Il y a presque 20 ans, la mise en évidence de mutations bi-alléliques inactivatrices du gène SMARCB1 dans les tumeurs rhabdoïdes établissait la première démonstration d’altérations du complexe SWI/SNF de remodelage de la chromatine en oncologie. Depuis, l’avènement des techniques d’analyse moléculaire à haut débit appliquées à la cancérologie a permis de montrer que des altérations dans d’autres gènes du complexe SWI/SNF était présentes dans un très grand nombre de cancers. A travers la présentation de plusieurs types de tumeurs SWI/SNF déficientes et de nos modèles d’étude des tumeurs rhabdoïdes, nous montrons que la perte de SMARCB1 est associée à une augmentation de la biosynthèse de la sérine et des voies métaboliques en aval importantes pour l’oncogenèse. Ces résultats pourraient aboutir à une option thérapeutique pour les tumeurs rhabdoïdes voire, plus généralement, pour d’autres modèles de tumeurs SWI/SNF-déficientes. Enfin, la mise en perspective de ces changements métaboliques avec les altérations épigénétiques observées dans les tumeurs SWI/SNF déficientes pourrait se révéler pertinente pour continuer d’approfondir nos connaissances sur ces tumeurs. / Nearly 20 years ago, the demonstration of truncated bi-allelic mutations in the SMARCB1 gene in rhabdoid tumors established the first demonstration of alterations in the SWI/SNF chromatin remodeling complex in oncology. Since then, the advent of high-throughput molecular analysis techniques applied to oncology has shown that alterations in other genes of the SWI/SNF complex are present in a wide variety of cancers. Through the presentation of several types of SWI/SNF deficient tumors and our models of rhabdoid tumors, we show that the loss of SMARCB1 is associated with an increase of the serine biosynthesis pathway and the downstream metabolic pathways important for oncogenesis.These results could lead to a therapeutic option for rhabdoid tumors or, more generally, for other models of SWI/SNF-deficient tumors. Finally, the prospect of these metabolic changes with the epigenetic alterations observed in SWI / SNF deficient tumors may be relevant to continue to deepen our knowledge of these tumors.

Chromatin remodelers are ATP-dependent multisubunit assemblies that regulate transcription and other processes by altering DNA-histone contacts. The mechanism of action is based on the transduction of energy released by ATP hydrolysis to translocation on DNA and ultimately the movement of histones in cis or trans. Though the critical ATP burning and translocation activities are fulfilled by a conserved ATPase domain in the catalytic subunit, there are accessory domains and subunits that are speculated to regulate these activities. Important questions in the field center around the identification of these domains and subunits, whether they affect complex formation, substrate affinity or a critical step in remodeling. If they do affect remodeling, what is the structural basis of the regulatory activity. In this study, these questions have been addressed using the prototype remodeler SWI/SNF from budding yeast. ySWI/SNF is a 12 subunit complex that includes the catalytic subunit Swi2/Snf2. It affects 6% of the yeast genome being primarily involved in gene activation. We employed a systematic protein or domain deletion strategy and characterized the mutant complexes in vitro and in vivo. A key finding was that SWI/SNF is organized in distinct structural modules and that the Snf2 module regulates most of its activities. Snf2 is a central subunit in this module and the function of conserved regions within Snf2 were studied. The N terminus preceding the HSA and ATPase domain has three major roles - complex assembly, recruitment and regulation of catalytic activity. A novel SnAC domain located C terminal to ATPase domain was identified to play critical role in coupling ATP hydrolysis to nucleosome movement by acting as a histone anchor. Finally the tandem AT-hooks between SnAC and bromodomain serve as DNA binding domains but also affect ATPase activity and nucleosome mobilization independent of its binding activity. Taken together, this study provides a comprehensive overview of the function of regulatory domains in SWI/SNF.

Thesis (Ph.D.)--Indiana University, 2009. / Title from screen (viewed on December 1, 2009). Department of Cellular and Integrative Physiology, Indiana University-Purdue University Indianapolis (IUPUI). Advisor(s): B. Paul Herring, Anthony B. Firulli, Frederick M. Pavalko, Simon J. Rhodes. Includes vitae. Includes bibliographical references (leaves 138-149).

Résumé: L’Imagerie par Résonance Magnétique fonctionnelle est devenue un des outils principaux pour mesurer l’activité cérébrale chez l’Homme de façon non-invasive. Le type de séquence plus fréquemment utilisé à ces fins est le signal dépendant du niveau d'oxvgène sanguin (BOLD signal) car il reflète les changements hémodynamiques associés à l’activité cérébrale et offr l’avantage d'être relativement facile à mesurer. Cependant, cette mesure est dépendante du niveau de désoxyhémoglobine, présent dans les veines. L'architecture structurelle de ces dernières varie considérablement d'une région du cerveau à l'autre et cela fait en sorte qu'il est ardu de savoir si les différences inter-régionales sont dues à des différences au niveau de l’activité neuronale ou de la structure vasculaire. C'est pour répondre à cette question que nous avons observé la relation entre les variations régionales de densité vasculaire (VAD) et l’amplitude du signal BOLD au repos et en présence d'un stimulus. Nous avons implémenté une méthode de segmentation des veines pour des images en pondération de susceptibilité (SWI). Nous avons également utilisé une méthode de segmentation des tissus (Morphométrie Basée sur les Voxels (VBM )) pour séparer les tissus et calculer une mesure de densité de matière. Nous avons trouvé qu'indépendamment de la taille des voxels, les variations régionales d'amplitude du signal BOLD au repos et du signal évoqué par une tâche sont mieux corrélées avec la VAD qu'avec la densité de matière grise. En utilisant un modèle linéaire général, nous avons observé qu'une grande partie des variations régionales au repos pouvait être modélisée par la VAD. En somme, nos résultats suggèrent que le signal BOLD au repos est intimement relié à la structure vasculaire. Utiliser la densité vasculaire afin de calibrer les mesures d'amplitude du signal BOLD au repos nous permettra d'interpréter de façon plus précise et d'obtenir de meilleures informations sur les différences observées entre plusieurs groupes de sujets et de patients. // Abstract: Functional Magnetic Resonance Imaging (fMRI) has become one of the primary tools used for non-invasively measuring brain activity in humans. For the most part, the blood oxygen level-dependent (BOLD) contrast is used, which reflects changes in heinodynamics associated with active brain tissue. The main advantage of the BOLD signal is that it is relatively easy to measure and thus is often used as a proxy for comparing brain function across population groups (i.e. control vs. patient). However, it is particularly weighted towards veins whose structural architecture is known to vary considerably across the brain. This makes it difficult to interpret whether differences in BOLD between cortical areas reflect true differences in neu-ral activity or vascular structure. We therefore investigated how regional variations of vascular density (VAD) relate to the amplitude of resting-state and task-evoked BOLD signals. To address this, we first developed an automated method for segmen-ting veins in images acquired with susceptibility weighted imaging (SWI), allowing us to visualize the venoms vascular tree across the brain. In 19 healthy subjects, we then applied Voxel-Based Morphometry (VBNI) to Ti-weighted images and compu-ted regional measures of gray matter density (GNID). We found that, independent of spatial scale. regional variations in resting-state and task-evoked fNIRI amplitude was better correlated to VAD compared to GRID. Using a general linear model (GLNI). it was observed that the bulk of regional variance in resting-state activity could be modelled by VAD. Taken together, our results suggest that resting-state BOLD signals are signifi-cantly related to the underlying structure of the brain vascular system. Calibrating resting BOLD activity by venous structure may result in a more accurate interpreta-tion of differences observed between cortical areas and/or individuals.

In this study the saltwater intrusion in coastal aquifers is briefly described and the prevention techniques are discussed. By using two computer models SWI and SHARP, the movement of freshwater and saltwater is analyzed on hypothetical cases and on one real aquifer in Marmaris in the coast of Mediterranean Region. Artificial recharge and subsurface barrier techniques are applied to hypothetical cases as means of controling the saltwater intrusion. The performance of strip recharge and subsurface barrier in reducing the salt water intrusion is analyzed by simulation of the groundwater flow with the codes mentioned above. The results obtained are compared with each other. The results of hypothetical cases are relatively in good agreement. For the real aquifer the results show discrepancy that cannot be ignored.

No description available.

Objectifs : Les thérapies régénératives cardiaques ont connu un essor considérable au cours des 10 dernières années. Malgré des effets positifs démontrés chez l’animal, les bénéfices cliniques obtenus chez l’homme sont encore relativement modestes. L’objectif de ce travail a été de mieux comprendre les facteurs liés à l’implantation des cellules souches grâce aux techniques de détection cellulaire en imagerie par résonance magnétique (IRM), afin d’optimiser la thérapie cellulaire cardiaque.Matériel et méthodes : Un protocole de détection cellulaire en IRM cardiaque in vivo ainsi qu’une méthode de détection des microvaisseaux en IRM cardiaque ex vivo haute résolution avec des séquences Susceptibility Weighted Imaging (SWI) ont été développés, puis mis en application pour l’étude de la vectorisation de progéniteurs des cellules endothéliales marqués magnétiquement par des nanoparticules d’oxyde de Fer et injectés par voie intraveineuse, ainsi que pour l’évaluation de l’intégration et de l’efficacité de cellules souches mésenchymateuses administrées via des patchs de fibrine cellularisés chez des rats adultes indemnes de toute pathologie (un groupe contrôle vs un groupe infarctus via ligature définitive de l’artère interventriculaire antérieure).Résultats : Après injection intraveineuse et malgré la vectorisation magnétique (n=16 rats), l’imagerie de détection cellulaire a montré qu’aucune cellule n’était implantée dans le myocarde et que les paramètres fonctionnels cardiaques n’étaient pas améliorés. Avec les patchs cellularisés (n=37 rats), la fraction d’éjection ventriculaire gauche (FEVG) était améliorée dans les groupes de patchs cellularisés par rapport aux groupes contrôles. La densité microvasculaire était augmentée dans la zone infarcie et peri-infarcie dans les groupes cellularisés par rapport aux groupes contrôles, à la fois en immunohistochimie et en IRM sur les séquences SWI. L’IRM a montré l’absence de migration des cellules dans le myocarde à partir du patch, confirmé en immunohistochimie. La persistance de cellules dans la zone d’implantation du patch à la surface épicardique à J21 post greffe et l’étude en cytométrie en flux des cytokines et facteurs de croissance produits par les cellules souches plaident pour une efficacité de la thérapie cellulaire en rapport avec la sécrétion de facteurs paracrines par les cellules souches.Conclusion : L’imagerie de susceptibilité magnétique permet d’une part d’étudier les vaisseaux myocardiques sur des séquences pondérées en SWI ex vivo et d’autre part d’évaluer l’implantation des cellules souches sur des séquences en écho de gradient T2* in vivo. Ces techniques ont permis de mieux caractériser le mode d’action des patchs cardiaques en tant que réservoir de facteurs paracrines pour le traitement de l’insuffisance cardiaque dans un modèle murin. Ces résultats confirment l’intérêt fort à développer et optimiser l’utilisation de biomatériaux intelligents délivrant spécifiquement des molécules d’intérêt comme les cytokines ou les facteurs de croissance et permettant ainsi de contourner les contraintes immunogènes et tératogènes liés aux cellules souches. / Objectives: Cardiac regenerative therapies have grown considerably over the past 10 years. Despite positive effects demonstrated in animals, the clinical benefits obtained in humans are still relatively modest. The objective of this work was to better understand the factors associated with implantation of stem cells through the cell detection techniques in magnetic resonance imaging (MRI) and to improve cardiac stem cell therapy in a murine model of myocardial infarction.Materials and methods: A protocol for cell detection with gradient echo T2* sequences in cardiac MRI in vivo and a method for detection of microvessels in cardiac MRI ex vivo with high resolution Susceptibility Weighted Imaging sequences (SWI) were developed and implemented for the study of vectorization of intravenously injected endothelial progenitors cells (EPC) and the integration and evaluation of the impact of mesenchymal stem cells (MSC) administered via cellularized fibrin patches. A permanent ligation of the left anterior coronary artery was performed in adult rats. The stem cells were magnetically labeled with iron oxide nanoparticles by endocytosis.Results: Cell detection imaging showed no cell implantation in the myocardium and no improvement in cardiac functional parameters after intravenous injection of EPC, despite the aid of magnetic vectorization (n = 16 rats). With a local administration of MSC via cardiac patches (n = 37 rats), the left ventricular ejection fraction (LVEF) was improved in cellularized patches groups compared to controls. Microvascular density was increased in the infarcted and peri – infarcted areas in cellularized patches groups compared to controls in immunohistochemistry and in MRI on SWI sequences. The MRI showed no migration of cells into the myocardium from the patch, as confirmed by immunohistochemistry and Perls staining. The persistence of MSCs on the epicardial surface at D21 after implantation and flow cytometry profiling of cytokines and growth factors produced by MSC argue for cell therapy effectiveness related to the secretion of paracrine factors by stem cells.Conclusion: Susceptibility imaging allows: (1) to study myocardial vessels on SWI sequences ex vivo and (2) to assess the implementation of stem cells on gradient echo sequences T2 * in vivo. These techniques have shown that cardiac patches act as a reservoir of soluble mediators which paracrinally target the angiogenesis in the treatment of heart failure in a murine model. This is in favor of a move towards “cell free” biomaterials containing only molecules of interest such as cytokines or growth factors to circumvent immunogenic and teratogenic constraints related to the use of stem cells.

This thesis focuses on the concept of Single Well Imaging (SWI) in which a seismic source and receivers are deployed in a borehole to investigate the surrounding geology. The Uniwell project (1997-1999) was the first attempt to develop the SWI method; it used a fluid-coupled downhole source, which unfortunately generated high amplitude guided waves in the borehole which obscured all other useful information. Initial research work detailed in this thesis focused on removing the high amplitude guided waves, known as tube waves. Two-step source signature deconvolution using first the recorded source signature, and then the tube-wave reflected from the bottom of the well, succeeded in compressing the tube wave. The results were not consistent across all receivers, but there is enough correlation to identify a P-wave. Further work concentrates on using a new technique called Empirical Mode Decomposition to separate the tube-wave mode from the data. This identifies three dominant modes and a possible body wave arrival, but the results are ambiguous due to the inability of the decomposition to focus on the narrow bandwidth of interest. The source signature deconvolution technique can also be used to process real-time vertical seismic profiling (VSP) data down-hole, during pauses in drilling, in what is referred to as a Seismic-While-Drilling (SWD) setup. Results show that the technique is versatile and robust, giving 1 ms precision on first-break picking even in very noisy data. I also apply the technique to normal VSP data to improve both the resolution and the signal-to-noise ratio. A major effort in this thesis is to consider the effect of a clamped downhole source to overcome the tube-wave problem, using a magnetostrictive source. Earlier work established that the use of a reaction mass tended to excite resonances in the tool which caused the transducer to break. A new design for the source was developed in cooperation with colleagues which utilises a hydraulic amplifier design and a low power coded waveform driving method exploiting the time-bandwidth product to extract the signal from the noise. My results show that as the run time increases the resolution improves. With a run length of 80s it is possible to resolve the signal transmitted 50 cm through a granite formation. This analysis led to a revised design of the source to improve its efficiency. I have used finite difference modelling, with a variable grid technique, to compare an ideal explosive source with an ideal clamped source. The fluid-coupled source emits high amplitude tube waves which virtually obscure the body wave, whereas the clamped source emits a clearly identifiable P-wave along with lower amplitude tube waves. This clearly illustrates the advantage of an ideal clamped source. To model the source more accurately the idealwavelet is replaced by the respective recorded source signatures, and the data is then processed by cross correlation with the appropriate signature. The results show that the coded waveform approaches the resolution of the ideal wavelet very well, with all major events being visible. However, the fluid-coupled source performs very poorly with only the highest amplitude tube-wave visible. This work illustrates that by replacing a fluid-coupled source by a clamped source driven by a coded waveform, and by processing the data using cross correlation or signature deconvolution, it is possible to minimise or eliminate tube-wave noise from a SWI survey. It is hoped that the results outlined here will provide the basis for a new SWI method than can be used to prolong the supply of North Sea oil.

Supersaturated water injection (SWI) is a novel remediation technology which is able to remove entrapped residual NAPLs from saturated porous media by both volatilization (partitioning of volatile contaminants into the gas phase) and mobilization (displacement of isolated NAPL residuals by gas clusters). The character of gas saturation evolution in-situ in saturated porous media during SWI results in high sweep efficiency. This work focuses on studying the recovery of entrapped residual NAPL by the mobilization mechanism during SWI, thus low-volatility NAPL residuals, kerosene and a kerosene-hexadecane mixture, are used as contaminants. A series of SWI recovery experiments are conducted to investigate the influence of grain size, low-permeability layering, and physical properties of the contaminants on the recovery behavior. For columns contaminated with kerosene, the residual saturation can be reduced to around 4% from an initial value of 16%, and over 70% of the residual kerosene is recovered by a combination of mobilization and volatilization in homogeneous sand packs. For columns contaminated with a kerosene-hexadecane mixture, the final residual saturation is 7.4% and the final NAPL recovery is lower than that in kerosene columns. Grain size has little influence on NAPL recovery, but low permeability layering has a significantly negative influence. Experiments designed to compare SWI to sparging, and water-gas co-injection showed that water-gas co-injection was able to effectively recovery residual NAPLs albeit not as efficiently as SWI, while steady gas sparging is completely ineffective at recovering residual NAPL by mobilization. Based on these experimental observations, a conceptual model, involving double displacements and NAPL bank formation, is purposed to explain the experimental observations.

Supersaturated water injection (SWI) is a novel remediation technology which is able to remove entrapped residual NAPLs from saturated porous media by both volatilization (partitioning of volatile contaminants into the gas phase) and mobilization (displacement of isolated NAPL residuals by gas clusters). The character of gas saturation evolution in-situ in saturated porous media during SWI results in high sweep efficiency. This work focuses on studying the recovery of entrapped residual NAPL by the mobilization mechanism during SWI, thus low-volatility NAPL residuals, kerosene and a kerosene-hexadecane mixture, are used as contaminants. A series of SWI recovery experiments are conducted to investigate the influence of grain size, low-permeability layering, and physical properties of the contaminants on the recovery behavior. For columns contaminated with kerosene, the residual saturation can be reduced to around 4% from an initial value of 16%, and over 70% of the residual kerosene is recovered by a combination of mobilization and volatilization in homogeneous sand packs. For columns contaminated with a kerosene-hexadecane mixture, the final residual saturation is 7.4% and the final NAPL recovery is lower than that in kerosene columns. Grain size has little influence on NAPL recovery, but low permeability layering has a significantly negative influence. Experiments designed to compare SWI to sparging, and water-gas co-injection showed that water-gas co-injection was able to effectively recovery residual NAPLs albeit not as efficiently as SWI, while steady gas sparging is completely ineffective at recovering residual NAPL by mobilization. Based on these experimental observations, a conceptual model, involving double displacements and NAPL bank formation, is purposed to explain the experimental observations.