1,25-(OH)2 vitamin D3 inhibits cell proliferation of a variety of cancers including prostate. In the human prostate cancer cell line LNCaP, 1,25-(OH)2 vitamin D3-mediated growth inhibition is attributed to cell cycle G1 accumulation which correlates with a robust decrease of cyclin-dependent kinase 2 (CDK2) activity and pronounced relocalization of CDK2 into the cytoplasm. Nuclear targeting CDK2 blocks the 1,25-(OH)2 vitamin D3-mediated growth inhibition and cell cycle G1 accumulation. Further, the nuclear targeted CDK2 blocks 1,25-(OH)2 vitamin D3-mediated inhibition of CDK2 activity and nuclear exclusion in LNCaP cells. Therefore, CDK2 cytoplasmic relocalization is the key mechanism for 1,25-(OH)2 vitamin D3 effects. Since cyclin E is important for CDK2 nuclear localization and activation, 1,25-(OH)2 vitamin D3 may exert its effects through regulation of cyclin E. Cyclin E but not a cyclin E mutant deficient in CDK2 binding reverses 1,25-(OH)2 vitamin D3-mediated antiproliferation which suggests the involvement of cyclin E as a mechanism. However, the studies showed no effects of 1,25-(OH)2 vitamin D3 on cyclin E levels, intracellular localization or binding to CDK2. In order to develop a model for studying 1,25-(OH)2 vitamin D3-mediated antiproliferative effects, LNCaP vitD.R cell line, a vitamin D resistant LNCaP derivative, was generated by continuously culturing of LNCaP cells in medium supplemented with 10 nM 1,25-(OH)2 vitamin D3 for over 9 months. The initial characterization of this cell line showed complete resistance to 1,25-(OH)2 vitamin D3-mediated effects. Analysis of vitamin D regulation of VDR target gene expression revealed that vitamin D resistance in LNCaP vitD.R cells was not due to deregulation of VDR signaling. HDAC inhibitor Trichostatin A (TSA) did not confer sensitivity of LNCaP vitD.R cells to vitamin D treatment suggested the resistance to 1,25(OH)2 vitamin D3 effect of LNCaP vitD.R cells is not due to histone deacetylase remodeling of the chromatin structure which leads to inhibition of gene transcription. While the partial sensitization of LNCaP vitD.R cells to 1,25(OH)2 vitamin D3 effect by demethylation reagent 5-Aza-2¡¯-deoxycytidine treatment suggested a set of genes involved in 1,25(OH)2 vitamin D3-mediated antiproliferative effects is silenced via hypermethylation in LNCaP vitD.R cells. These results suggested LNCaP vitD. R cell line is a useful tool and further studies to elucidate the genes involved in this effect will help uncover the mechanisms of 1,25(OH)2 vitamin D3-mediated antiproliferative effects.

Les procédures gastro-intestinales de l’oesophage impliquent un contrôle ou une surveillance périodique de l'anatomie interne (réalisation de multiples biopsies le long de l’oesophage). Le suivi et la relocalisation inter-opératoires de ces sites de biopsies (pour un même patient opéré plusieurs fois) est un challenge bien connu. L'objectif de cette thèse est de proposer une solution informatisée afin de guider le gastroentérologue pendant de telles procédures. Nous proposons un cadre novateur utilisant un système de suivi électromagnétique pour réaliser des enregistrements d'intervention de l’oesophage, couplant la vidéo à la profondeur de l'endoscope inséré. Ces enregistrements sont ensuite utilisés afin de repositionner l'endoscope de façon précise sur des sites de biopsie préalablement ciblés. Cette navigation consiste en une synchronisation vidéo entre la vue endoscopique courante et celles des surveillances endoscopiques précédentes enregistrées. Une première version de notre système est évaluée de manière incrémentale sur des données d'abord synthétiques puis réelles recueillies sur des cochons. Les résultats montrent que la relocalisation est obtenue avec une précision de l'ordre de 10mm, considérée comme largement acceptable par les experts. En outre, une expérience qualitative simulant une tâche réelle de relocalisation de site de biopsie, évaluée par 10 gastroentérologues, démontre les avantages du système de guidage assisté. Ce cadre est finalement étendu afin d'améliorer encore la précision de la relocalisation à partir d'une sélection optimale de l'image vidéo pré-enregistrée dont le point de vue est le plus proche de celui de l'image endoscopique courante / Gastrointestinal (GI) procedures, specifically, oesophageal interventions involve periodic monitoring or surveillance of the internal anatomy, which involve obtaining biopsies at different regions along the oesophagus. The tracking and relocalization of these biopsy sites ``inter-operatively'' poses a significant challenge for providing targeted treatments. This thesis, clarifies the concept of relocalization, and analyses the need for a platform to aide GI endoscopy. Based on the understanding of the clinical context in oesophageal procedures; a novel framework to use electromagnetic tracking system is proposed, which is used to perform a ``recording'' of an intervention. This framework and the recording is then used to provide a guided navigation to the GI expert, during a follow-up surveillance endoscopy; for accurate re-positioning of the endoscope at previously targeted sites. This is achieved using inter-operative video synchronization, and the various steps involved in achieving this are described in this thesis. A careful analysis of noise affecting the system is performed, to propose quantitative analysis using synthetic and realdata collected on pigs. A set of qualitative experiments were also proposed using 10 experts to indicate benefit to the GI community. The quantitative experiment indicated that the relocalization was achieved with an accuracy of 10mm, and the qualitative experiments showed that the biopsy site relocalization rate improved from 47.5% to 94%. The thesis then proceeds to provide two additional improvements using additional information collected during the GI intervention for a complete solution

The Transition movement is a grassroots movement working to build community resilience in response to the challenges of climate change, fossil fuel depletion, and economic insecurity. Rather than focusing on the state as a site for contestation or change, the movement adopts a "do it ourselves" approach, prioritizing autonomy and prefigurative action. It also places importance on relationships and community in the context of local places. It is open-ended and characterized by an ethos of experimentation and learning. Transition shares these place-based and prefigurative features in common with many other contemporary movements, from the Zapatistas to alternative globalization movements, to popular movements in Latin America, to most recently the Occupy movement. Though often not seen as "political" by conventional definitions that understand social movements in relation to the state, I argue that Transition's choice of practical, place-based forms and commitments is an ethical-political one, based on the state's failure to meet crises of our times, and it has political effects. In exploring the movement in its own terms, this ethnographic study of the Transition movement in the northeast US demonstrates the ways in which activists are locating power and possibility in the local and the everyday. Operating in the terrain of culture and knowledge production, the Transition movement is engaged in an effort to shift subjectivities and social relations, and to resignify power, security, economy, and democracy. Paying attention to the Transition movement's specifically place-based, prefigurative features provides a better understanding of the potential of this approach and its political significance. It also sheds light on tensions, which in the US context include challenges in addressing racism, inequality, and the neoliberal state.

Au début des années 2000, un mouvement de pensée politique se forme en France autour du terme « décroissance ». Il formule une critique radicale des sociétés contemporaines dont l’organisation ne tient pas compte des limites écologiques de la planète. L’une des réponses apportées est la relocalisation ; elle est étudiée en tant que dimension spatiale structurante de la décroissance. Cette thèse est fondée sur une enquête par immersion de longue durée dans le réseau français des militant-es politiques pour la décroissance, ainsi qu’une enquête de terrain plus courte à Montréal, associant observation directe et participante, entretiens et récolte documentaire. L’analyse montre d’abord le rapport entre les ressources et dispositions des militant-es et les modes de structuration et de fonctionnement des organisations politiques visant l’échelle nationale. Elle distingue ensuite une pluralité de modes d’actions défiant les frontières établies entre champ intellectuel, champ politique, mouvements contestataires et alternatives locales. L’étude de séquences de mobilisations montre l’ancrage des militant-es dans la gauche de (la) gauche écologiste tandis que l’analyse de trajectoires d’engagement dévoile la valorisation des alternatives concrètes dans le répertoire d’actions collectives des militant-es pour la décroissance. La multipositionnalité apparaît alors comme un moyen de garantir la reconnaissance militante et l’engagement local comme une condition de la mise en cohérence de soi. La relocalisation, mise en jeu dans le répertoire contestataire des militant-es, est finalement présentée comme la (re)construction collective d’espaces de vie appropriés, point de départ de la transformation sociale souhaitée / An activist movement around the political concept ‘degrowth’ originated in France in the early 2000s. It formulates a radical critique of unsustainable contemporary development patterns and ways of life. ‘Relocalization’, which the movement puts forward as an alternative, is analyzed as degrowth’s fundamental spatial dimension. This thesis uses data gathered through multi-sited ethnography in the French degrowth political network and a political organization in Montreal, including participant observation and interviews. The analysis begins by showing a relationship between activists’ critical dispositions and national political organizations’ modes of structuration and functioning. Furthermore, it identifies several modes of action that blur the distinctions between intellectual and political fields, social movements and local alternatives. The analysis of mobilization sequences shows activists’ affiliation to the ecological and radical left. Their careers reveal how concrete alternatives are valued within degrowth militants’ collective action repertoires. Maintaining multiple commitments becomes a way of guaranteeing activist recognition and local activism a condition of individual coherence. Within the action repertoires, relocalization emerges as the collective (re)construction of appropriated living spaces, a starting point for the social change wished

Le génome de la levure de boulanger Saccharomyces cerevisiae a évolué à partir d'un ancêtre chez lequel une profonde décompaction du génome s'est produite à la suite de la perte de la méthylation de la lysine 9 de l'histone H3, il y a environ 300 millions d'années. Il a été proposé que cette décompaction du génome a entraîné une capacité accrue des levures à évoluer par des mécanismes impliquant des taux de recombinaison méiotique et de mutation exceptionnellement élevés. La capacité à évoluer accrue qui en résulte pourrait avoir permis des adaptations uniques, qui en ont fait un eucaryote modèle idéal et un outil biotechnologique. Dans cette thèse, je présenterai deux exemples de la façon dont les adaptations locales et globales du génome se reflètent dans les changements des propriétés mécaniques de la chromatine qui, à leur tour, indiquent un phénomène de séparation de phase causée par les modifications post-traductionnelles des histones et des changements dans les taux d'échange des histones. Dans un premier manuscrit, je présente des preuves d'un mécanisme par lequel la relocalisation du locus INO1, gène actif répondant à la déplétion en inositol, du nucléoplasme vers l'enveloppe nucléaire, augmente la vitesse d'adaptation et la robustesse métabolique aux ressources fluctuantes, en augmentant le transport des ARNm vers le cytosol et leur traduction. La répartition d'INO1 vers l'enveloppe nucléaire est déterminée par une augmentation locale des taux d'échange d'histones, ce qui entraîne sa séparation de phase du nucléoplasme en une phase de faible densité plus proche de la périphérie nucléaire. J'ai quantifié les propriétés mécaniques de la chromatine du locus du gène dans les états réprimé et actif en analysant le déplacement de 128 sites LacO fusionnés au gène liant LacI-GFP en calculant diffèrent paramètres tel que la constante de ressort effective et le rayons de confinement du locus. De plus, j'ai mesuré l'amplitude et le taux d'expansion en fonction du temps du réseau LacO et j'ai observé une diminution significative du locus à l'état actif, ce qui est cohérent avec le comportement de ressort entropique de la chromatine décompactée. J'ai montré que les séquences d'éléments en cis dans le promoteur du locus, essentielles à la séparation de phase, sont des sites de liaison pour les complexes de remodelage de la chromatine effectuant l'acétylation des histones. Ces modifications de la chromatine entraînent une augmentation des taux d'échanges des sous-unités des complexes d'histones, et une séparation de phase locale de la chromatine. Enfin, je présente l’analyse de simulations in silico qui montrent que la séparation de phase locale de la chromatine peut être prédite à partir d'un modèle de formation/disruption des interactions multivalentes protéine-protéine et protéine-ADN qui entraîne une diminution de la dynamique de l'ADN. Ces résultats suggèrent un mécanisme général permettant de contrôler la formation rapide des domaines de la chromatine, bien que les processus spécifiques contribuant à la diminution de la dynamique de l'ADN restent à étudier. Dans un second manuscrit, je décris comment nous avons induit la « retro-évolution » de la levure en réintroduisant la méthylation de la lysine 9 de l'histone H3 par l'expression de deux gènes de la levure Schizosaccaromyces pombe Spswi6 et Spclr4. Le mutant résultant présente une augmentation de la compaction de la chromatine, ce qui entraîne une réduction remarquable des taux de mutation et de recombinaison. Ces résultats suggèrent que la perte de la méthylation de la lysine 9 de l'histone H3 pourrait avoir augmenté la capacité à l'évoluer. La stabilité inhabituelle du génome conférée par ces mutations pourrait être utile pour l'ingénierie métabolique de S. cerevisiae, dans laquelle il est difficile de maintenir des gènes exogènes intégrés pour les applications de nombreux processus biotechnologiques courants tels que la production de vin, de bière, de pain et de biocarburants. Ces résultats soulignent l'influence des propriétés physiques d'un génome sur son architecture et sa fonction globales. / The genome of the budding yeast Saccharomyces cerevisiae evolved from an ancestor in which a profound genome decompaction occurred as the result of the loss of histone H3 lysine 9 methylation, approximately 300 million years ago. This decompaction may have resulted in an increased capacity of yeasts to evolve by mechanisms that include unusually high meiotic recombination and mutation rates. Resultant increased evolvability may have enabled unique adaptations, which have made it an ideal model eukaryote and biotechnological tool. In this thesis I will present two examples of how local and global genome adaptations are reflected in changes in the mechanical properties of chromatin. In a first manuscript, I present evidence for a mechanism by which partitioning of the active inositol depletion-responsive gene locus INO1 from nucleoplasm to the nuclear envelope increases the speed of adaptation and metabolic robustness to fluctuating resources, by increasing mRNA transport to the cytosol and their translation. Partitioning of INO1 to the nuclear envelope is driven by a local increase in histone exchange rates, resulting in its phase separation from the nucleoplasm into a low-density phase closer to the nuclear periphery. I quantified the mechanical properties of the gene locus chromatin in repressed and active states by monitoring mean-squared displacement of an array of 128 LacO sites fused to the gene binding LacI-GFP and calculating effective spring constants and radii of confinement of the array. Furthermore, I measured amplitude and rate of time-dependent expansion of the LacO array, and observed a significant decrease for the active-state locus which is consistent with entropic spring behavior of decompacted chromatin. I showed that cis element sequences in the promoter and upstream of the locus that are essential to phase separation are binding sites for chromatin remodeling complexes that perform histone acetylation among other modifications that result in increased histone complex exchange rates, and consequent local chromatin phase separation. Finally, I present analytical simulations that show that local phase separation of chromatin can be predicted from a model of formation/disruption of multivalent protein-protein and protein-DNA interactions that results in decreased DNA dynamics. These results suggest a general mechanism to control rapid formation of chromatin domains, although the specific processes contributing to the decreased DNA dynamics remain to be investigated. In a second manuscript, I describe how we retro-evolutionarily engineered yeast by reintroducing histone H3 lysine 9 methylation through the expression of two genes from the yeast Schizosaccaromyces pombe Spswi6 and Spclr4. This mutant shows an increase in compaction, resulting in remarkable reduced mutation and recombination rates. These results suggest that loss of histone H3 lysine 9 methylation may have increased evolvability. The unusual genome stability imparted by these mutations could be of value to metabolically engineering S. cerevisiae, in which it is difficult to maintain integrated exogenous genes for applications for many common biotechnological processes such as wine, beer, bread, and biofuels production. These results highlight the influence of the physical properties of a genome on its overall architecture and function.

This project explores the agricultural heritage and current social landscape of the Stinking Creek community of Knox County, Kentucky, and the legacy of the local nonprofit organization the Lend-A-Hand Center. Through participatory research, this project presents a reflexive account of the Lend-A-Hand Center Grow Appalachia Gardening Program examining the diverse economy of the Stinking Creek watershed and possibilities for new economic imaginings and post-coal futures for central Appalachia. This dissertation includes an oral history project, a theoretical examination, and an ethnographic reflection, bridging several literatures in the fields of agricultural history, Appalachian Studies, Participatory Action Research, research within the diverse economy framework, and feminist political ecology. For three years I coordinated the Grow Appalachia program through the Lend-A-Hand Center, developing agricultural initiatives in Knox County, working to re-localize food systems through home gardens, community gardens, and the establishment of the Knox County Farmers’ Market, and gathering stories through oral histories on the Creek. Problematizing the 1967 book Stinking Creek, by John Fetterman, this account of the community seeks to call attention to the importance of critical analyses of representations of people, processes, and places. In the face of pressing social issues in central Appalachia and renewed interest in the discourses of development, local food, and post-coal transition, this work seeks to intervene in region-wide discussions and suggest avenues for change and possibility. The Lend-A-Hand Center Grow Appalachia Gardening Program illustrates the potentials for community-based agriculture projects in the region to promote a variety of economic processes, foster and preserve agricultural traditions, and impact the conversation about outlooks for the region. This research provides policy and programmatic suggestions regarding the importance of relocalization of food systems and different (re)presentations of community narratives as part of a multifaceted agenda toward a just, sustainable future for eastern Kentucky and the region.

Visual simultaneous localization and mapping (SLAM) as field has been researched for ten years, but with recent advances in mobile performance visual SLAM is entering the consumer market in a completely new way. A visual SLAM system will however be sensitive to non cautious use that may result in severe motion, occlusion or poor surroundings in terms of visual features that will cause the system to temporarily fail. The procedure of recovering from such a fail is called relocalization. Together with two similar problems localization, to find your position in an existing SLAM session, and loop closing, the online reparation and perfection of the map in an active SLAM session, these can be grouped as visual location recognition (VLR). This thesis presents novel results by combining the scalability of FabMap and the precision of 13th Lab's tracking yielding high-precision VLR, +/- 10 cm, while maintaining above 99 % precision and 60 % recall for sessions containing thousands of images. Everything functional purely on a normal mobile phone. The applications of VLR are many. Indoors, where GPS is not functioning, VLR can still provide positional information and navigate you through big complexes like airports and museums. Outdoors, VLR can improve the precision of GPS tenfold yielding a new level of navigational experience. Virtual and augmented reality applications are other areas that benefit from improved positioning and localization.

Interactome of IL-1α N-terminal domain Cytokines are highly effective mediators produced by various cell types within and outside of the immune system with the aim to influence the orientation, intensity, and duration of the immune response and inflammatory process. Their biological effects mediated through binding the high-affinity membrane receptors and triggering the signal transduction pathway are usually well defined. However, as it is more and more frequently observed, in addition to the exocrine function, some cytokines may show intracrine effects. For this type of cytokines, the term "dual function cytokines" has been adopted. One of these cytokines is Interleukin-1α, in which the recent research has concentrated on determining its intracellular functions. The intracellular function of interleukin-1α has not been clearly defined so far. However, apart from the absence of the conventional hydrophobic sequence, its existence is supported by the fact that the N-terminal peptide included in its precursor is highly conserved and contains nuclear localization signal. The aim of this work is to define the conditions of localization of the interleukin-1α N- terminal domain in different cellular compartments and to study proteins potentially interacting with it using fluorescent microscopy. Key words:...