Les gènes codant pour des protéines peuvent souvent être regroupés et intégrés en modules fonctionnels par rapport à un organelle. Ces modules peuvent avoir des composantes qui suivent une évolution corrélée pouvant être conditionnelle à un phénotype donné. Les gènes liés à la motilité possèdent cette caractéristique, car ils se suivent en cascade en réponse à des stimuli extérieurs. L’hyperthermophilie, d’autre part, est interreliée à la reverse gyrase, cependant aucun autre élément qui pourrait y être associé avec certitude n’est connu. Ceci peut être dû à un déplacement de gènes non orthologues encore non résolu. En utilisant une approche bio-informatique, une modélisation mathématique d’évolution conditionnelle corrélée pour trois gènes a été développée et appliquée sur des profils phylétiques d’archaea. Ceci a permis d’établir des théories quant à la fonction potentielle du gène du flagelle FlaD/E ainsi que l’histoire évolutive des gènes lui étant liés et ayant contribué à sa formation. De plus, une histoire évolutive théorique a été établie pour une ligase liée à l’hyperthermophilie. / Protein coding gene may often be grouped and integrated in functional modules with respect to an organelle. These modules may have constituents that follow a conditional correlated evolution to a given phenotype. Genes linked to motility posses this characteristic as they follow a cascade in response to external stimuli. Similarly, hyperthermophily is related to reverse gyrase, however no other element that could be associated with certainty is known. This may be caused by an unresolved case of non-orthologous gene displacement. Using a bioinformatic approach, a mathematical model for conditional correlated evolution for three genes has been developed and applied to the phyletic profiles of archaea. This has helped to develop theories about the potential functions of the flagellar gene FlaD/E and the evolutionary history of the genes that are linked to it and that may have contributed to its formation. In addition, a theoretical evolutionary history has been established for a ligase associated with hyperthermophily.

This dissertation investigates the role of information technology (IT) in organizational strategy. Specifically, it examines how organizations can persist in turbulent competitive landscapes characterized by IT innovations. Underlying premises for this dissertation are that: (1) ubiquitous IT implies constant disruptions from digital innovation, (2) IT and practice are becoming fused, and (3) organizational strategies are dynamically linked with practice, i.e. they are reciprocally related through what organizations do rather than have. To investigate such IT strategizing processes, I outline a conceptual framework for analyzing how organizations can generate digital capability, i.e. a collection of routines for strategizing by leveraging digital assets to create differential value. Digital assets here refer to the complement of available resources and competencies for IT design and implementation. Based on the notion of dynamic capability and evolutionary theory, this framework emphasizes the importance of sensing, seizing and transforming abilities for generating digital capability. As organizational practices are becoming fused with IT scholars have argued that attempting to disentangle them analytically is futile. In a similar vein, organizational strategy is increasingly reliant on available IT resources for both formulation and execution. In the IS field it is widely acknowledged that IT has both enabling and inhibiting consequences for organizations. Drawing on the resource-based view of the firm and theory on organizational capabilities, the notion of IT capability has been widely used as a conceptual tool for analyzing these dual strategic effects of IT. Considering the explosive advances in computing, network and interaction that have resulted in IT being ubiquitous and deeply embedded in contemporary practices, recent research argues for the need to move beyond the functional view of technology implicit in the IT capability notion. A key aspect to address for such broadening of the perspective is the coevolution of IT and business practices, i.e. who (or what) leads, who or what follows, and whether such a causal distinction is meaningful. Grounded in the outlined conceptual framework, this dissertation examines how organizations can build digital capability to both enable large variation and complexity of feasible competitive actions, and reduce inhibiting effects of IT. The empirical investigation is situated in three distinct domains: boundary spanning IT innovation, transformation of existing IT resources, and hybridization of technology through digitalization of production equipment. These investigations are presented in five research papers. The dissertation contribute to knowledge of IT strategy by: (1) explicating the construct of digital capability, (2) providing a framework for coevolutionary strategizing processes, (3) presenting an empirical illustration of the coevolution of IT and business strategies, and (4) offer specific insights on design and orchestration of processes for digital capability generation.

L’Integrase du VIH est une ADN recombinase catalysant deux réactions qui permettent l'intégration de l'ADN viral dans l'ADN hôte. L’intégrase du VIH comprend 3 domaines : N-terminal impliqué dans la réaction de « 3' processing » et le transfert de brin, le domaine catalytique contenant le site actif et le domaine C-terminal liant l'ADN non-spécifiquement (CTD). Des recherches récentes mettent en évidence l'importance du CTD dans la liaison avec d'autres protéines virales comme la transcriptase inverse. Le but de la thèse était de comprendre les rôles et l'importance du domaine C-terminal de l’intégrase dans deux contextes : l'intégration dans la chromatine et la coévolution, avec l'objectif de comprendre le rôle de la multimerisation dans la fonction de l’intégrase. Globalement, les résultats de mon projet indiquent que l'IN-CTD joue un rôle important, en contribuant à la formation de multimères d'ordre supérieur importants pour la fonction de l’IN. / HIV Integrase is a DNA recombinase that catalyzes two endonucleolytic reactions that allow the viral DNA integration into host DNA for replication and subsequent viral protein production. HIV Integrase consists of 3 structural and functional domains: The N-terminal zinc domain involved in 3’ processing and strand transfer, the catalytic core domain which contains the active site, and the C-terminal domain that binds DNA non- specifically. Recent research highlights the importance of the CTD in binding with other viral proteins such as Reverse Transcriptase. The aim of the thesis was to understand the roles and importance of the C-terminal domain of HIV-1 Integrase in two contexts: chromatin integration, and co-evolution, with the overall purpose of understanding the role of multimerization in IN function. Overall, results from my project indicate that the IN-CTD plays an important role, by contributing to the formation of higher order multimers that are important for IN functionality.

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The study analyzes genealogy and coevolutionary relationships between the bloodsucking louse Polyplax serrata (Anoplura) and its host of the genus Apodemus (Rodentia). It uses the tools of molecular biology and phylogenetics for interpretation of the parasite distribution in respect to the georaphy and host specificity

O continente sul-americano é a única região biogeográfica onde podemos encontrar um grupo estenohalino de elasmobrânquios: as arraias da família Potamotrygonidae. Entre 19 e 21 espécies de potamotrigonídeos estão taxonomicamente organizadas em três gêneros, distribuídas pelas bacias dos rios Atrato, Magdalena, Maracaibo, Orinoco, Essequibo, Amazonas e do Prata, os quais desembocam no Oceano Atlântico e no Mar do Caribe. Diversos cenários biogeográficos postulados para explicar a presença de linhagens predominantemente marinhas nos sistemas fluviais da América do sul foram propostos. O mais aceito para a origem e diversificação de Potamotrygonidae é a de invasão de um ancestral caribenho no sistema fluvial sul-americano durante as ingressões marinhas do Mioceno inferior no noroeste do continente, seguido de isolamento por alteração dos padrões de drenagens do Orinoco e formação dos Andes. A fauna parasitária de Potamotrygonidae está representada predominantemente por membros de Cercomeromorpha, um clado composto por linhagens de platelmintos membros de Cestoda e Monogenoidea. Dois gêneros de monogenóideos parasitas branquiais podem ser encontrados em potamotrigonídeos: Potamotrygonocotyle (Monocotylidae), para o qual 12 espécies são conhecidas, e a monotípica Paraheteronchocotyle amazonense (Hexabothriidae). O objetivo desta tese é propor uma hipótese de relacionamento filogenético baseada em dados moleculares para as espécies de Potamotrygonocotyle, e discutir padrões de evolução da espécie P. aramasae e seu hospedeiro Paratrygon aiereba, distribuídos em diferentes rios amazônicos. Sequências nucleotídicas do gene mitocondrial cox1 e nuclear ITS1 foram utilizadas simultaneamente em uma busca de uma hipótese filogenética para todas as espécies conhecidas de Potamotrygonocotyle. Os resultados recuperaram o status monofilético de cinco espécies, sugeriram complexos de linhagens crípticas para três espécies nominais e revelaram relacionamentos de grupo-irmão não detectados na hipótese filogenética mais recente para o gênero, baseada em dados morfológicos. Adicionalmente, os resultados apresentados suportam decisões taxonômicas recentes envolvendo sinonímias entre espécie nominais de Potamotrygonocotyle. Finalmente, os relacionamentos filogenéticos de haplótipos de diferentes populações de P. aramasae e seu hospedeiro P. aiereba foram acessados pela análise cladística de múltiplos marcadores mitocondriais, com o objetivo de se detectar possíveis padrões filogeográficos e testá-los sob predições filogenéticas de três hipóteses de diversificação amazônica (Hidrogeológica, de Museu e Paleogeográfica). Sequências dos genes ribossomal 16S e citocromo oxidase 1 foram obtidas para espécimes de parasitas de seis sub-bacias amazônicas. Os hospedeiros foram amostrados em 10 sub-bacias amazônicas e na sub-bacia do rio Essequibo, para os quais foram obtidas sequências nucleotídicas dos genes mitocondriais citocromo oxidase 1, citocromo b e ATPase. Os resultados sugerem a ausência de padrões filogeográficos para o parasita, cujos resultados indicam um modelo de alta dispersão. Em contraste, P. aireba é caracterizada por populações bem estruturadas, de acordo com as sub-bacias amostradas. O padrão filogeográfico geral desta espécie é concordante com as predições da Hipótese de Museu (linhagens mais antigas em rios dos escudos pré-cambrianos; linhagens apicais na bacia sedimentar amazônica). / South America is the only biogeographical region in the world where is possible to find an exclusive stenohalin group of elasmobranchs: the Potamotrygonidae stingrays. Between 19 and 21 species of potamotrygonid stingrays are taxonomically organized in three genera, distributed in the Atrato, Magdalena, Maracaibo, Orinoco, Essequibo, Amazonas e la Plata river Basins, discharging in both Atlantic and Caribbean waters. Distinct biogeographical scenarios have been proposed to explain the presence of predominantly marine lineages in the south American fluvial systems. The most accepted theory for Potamotrygonidae is the invasion of a Caribbean ancestor in the south-American freshwater system during the marine ingression of the early Miocene in the northwest of the continent, followed by its isolation due alterations of Orinoco rivers drainage patterns, as well as formation of Andes. The parasitic fauna of potamotrygonids is predominantly represented by members of Cercomeromorpha, a clade composed by members of Cestoda and Monogenoidea. Two genera of gill parasites monogenoidean might be found in potamotrygonids: Potamotrygonocotyle (Monocotylidae), for which 12 species are currently recognized, and the monotypic Paraheteronchocotyle amazonense (Hexabothriidae). The goal of this study is to propose a phylogenetic hypothesis based in molecular data for members of Potamotrygonocotyle, as well as to discuss evolutionary patterns of the species P. aramasae and its host Paratrygon aiereba, distributed through different amazon rivers. Nucleotide sequences of the mitochondrial gene cox1, and the nuclear gene ITS1 were simultaneously used to infer phylogenetic sister-group relationships among allrecognized species of Potamotrygonocotyle. The results recovered the monophyletic status of five species, suggested cryptic lineages for three species complexes, and revealed sister-groups relationships not detected previously by the phylogenetic analysis of morphological data. Additionally, the results supports recent taxonomic decisions involving synonyms among nominal species within the genus. The phylogenetic relationships of haplotypes from distinct populations of the parasite P. aramasae, as well as from its host Paratrygon aiereba, were accessed by the cladistic analysis of mitochondrial markers, in an attempt of detecting possible phylogeographic patterns, and to test them against phylogenetic predictions of three amazonian bio-diversification hypotheses (Hydrogeology, Museum, Paleogeography). Sequences of the ribosomal 16S gene and cytochrome oxidase 1 were obtained from parasite specimens collected in six amazon sub-basins. The hosts were sampled in 10 amazon sub-basins, as well as in the Essequibo sub-basin, for which cythocrome oxidase 1, cythocrome b, and ATPase sequences were obtained. No clear phylogeographic patterns were revealed for theparasite haplotypes, and the results suggest a high dispersion model. In contrast, P. aiereb is characterized by strongly structured populations, according to the sub-basin sampled. The general phylogeographic pattern recovered for this species is in agreement with the Museum Hypothesis predictions (older lineages in rivers of the pre-cambrian shields; apical lineages inhabiting the sedimentary amazon basin).

Recentemente, tornou-se acessível a análise filogenética com base em caracteres contínuos. Isso amplia a quantidade de caracteres que podem ser utilizados em análises filogenéticas baseadas em morfologia, mas não há ainda um consenso sobre como esse tipo de caráter deve ser codificado e analisado. Este trabalho analisa o uso de caracteres contínuos em filogenias com dois diferentes enfoques: simulações em computador e aplicação em uma análise com dados reais. As simulações realizadas indicam que de fato pode-se recuperar filogenias com base em caracteres contínuos, com alguns cuidados. O mais importante deles é o uso de pesagem implícita. Mesmo com esse cuidado, os ramos pouco suportados podem ser incorretos, provavelmente devido a um efeito de atração de ramos longos. Na análise do gênero Anchylorhynchus, utilizei caracteres discretos e contínuos, em separado e combinados. As árvores obtidas com as matrizes separadas são bastante diferentes, e a árvore da matriz combinada é semelhante àquela obtida somente com os caracteres discretos. O suporte dos ramos, contudo, cresce com a adição dos caracteres contínuos. Os caracteres contínuos, portanto, não devem ser vistos como uma alternativa, mas como um acréscimo às análises tradicionais. A revisão taxonômica de Anchylorhynchus resultou na descrição de nove espécies novas e reconhecimento de quatro sinônimos novos. O gênero resultou ser um grupo monofilético com um total de 24 espécies reconhecidas. Além disso, as informações sobre a biologia e a distribuição geográfica desses gorgulhos foi atualizada. Em conjunto com a filogenia obtida, essas informações basearam reconstruções biogeográficas e da associação histórica com as plantas hospedeiras. / Recently, phylogenetic analysis based on continuous characters was made accessible. This increases the pool of characters available for morphology-based phylogenetic analyses, but there is still no consensus on how this kind of characters should be coded and analyzed. In the present study, I assessed the use of continuous characters in phylogenies from two distinct perspectives: computer simulations and an application to real data. The simulations indicate that one can indeed recover phylogenies based on continuous characters, given some precautions. The most important of them is the use of implied weighting. Even when this is done, poorly supported branches may be incorrect, probably due to long-branch attraction. For the phylogenetic analysis of Anchylorhynchus, I used both continuous and discrete characters, separately or combined. Trees obtained with separate matrices were significantly different, and the combined matrix resulted in a tree very similar to the tree obtained with discrete characters alone. Branch supports, however, increased with the addition of continuous characters. Continuous characters, therefore, should not be considered an alternative to traditional analyses. Rather, they should be added to discrete-character matrices. The taxonomic revision of Anchylorhynchus resulted in nine new species described and four new synonyms recognized. The genus resulted to be a monophyletic group containing 24 recognized species. Moreover, the information on weevils\' biology and geographical distribution was updated. Together with the phylogeny this information embased reconstructions of host relationships and biogeography.

Orientador: Louis Bernard Klaczko / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-22T19:31:56Z (GMT). No. of bitstreams: 1 Ventura_IuriMatteuzzo_M.pdf: 2580161 bytes, checksum: ec78d3ac3a9cb1dcb0d410ab56b4d99c (MD5) Previous issue date: 2013 / Resumo: O resumo poderá ser visualizado no texto completo da tese digital / Abstract: The abstract is available with the full electronic document / Mestrado / Genetica Animal e Evolução / Mestre em Genética e Biologia Molecular

Orientador: Wilson Castro Ferreira Junior / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Matemática, Estatística e Computação Científica / Made available in DSpace on 2018-08-20T05:05:37Z (GMT). No. of bitstreams: 1 Assis_RaulAbreude_D.pdf: 6617583 bytes, checksum: 80b80410952f2ac47edc7cf71466fb07 (MD5) Previous issue date: 2012 / Resumo: Neste trabalho apresentamos modelos matemáticos de processos evolutivos, utilizando como abordagem principal a descrição da frequência de fenótipos em populações. São propostos diversos modelos baseados em equações diferenciais parciais, ordinárias e equações de recorrência. São apresentados resultados de suas análises, bem como comparações com modelos genéticos aditivos. Como uma ilustração do tipo de abordagem proposto, criamos um modelo de um sistema do tipo parasita-hospedeiro (Maculinea-Myrmica) utilizando-o com o objetivo de analisar comportamento de especificidade de hospedeiro. Finalmente, apresentamos generalizações dos modelos em espaços de fenótipos e indicamos direções para aprofundamento de pesquisa / Abstract: In this thesis we present models of evolutionary dynamics that describe the changes in frequencies of phenotypes in populations. The models proposed are based on ordinary and partial differential equations and difference equations. Results from the analysis of the models and comparisons with the behavior of additive genetic models are presented. We develop a model for a host-parasite system (Maculinea-Myrmica) using the phenotypic space aprroach with the objective of analysing the hostspecificity behavior of the species. Finally, we present generalizations of the models of phenotypic spaces and indicate directions for further research in the area / Doutorado / Matematica Aplicada / Doutor em Matemática Aplicada

The practices related to the growing, harvesting, preparation, and celebration of food over millennia have given rise to diverse biocultural landscapes the world over. These landscapes – rich in biological and cultural diversity – are often characterised by persistent poverty, and, as such, are often the target of development interventions. Yet a lack of understanding of the interdependencies between human well-being, nature, and culture in these landscapes means that such interventions are often unsuccessful - and can even have adverse effects, exacerbating the poverty they were designed to address. This thesis investigates different conceptualisations of persistent poverty in rural biocultural landscapes, the consequences of these conceptualisations, and the ways in which development interventions can benefit from, rather than erode, biocultural diversity. The thesis first reviews conceptualisations of persistent poverty and specifically, the notion of a poverty trap (Paper I), and examines the consequences of different conceptualisations of traps for efforts to alleviate poverty (Paper II). Paper I argues that the trap concept can be usefully broadened beyond a dominant development economics perspective to incorporate critical interdependencies between humans and nature. Paper II uses multi-dimensional dynamical systems models to show how nature and culture can be impacted by different development interventions, and, in turn, how the degradation of both can undermine the effectiveness of conventional poverty alleviation strategies in certain contexts. In the second section, the thesis focuses on the effects of, and responses to, trap-like situations and development interventions in a specific context of high biocultural diversity: the Pamir Mountains of Tajikistan. Paper III advances a typology of responses to traps based around the mismatch of desires, abilities and opportunities. Observing daily practice provides a way to study social-ecological relationships as a dynamic process, as practices can embody traditional and tacit knowledge in a holistic way.  Paper IV examines the diverse effects of a development intervention on the coevolution of biocultural landscapes and the ways in which everyday practice – particularly around food – can be a source of both innovation and resilience. Papers I-IV together combine insights from diverse disciplines and methodologies, from systematic review to dynamic systems thinking and participant observation. Paper V provides a critical analysis of the opportunities and challenges involved in pursuing such an approach in sustainability science, underscoring the need to balance methodological groundedness with epistemological agility. Overall, the thesis contributes to understanding resilience and development, highlighting the value of viewing their interrelation as a dynamic, coevolving process. From this perspective, development should not be regarded as a normative endpoint to be achieved, but rather as a coevolving process between constantly changing ecological and social contexts. The thesis proposes that resilience can be interpreted as the active and passive filtering of practices via the constant discarding and retention of old and new, social and ecological, and endogenous and exogenous factors. This interpretation deepens understanding of resilience as the capacity to persist, adapt and transform, and ultimately shape new development pathways. The thesis also illustrates how daily practices, such as the growing, harvesting, and preparation of food, offer a powerful heuristic device for understanding this filtering process, and therefore the on-going impact of development interventions in rural landscapes across the world. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>