Three different studies are included in this dissertation.The first chapter is a preformulation study of the anticancer drug NSC-726796. A stability-indicating HPLC method to quantify the compound and its three main degradation products was developed. This method was used to investigate its degradation kinetics and mechanism. The reaction follows first-order kinetics and appears to be base-catalyzed with a maximum stability at pH 1. The degradation products were identified as 2-(2,4-difluorophenylcarbamoyl)-3,4,5,6-tetrafluorobenzoic acid (NSC-749820), 2,4-difluoroaniline and 3,4,5,6-tetrafluorophthalic acid. The mono acid was synthesized and its structure was confirmed by single crystal crystallography. That compound is found to be more soluble and more stable than the parent drug in aqueous media.The purpose of the research reported in the second chapter is to investigate the pH-stability of an anticancer cytidine derivative and a cytidine deaminase inhibitor, individually and in combination. A stability indicating HPLC method for the quantification of 5-fluoro-2-deoxycytidine (FdCyd, NSC-48006), tetrahydrouridine (THU, NSC-112907) and their degradants was developed using a ZIC®-HILIC column. The effect of THU and FdCyd on the in vitro degradation of each other was studied as a function of pH from 1.0 to 7.4. The degradation of FdCyd appears to be first-order and acid-catalyzed. THU equilibrates with at least one of its degradants. Results show that the combination of FdCyd and THU in solution does not affect the stability of either compound. The stability and compatibility of FdCyd and THU in the solid state at 40 C/ 75% relative humidity (RH) and at ambient temperature are also evaluated.In chapter three, the effect of polarity on acid-base dissociation in ionic micellar systems is discussed. The dissociation constant of a compound (i.e., pKa) can shift when it is incorporated in or on a micelle. The magnitude of the pKa shift can be attributed to the effect of the surface potential of the micelle and the dielectric constant of the system. Currently, there is no reliable relationship to quantitate the dependence of pKa on the polarity of the drug. Experimental data for pKa of acids in cationic and anionic micelles were compiled from the literature. The increase in the pKa of weak acids upon incorporation into sodium dodecyl sulphate micellar is shown to be proportional to their ClogP values.

Neurotrophins are a family of growth factors necessary for the development and maintenance of the nervous system. They produce their effects through receptor mediated signaling mechanisms that are highly regulated by sophisticated intracellular transport networks. The impairment of intracellular trafficking of neurotrophins in motor neurons has been identified as one possible factor in the development of motor neuron diseases, but remains inadequately studied. Aided by advances in imaging technology and the development of more powerful and sensitive detection tools for in-vitro studies, the dynamics of intracellular transport of neurotrophins are beginning to be unraveled. However, a primary limiting factor in the study of neurotrophin-transport dynamics in motor neurons has been the lack of alternative and easily available in-vitro systems able to substitute the often difficult and costly primary motor neuron cultures. The aim of this project was to develop a suitable motor neuron model using the NSC-34 cell line for the study of receptor mediated trafficking events through endosomal transport pathways. Successful evaluation and characterization of NSC-34 cells for motor neuron specific markers would result in the investigation of the p75 neurotrophin receptor (p75NTR) trafficking pathways in the presence of exogenous neurotrophins, with a variety of confocal imaging techniques. Chapter 3 describes the optimisation of NSC-34 cell culture conditions through media modification and the development of a suitable growth substrate matrix, which significantly improved cell adhesion, differentiation and the ability to culture the cells for extended time periods in serum free conditions. Quantitative measurements of cell proliferation, culture viability, cell-body size and neurite length are described to highlight the increased value of the cell line for long-term culture and experiments examining a broad range of issues relevant to motor neurons. In Chapter 4, multiple experimental approaches were used to extensively screen the NSC-34 cell line for the presence of motor neuron-specific markers, neurotrophin receptors and proteins involved in regulation of endosomal transport. This characterization established the presence of a developing motor neuron-like neurotrophin receptor profile (p75NTR, TrkB and TrkC), a genetic marker of developing motor neurons, cholinergic markers, proteins regulating transport within the endosomal pathway, and additional proteins previously shown to directly interact with neurotrophin receptors, including sortilin, and the lipid raft associated ganglioside GT1b. Furthermore, evidence is provided that NSC-34 cells undergo apoptosis in response to exogenous nerve growth factor (NGF) or neurotrophin-3 (NT-3), but not brain derived neurotrophic factor (BDNF) or neurotrophin-4 (NT-4). In addition characterization of mouse specific p75NTR antibodies is presented to establish their suitability for internalization studies without altering the binding of exogenous neurotrophins to the receptor. Subsequent confocal microscopy examination focusing on p75NTR trafficking in Chapter 5 revealed that internalization and intracellular transport of this receptor is regulated by exogenous neurotrophins at the cell surface where ligand binding and internalization occur, and in endosomal compartments where the bulk of receptors and ligands are targeted to their specific destinations. Evidence is provided showing that p75NTR internalization is altered in the presence of NGF, NT-3, or NT-4, but not BDNF, and the receptor is diverted into non-clathrin mediated endosomal pathways in response to NGF but not BDNF. Immunofluorescence confocal microscopy suggests that p75NTR recycles to the plasma membrane in a Rab4 GTPase dependent manner in the absence of neurotrophins. Addition of neurotrophins diverted p75NTR from the recycling Rab4 positive pathway, into EEA-1 positive sorting endosomes in the presence of NGF or NT-3, or lysosomal degradation in the presence of BDNF or NT-4. This study clearly demonstrates the suitability of the NSC-34 cell line as an alternate in-vitro system for the study of motor neuron biology, particularly the study of neurotrophin receptor trafficking. Taken together the results represented in this study suggest for the first time, that the fate of the p75NTR receptor depends on which neurotrophin is bound. These findings have important implications for understanding the dynamic mechanisms of action of p75NTR in normal neuronal function, and may also offer further insight into the potential role of neurotrophins in the treatment of neurodegenerative diseases.

Delta-like homologue 1 (Dlk1) and Dlk2 encode vertebrate-specific transmembrane proteins belonging to the Jagged/Delta/Serrate family of Notch ligands. Murine Dlk1 is widely expressed during embryonic development and targeted deletion results in defects in numerous developmental processes, such as adipogenesis, haematopoiesis, neurogenesis and skeletal muscle formation. However, the mechanisms by which DLK1 regulates these processes remains unclear. The purpose of this project is to examine the function of these genes using zebrafish as an in vivo model, allowing insight to the ancestral functions of these genes. We have strong evolutionary evidence that dlk2 is the ancestral version of the gene from which dlk1 is derived; therefore, the thesis focuses primarily on the role of dlk2 in the zebrafish system. I initially examine the expression of zebrafish dlk1 and dlk2 during embryonic development and in the adult brain, determining similarities and differences between mouse and zebrafish. In particular, dlk1 and dlk2 in the fish exhibit a pattern that is more reminiscent of Dlk2 in the mouse. This developmental expression pattern is essential for the interpretation of the modulation of Dlk2 in later chapters, and is aided by the generation of a mammalian Dlk2 antibody that cross-reacts with zebrafish. We obtained a dlk2 mutant and used this line to examine the role of the DLK2 protein in development and in the adult brain. I demonstrate that, in the absence of DLK2, a population of neural precursor cells appear to over-proliferate early in zebrafish development. Later, by larval stages, these cells are absent, suggesting a premature activation and subsequent depletion of the progenitor cell pool in the mutant, reminiscent of the Dlk1 mutant in mouse. Associated with this phenotype are larval behavioral defects in motor response. In this thesis, it will be shown that in the adult dlk2 mutant zebrafish, the radial glial cell population in the telencephalon is completely depleted. These radial glial cells are thought to be responsible for adult neural regeneration in zebrafish, and our characterization of a mutant completely lacking this cell population provides a rich model to further examine and understand the functions of this well-studied but poorly understood cell population. These findings have both functional and evolutionary implications for the relative roles of these two vertebrate specific atypical Notch ligands.

L'atmosphère terrestre est un milieu très complexe, perpétuellement en interaction, dont sa composition est fortement influencée par les activités humaines qui émettent de nombreux composés. Peu d'études liées aux émissions de composés organiques volatils (COV) en air intérieur à partir des sources de combustion (différents modes de chauffage, cuisine, ...) ont été conduites à ce jour. En effet, l'utilisation de cheminées ne peut que s'accentuer ces prochaines années compte tenu de l'augmentation importante du coût du pétrole et de la valorisation du bois en tant que source alternative. Une partie de la carence en études dans de domaine est liée au manque de techniques analytiques permettant d'accéder aux composés émis à des niveaux très faibles.Le travail entrepris a pour principal objectif l'évaluation de l'impact des émissions de COV dû à la combustion du bois, plus particulièrement dans les atmosphères intérieures. Afin de mieux appréhender le rôle des composés émis sur la qualité de l'air et la santé, une étude cinétique de photodégradation d'un traceur spécifique de la combustion a été réalisée : le créosol. Ainsi après avoir étudié les possibilités de nouveaux supports analytiques à base de nanostructures de carbone (NSC) nous nous sommes attachés à évaluer les caractéristiques des émissions de différents foyers individuels à bois. Cette étude a montré qu'il était possible d'isoler certains composés « traceurs » en relation avec le type de combustion et l'essence de bois brûlé. Les NSC ont montré des qualités analytiques inégales à ce jour et demande encore des études complémentaires. Un traceur type : le créosol, à été mis en évidence dont son étude cinétique a montré qu'il était très réactif avec une constante très élevée et qu'il était à l'origine de composés secondaires parfois plus toxiques pour la santé humaine (composés oxydés).

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This thesis sets out to address the challenges with the comparison of Amphetamine material in determining whether they originate from the same source or different sources using pairwise ratios of peak areas within each chromatogram of material and then modeling the difference between the ratios for each comparison as a basis for evaluation. The evaluation of an existing method that uses these ratios to determine the sum of significant differences between each comparison of material that is provided is done. The outcome of this evaluation suggests that there the distributions for comparison of samples originating from the same source and the comparison of samples originating from different sources have an overlap leading to uncertainties in conclusions. In this work, the differences between the ratios of peak areas have been modeled using a feature-based approach. Because the feature space is quite large, Discriminant Analysis methods such as Linear Discriminant Analysis (LDA) and Partial least squares Discriminant Analysis (PLS-DA) have been implemented to perform classification by dimensionality reduction. Another popular method that works on the principle of nearest centroid classifier called as Nearest shrunken centroid is also applied that performs classification on shrunken centroids of the features. The results and analysis of all the methods have been performed to obtain the classification results for classes +1 (samples originate from the same source) and  ́1 (samples originate from different sources). Likelihood ratios of each class for each of these methods have also been evaluated using the Empirical Cross-Entropy (ECE) method to determine the robustness of the classifiers. All three models seem to have performed fairly well in terms of classification with LDA being the most robust and reliable with its predictions.

Many human tumors harbor persistently-active Signal Transducer and Activator of Transcription (ST AT)3 protein. There is substantial evidence that aberrantly-active STAT3 is a master regulator of events that promote carcinogenesis and human tumor formation. Abnormal STAT3 activity induces uncontrolled growth and survival of cells, thereby contributing to neoplastic transformation and progression. Cisplatin is a major chemotherapeutic modality for ovarian cancer, but is frequently challenged by drug resistance. Given that STAT3 is aberrantly-active in many human tumors, including ovarian cancer, there is the potential that it contributes to the development of Cisplatin resistance, a problem ripe for investigation. This study was conducted to explore the potential that the aberrant STAT3 present in ovarian cancer cells contributes to the decreased sensitivity to Cisplatin observed for ovarian cancer cells. The investigation revealed that STAT3 is aberrantly activated in cancer cell lines resistant to Cisplatin, but not in sensitive cells. Inhibition of aberrant STAT3 activity by the small-molecule STAT3 inhibitor, NSC 74859, increased growth inhibition induced by Cisplatin in resistant ovarian cancer cells. Furthermore, NSC 74859 enhanced apoptosis induced by Cisplatin in resistant cells in vitro by nearly 52%. Collectively, these observations indicate that inhibition of hyperactive STAT3 increases Cisplatin sensitivity, and therefore effectiveness, in resistant cells. Thus, STAT3 represents a viable target for enhancing the sensitivity of ovarian cancer cells to Cisplatin.

Une activité germinale persiste après la naissance dans des niches spécialisées du cerveau des mammifères, à savoir le gyrus denté de l'hippocampe et la zone sous-ventriculaire (SVZ) bordant le ventricule latéral. Les cellules souches neurales (NSC) de la SVZ postnatale se différencient en progéniteurs transitoires qui vont générer des neuroblastes migrant à travers la voie de migration rostrale vers le bulbe olfactif, où ils se différencient en neurones. La SVZ génère également des progéniteurs gliaux qui se dispersent dans le parenchyme voisin. Les travaux récents auxquels j'ai participé soulignent la nature hétérogène de la SVZ postnatale, composée de différents microdomaines générant des lignées neurales distinctes. Les objectifs de mon travail de thèse ont permis de : 1) développer de nouveaux moyens pour explorer l'hétérogénéité de la SVZ; et 2) d'identifier et d'étudier le rôle d'un facteur de transcription exprimé par une sous population des NSCs de la SVZ. Objectif 1: La SVZ est une région hautement complexe et irrégulière dans laquelle une forte activité germinale persiste après la naissance. Le caractère hétérogène de la SVZ est évident et des études récentes ont généré une très grande base de données de transcrits, qui sont différentiellement exprimés entre les microdomaines. Cependant, un outil approprié pour l'analyse rapide du niveau d'expression d'une protéine d'intérêt, le long des axes rostro-caudal et dorso-ventral de la SVZ est toujours manquant et nécessaire. Par conséquent, j'ai développé "FlashMap", un logiciel semi-automatique qui permet une analyse rapide des niveaux d'expression de protéines dans le SVZ, basé sur des mesures de densité optique après immunohistochimie. "FlashMap" génère des cartes thermiques facilement lisibles en deux dimensions, qui peuvent être superposées avec précision aux reconstructions tridimensionnelles du système ventriculaire pour une visualisation spatiale fine et rapide. Cette nouvelle approche accélérera la recherche sur la régionalisation de la SVZ, en permettant l'identification de marqueurs (e.g. facteurs de transcription) exprimés dans des régions discrètes de la SVZ. Objectif 2: J'ai utilisé des approches de transcriptomique et de « fate mapping » des NSCs pour étudier la relation entre l'expression régionale de facteurs de transcription et leur différenciation dans des lignées neurales distinctes. Mes résultats supportent un amorçage précoce des NSCs à produire différents types cellulaires en fonction de leur localisation spatiale dans la SVZ. Nos données identifient Hopx comme un marqueur d'une sous population de NSCs qui génère principalement des astrocytes. De façon intéressante, la manipulation de l'expression de Hopx montre des effets mineurs sur l'astrogénèse, mais entraîne des changements marqués quant au nombre de NSCs et de leur descendance. Dans son ensemble, Mes résultats mettent en évidence à la fois une hétérogénéité spatiale des NSCs postnatales ainsi que leur amorçage précoce à produire des types cellulaires distincts / Germinal activity persists in the postnatal mammalian brain in specialized niches, namely the dentate gyrus of the hippocampus and the subventricular zone (SVZ) surrounding the lateral ventricle. Neural stem cells (NSCs) of the postnatal SVZ differentiate into transient amplifying progenitors that will generate neuroblasts migrating through the rostral migratory stream, into the olfactory bulb, where they differentiate into neurons. The SVZ additionally generates glial progenitors that invade the nearby parenchyma. Recent work to which I have participated, highlights the heterogeneous nature of the postnatal SVZ in respect to different microdomains generating distinct neural lineages. The objectives of my PhD work were twice: 1) to develop new means to explore the heterogeneity of the SVZ; and 2) to identify transcription factors expressed by subpopulations of NSCs of the SVZ and acting in their differential specification. Objective 1: The SVZ is a highly complex and irregular region of ongoing postnatal germinal activity. The heterogeneous character of the SVZ is evident and recent studies generated enormous datasets of transcripts, which are differentially expressed between divergent microdomains. However, an appropriate tool for fast analysis of the protein level along the full rostro-caudal and dorso-ventral extend of the SVZ is still missing. Therefore, I developed “FlashMap”, a semi-automatic software that allows rapid analysis of protein levels in the full SVZ, based on optical density measurements after immunohistochemistry. “FlashMap” generates easy readable heatmaps in two dimensions, which can be accurately superimposed on three-dimensional reconstructions of the ventricular system for rapid spatial visualization and analysis. This new approach will fasten research onto SVZ regionalization, by guiding the identification of markers, such as transcription factors expressed in specific SVZ microdomains. Objective 2: I used transcriptomic as well as fate mapping approaches to investigate the relation between regional expression of transcription factors by NSCs and their acquisition of distinct neural lineage fates. Our results support an early priming of NSCs to produce defined cell types depending of their spatial location in the SVZ and identify Hopx as a marker of a subpopulation biased to generate astrocytes. Interestingly, manipulation of Hopx expression showed minor effects on astrogenesis, but resulted in marked changes in the number of NSCs and of their progenies. Taken together, our results highlight transcriptional and spatial heterogeneity of postnatal NSCs, as well as their early priming toward specific lineages and suggest a role for Hopx in the evolution of SVZ germinal activity

Inflammatory bowel disease encompasses a variety of heterogeneous chronic inflammatory diseases that affect the gastrointestinal tract, where Crohn’s disease and ulcerative colitis are the principal examples. The etiology of these, and many other complex human diseases, remain largely unknown and therefore pose relevant targets for novel research strategies. One such strategy is the in silico application of network theory derived methods to data sourced from publicly available repositories of e.g. gene expression data. Specifically, methods generating graphs of interconnected elements enriched by differentially expressed genes—disease modules—were inferred with data available through the Gene Expression Omnibus. Based on a previous method, the current project aimed to evaluate disease modules, combined from stand-alone inferential methods, in disease consensus modules: representing pathophenotypical motifs for the diseases of interest. The modules found to be significantly enriched by genome-wide association study inferred single-nucleotide polymorphisms, as validated using the Pathway Scoring Algorithm, were subsequently subjects for further analysis using Kyoto Encyclopedia of Genes and Genomes-pathway enrichment, and literature searches. The results of this study adheres to previous findings relating to the employed method, but lack any novelty pertaining the diseases of interest. However, the results substantiate the preceding methods’ conclusion by including parameters that increase statistical validity. In addition, the study contributed to peripheral results concerning both the methodology of consensus module methods, and the elucidation of inflammatory bowel disease etiology and disease subtype differentiation, that pose interesting subjects for future investigation.

A complex regulatory framework underlies the generation of newborn neurons in the adult mammalian brain, including the lifelong maintenance of neural stem cell (NSC) quiescence and instructing NSC entry to and exit from quiescence. Future therapies targeting endogenous repair of the aging or afflicted brain, including neurodegenerative pathologies, rely on present efforts to define and characterize the mechanisms underlying the regulation of adult NSC fate. In this dissertation, we demonstrate a requirement for the Rb/E2F axis in the regulation of the molecular program instructing adult NSC quiescence and activation, with a potential role in the impaired hippocampal function observed in Alzheimer's disease pathology. While Rb plays a role in the production and survival of hippocampal newborn neurons, we identify a collective requirement for Rb family proteins — pRb, p107 and p130 — as well as their targets, E2F family transcriptional activators E2F1 and E2F3, in the regulation of NSC quiescence and activation. We further demonstrate that this is mediated through pivotal factors REST and ASCL1, identified as direct molecular targets of the Rb/E2F axis, and that REST inactivation can partially rescue NSC depletion following Rb family loss. We finally demonstrate impaired NSC activation and a return to quiescence in the 3xTG-AD model of Alzheimer's disease, with altered expression of Rb/E2F genes observed within cell population-specific defects. Ultimately, this work addresses the key issue of how transcriptional signatures of quiescence and activation among adult NSCs are co- ordinated with cell cycle control, and demonstrates that Rb family proteins serve as master regulators of the molecular program instructing adult NSC exit from and re-entry into quiescence.