic theory and complex systems like links between biological processes and architectural design processes, with implications in emergence and innovation in architecture 3. Analyses of study cases about design processes and digital production integration recurrent from the interrelationship between architecture and biology.

Made available in DSpace on 2014-06-11T19:30:54Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-12Bitstream added on 2014-06-13T19:00:58Z : No. of bitstreams: 1 murakami_mt_dr_sjrp.pdf: 4603266 bytes, checksum: 354af33ced476bc60fd37bac536c3729 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / This work presents some features of essential biological processes such as the haemostatic system, integrity of biological membranes and thermostability of proteins. Crystallographic, spectroscopic and in silico tools have been used to obtain information at the molecular level of macromolecular complexes, action mechanisms and inhibition pathways. Worms, snakes, ticks, leeches and spiders produce a variety of proteins, which interfere in the regulation of these systems. Different toxins isolated from these organisms were characterized providing necessary information for the development of a new anti-myonecrotic molecule and reveal a new factor Xa exosite that is important for macromolecular substrates recognition and inhibition. The first crystal structure of a member of the sphingomyelinases D family was determined by the quick cryo-soaking technique and the catalytic mechanism was proposed, which involves a magnesium-binding site and two catalytic histidines. An alternative activation of the protein C pathway that does not require thrombomodulin was structurally characterized and revealed the dual role of the elestrotatic surface charge around the active site and the three strategically positioned carbohydrate moieties in the approach, recognition and activation of protein C.

FundaÃÃo Cearense de Apoio ao Desenvolvimento Cientifico e TecnolÃgico / Este trabalho avaliou a viabilidade dos processos biolÃgicos aerÃbios e oxidativos avanÃados (POAs) como pÃs-tratamento de lixiviados antigos provenientes de lagoas de estabilizaÃÃo em sÃrie. Paralelamente, desenvolveu-se uma metodologia analÃtica para detecÃÃo e quantificaÃÃo de compostos aromÃticos, organoclorados, Ãsteres ftalatos e hormÃnios, considerados como compostos recalcitrantes e raramente investigados em lixiviados tratados, principalmente nas ETEs localizadas no estado do CearÃ. Inicialmente foi realizada uma caracterizaÃÃo fÃsico-quÃmica e especiaÃÃo de metais sendo verificado que DQO e amÃnia estavam acima dos limites permitidos pelas normas ambientais, bem como alguns metais. No desenvolvimento da metodologia analÃtica para detecÃÃo e quantificaÃÃo por GC/FID verificou-se que a extraÃÃo em fase sÃlida empregando C-18 foi a melhor tÃcnica para extraÃÃo e prÃ-concentraÃÃo dos compostos recalcitrantes e que os melhores resultados de recuperaÃÃo dos compostos foram obtidos para os compostos aromÃticos e Ãsteres ftalatos. Nos experimentos de pÃs-tratamento empregando os reatores biolÃgicos, reator aerado submerso (RAS) e reator em batelada seqÃencial (RBS), todos foram eficientes na nitrificaÃÃo do lixiviado com percentuais superiores a 90% de remoÃÃo da amÃnia, contudo, nÃo foram eficazes na remoÃÃo de fÃsforo. Em termos de remoÃÃo dos compostos recalcitrantes, o RBS apresentou melhores resultados em relaÃÃo ao RAS para os compostos aromÃticos e Ãsteres ftalatos. No processo de oxidaÃÃo avanÃada UV/H2O2 foi obtida remoÃÃes de DQO, turbidez e descoloraÃÃo da amostra superior a 90%, a partir de 120 minutos de reaÃÃo, em sistema de batelada com recirculaÃÃo. O sistema UV/H2O2 foi eficiente na remoÃÃo dos compostos aromÃticos e, eficaz para os Ãsteres ftalatos benzil-butilftalato (BBP) e dietil-hexilftalato (DEHP) com 100% de remoÃÃo. O processo foto-Fenton com radiaÃÃo solar estudado com o lixiviado de Portugal apresentou-se como uma excelente opÃÃo no pÃs-tratamento do lixiviado em relaÃÃo aos outros sistemas estudados (UV/H2O2 e TiO2/UV) devido a mineralizaÃÃo dos compostos orgÃnicos terem sido de aproximadamente 80% de remoÃÃo do carbono orgÃnico dissolvido (COD), reduÃÃo da aromaticidade e descoloraÃÃo, alÃm de aumentar a biodegradabilidade do lixiviado. A concentraÃÃo Ãtima de ferro para o lixiviado estudado foi de 60 mg L-1 Fe+2, com consumo de H2O2 de 310, 6 mM e aproximadamente 110 kJ L-1 de energia acumulada., mas nÃo foi eficiente na remoÃÃo do Ãster dietil-hexil ftalato (DEHP), um dos principais ftalatos considerado como interferente endÃcrino. Os processos UV/H2O2 e TiO2/UV utilizando energia solar nÃo foram favorÃveis devido a reaÃÃo ser mais lenta em comparaÃÃo com o processo foto-Fenton e terem sido obtidos baixos valores de remoÃÃo de COD, indicando baixa mineralizaÃÃo dos compostos orgÃnicos presentes no lixiviado. / This work assessed the feasibility of using biological and advanced oxidation processes (AOP) as post-treatments for old leachate from stabilization ponds in series. Additionally, an analytical methodology for detection and quantification of aromatic compounds, organochlorides, phthalate esters and hormones, was developed. These compounds are considered as recalcitrant and rarely investigated in treated leachates, mainly in wastewater treatment plants located in the state of CearÃ. Initially, a physico-chemical characterization and a metal speciation was carried out, from which it was verified that COD and ammonia were above the limits permitted by environmental legislation, and also some metals. In the development of the analytical methodology for detection and quantification by GC/FID, the solid phase extraction using C-18 was the best technique for extraction and pre-concentration of the recalcitrant compounds and the best results in terms of recuperation were achieved for the aromatic compounds and phthalate esters. In the post-treatment experiments using biological reactors, aerated submerged reactor (ASR) and sequential batch reactor (SBR), both were efficient in the leachate nitrification reaching ammonia removal efficiencies above 90%. However, they were not efficient on phosphorus removal. In terms of recalcitrant compounds removal, SBR presented better results when compared with ASR for the aromatic compounds and phthalate esters. The advanced oxidation process UV/H2O2 reached turbidity and COD removal and decolourisation efficiencies above 90% from a reaction time of 120 minutes by using recirculation batch mode. The UV/H2O2 system was efficient in the removal of aromatic compounds and the phthalate esters benzyl butyl phthalate (BBP) and diethyl hexyl phthalate (DEHP), achieving 100% removal. The photo-Fenton process with solar radiation assessed with the leachate from Portugal showed to be an excellent option for the leachate post-treatment when compared to the other systems studied (UV/H2O2 and TiO2/UV). Mineralization of organic compounds has reached approximately 80% reduction of dissolved organic carbon (DOC), beside aromaticity and decolourisation reductions and increasing leachate biodegradability. The optimal iron concentration for the leachate studied was 60 mg L-1 Fe+2, with H2O2 consumption of 310.6 mM and approximately 110 kJ L-1 of accumulated energy. However, it was not efficient in the removal the ester DEHP, one of most important phthalates, which is considered an endocrine disruptor. The UV/H2O2 and TiO2/UV processes using solar energy were slower than the photo-Fenton process and low COD removals were achieved, which indicated low mineralization of the organic compounds present in the leachate.

Biological processes at the cellular level take place in heterogeneous environments, and usually involve only a small number of molecules. They tend to exhibit strong time dependent fluctuations, as a result, and are, therefore, intrinsically stochastic. The present thesis describes some of the efforts I have made during the course of my research work to develop simple, analytically tractable models of a selection of biologically-inspired problems in which this kind of stochasticity is a central ingredient. These problems are: (i) single molecule enzyme activity (ii) intermittency in single enzymes, (iii) liquids crystal dynamics (iv) modulation of electron transfer kinetics during photosynthesis, and (v) anomalous polymer translocation dynamics. All of these problems can be defined in terms of quantity that changes randomly in time because of environmental fluctuations with broad distributions of relaxation times. In this thesis I show that a generalization of a model that describes simple Brownian Motion can be used to understand many of the dynamical aspects of these problems.