Chez les eucaryotes, le génome est organisé en chromatine, une structure nucléoprotéique essentielle pour la régulation de l’expression génique ainsi que pour le maintien de la stabilité du génome. Les ciliés sont d’excellents organismes modèles pour étudier les mécanismes généraux qui maintiennent l’intégrité du génomes eucaryote. Chez Paramecium tetraurelia, la différentiation du génome somatique à partir du génome germinal est caractérisée par des événements massifs et reproductibles d’élimination d’ADN. D’une part, des éléments répétés (transposons,régions minisatellites), de plusieurs kilobases de long, sont imprécisément éliminés.D’autre part, 45000 séquences courtes et uniques, appelées IES, sont précisément éliminées au nucléotide près. Une classe de petits ARN, appelé scnRNAs, est impliquée dans la régulation epigénétique de l’élimination d’ADN, mais comment les scnRNA contrôlent l’élimination d’ADN reste mystérieux. Nous avons testé l’hypothèse selon laquelle une organisation particulière de la chromatine, en particulier des modifications post-traductionelles des histones associées à des formes répressives de la chromatine, est impliquée dans le processus d’élimination d’ADN. Nous avons montré que la triméthylation de l’histone H3 sur la lysine 9 et la lysine 27 (H3K9me3 et H3K27me3)apparaît transitoirement dans le noyau somatique en développement au moment où se produisent les événements d’élimination d’ADN. Nous avons identifié la protéine de type Polycomb, Ezl1, et montré qu’elle est une histone methyltransferase qui présente une dualité de substrat et catalyse à la fois la mise en place de K9me3 et K27me3 sur l’histone H3. Nous avons montré que la déposition de H3K9me3 et H3K27me3 dans le noyau en développement requiert les scnRNAs. Des analyses de séquençage haut débit ont montré que Ezl1 est requise pour l’élimination des longues séquences répétées germinales, suggérant que les scnRNA guident la déposition des marques d’histones au niveau de ces séquences. Au contraire des régions répétées du génome, les IES montrent une sensibilité différente aux scnRNAs et à Ezl1, suggérant que plusieurs voies partiellement chevauchantes sont impliquées dans leur élimination. Notre étude montre que des caractéristiques intrinsèques des séquences d’ADN, telles que leur taille, peut contribuer à la définition des séquences germinales à éliminer. De manière intéressante, nous avons aussi montré que Ezl1 est requise pour la répression transcriptionnelle des éléments transposables. Nous suggérons que les voies H3K9me3et H3K27me3 coopèrent et contribuent à préserver le génome somatique de Paramecium des parasites génomiques. / Eukaryotic genomes are organized into chromatin, a complex nucleoprotein structureessential for the regulation of gene expression and for maintaining genome stability.Ciliates provide excellent model organisms with which to gain better understandinginto the regulation of genome stability in eukaryotes. In the ciliate Parameciumtetraurelia, differentiation of the somatic genome from the germline genome ischaracterized by massive and reproducible programmed DNA elimination events. Longregions of several kilobases in length, containing repeated sequences and transposableelements are imprecisely eliminated, whereas 45,000 short, dispersed, single-copyInternal Eliminated Sequences (IESs) are precisely excised at the nucleotide level. Aspecific class of small RNAs, called scnRNAs, is involved in the epigenetic regulation ofDNA deletion. How scnRNAs may guide DNA elimination in Paramecium remains tobe discovered. Here, we investigated whether chromatin structure, in particular histonepost-translational modifications known to be associated with repressive chromatin,might control DNA elimination. We showed that trimethylated lysine 9 and 27 onhistone H3 (H3K9me3 and H3K27me3) appear in the developing somaticmacronucleus when DNA elimination occurs. We identified the Polycomb-groupprotein, Ezl1, and showed that it is a dual histone methyltransferase that catalyzes bothH3K9me3 and H3K27me3 in vitro and in vivo. Genome-wide analyses show thatscnRNA-mediated H3K9me3 and H3K27me3 deposition is necessary for theelimination of long, repeated germline DNA. Conversely, single copy IESs displaydifferential sensitivity to depletion of scnRNAs and Ezl1, unveiling the existence ofpartially overlapping pathways in programmed DNA elimination. Our study revealsthat cis-acting determinants, such as DNA length, also contribute to the definition ofgermline sequences to delete. We further showed that Ezl1 is required fortranscriptional repression of transposable elements. We suggest that H3K9me3 andH3K27me3 pathways cooperate and contribute to safeguard the Paramecium somaticgenome against intragenomic parasites.

Les introns de groupe II forment une classe d'ARN connus avant tout pour leur activité ribozymique, qui leur permet de catalyser leur propre réaction d'épissage. Sous certaines conditions, ces introns peuvent s'exciser des ARN précurseurs dont ils font partie et assurer la ligation des exons qui les bordent sans l'aide d'aucune protéine. Les introns de groupe II sont généralement excisés sous forme d'un lariat, semblable à celui formé par les introns des prémessagers nucléaires, dont l'épissage est assurée par le spliceosome. De telles similarités dans le mécanisme d'épissage suggèrent que les introns de groupe II et les introns des prémessagers nucléaires pourraient avoir un ancêtre évolutif commun.Malgré leurs séquences très diverses, les introns de groupe II peuvent être définis par une structure secondaire commune, hautement conservée. Celle-ci est formée de six domaines (domaine I à domaine VI ; D1-D6), émergeant d'une roue centrale. L'épissage des introns de groupe II comprend deux étapes, et autant de réactions de transestérification, qui produisent les exons liés et l'intron excisé sous forme lariat. Il est généralement admis que la structure du ribozyme subit des changements conformationnels entre les deux étapes de l'épissage et que le domaine VI est un acteur clé dans ce phénomène. Cependant, malgré l'identification d'un certain nombre d'interactions tertiaires entre domaines, ni la RMN, ni les études faisant appel à des modifications chimiques ne sont parvenues à déterminer l'environnement immédiat, au niveau du site actif du ribozyme, de l'adénosine qui sert de point de branchement de la structure en lariat, ainsi que des nucléotides qui entourent cette adénosine au sein du domaine VI. A l'aide d'analyses phylogénétiques et d'une modélisation moléculaire tridimensionnelle, nous avons identifié plusieurs sections du ribozyme susceptibles de constituer le site de fixation du domaine VI au cours de l'étape de branchement. Des mutations ont été introduites dans ces sites de fixation potentiels et la cinétique de réaction des ARN mutants résultants a été déterminée. Afin de démontrer formellement l'interaction du domaine VI avec le site récepteur le plus probable, une molécule de ribozyme dont la réaction de branchement est assurée par l'addition d'oligonucléotides ADN ou ARN qui positionnent correctement le domaine VI vis-à-vis de son partenaire a été construite. En combinant l'information apportée par différentes expériences de ce type, nous avons pu générer un modèle à résolution atomique du complexe formé par le domaine VI, son site de branchement et le reste de l'intron au moment où l'épissage est initié.

Determining the properties of mutations is fundamental to understanding the mechanisms of adaptive evolution. The major goal of this thesis is to investigate the mechanisms of bacterial adaptation to new environments using experimental evolution. Different types of mutations were under investigations with a particular focus on genome rearrangements. Adaptive evolution experiments were focused on the development of bacterial resistance to antibiotics. In paper I, we performed stochastic simulations to examine the role of gene amplification in promoting the establishment of new gene functions. The results show that gene amplification can contribute to creation of new gene functions in nature. In paper II, the evolution of β-lactam resistance was studied by evolving S. typhimurium carrying a β-lactamase gene towards increased resistance against cephalosporins. Our results suggest that gene amplification is likely to provide an immediate solution at the early stage of adaptive evolution and subsequently facilitate further stable adaptation. In paper III, we isolated spontaneous deletion mutants with increased competitive fitness, which indicated that genome reduction could be driven by selection. To test this hypothesis, independent lineages of wild type S. typhimurium were serially passaged for 1000 generations and we observed fixation of deletions that significantly increased bacterial fitness when reconstructed in wild type genetic background. In paper IV, we developed a new strategy combining 454 pyrosequencing technology and a ‘split mapping’ computational method to identify unique junction sequences formed by spontaneous genome rearrangements. A high steady-state frequency of rearrangements in unselected bacterial populations was suggested from our results. In paper V, the rates, mechanisms and fitness effects of colistin resistance in S. typhimurium were determined. The high mutation rate and low fitness costs suggest that colistin resistance could develop in clinical settings. In paper VI, a novel Metallo-β-lactamase (MBL) with low resistance against β-lactam antibiotics was employed as the ancestral protein in a directed evolution experiment to examine how an enzyme evolves towards increased resistance. For most isolated mutants, in spite of their significantly increased resistance, both mRNA and protein levels were decreased as compared with the parental protein, suggesting that the catalytic activity had increased.

The main motivation behind this thesis is the lack of belief subjectivity in problems of contracting, and especially in problems of demand for insurance. The idea that an underlying uncertainty in contracting problems (e.g. an insurable loss in problems of insurance demand) is a given random variable on some exogenously determined probability space is so engrained in the literature that one can easily forget that the notion of an objective uncertainty is only one possible approach to the formulation of uncertainty in economic theory. On the other hand, the subjectivist school led by De Finetti and Ramsey challenged the idea that uncertainty is totally objective, and advocated a personal view of probability (subjective probability). This ultimately led to Savage's approach to the theory of choice under uncertainty, where uncertainty is entirely subjective and it is only one's preferences that determine one's probabilistic assessment. It is the purpose of this thesis to revisit the "classical" insurance demand problem from a purely subjectivist perspective on uncertainty. To do so, we will first examine a general problem of contracting under heterogeneous subjective beliefs and provide conditions under which we can show the existence of a solution and then characterize that solution. One such condition will be called "vigilance". We will then specialize the study to the insurance framework, and characterize the solution in terms of what we will call a "generalized deductible contract". Subsequently, we will study some mathematical properties of collections of vigilant beliefs, in preparation for future work on the idea of vigilance. This and other envisaged future work will be discussed in the concluding chapter of this thesis. In the chapter preceding the concluding chapter, we will examine a model of contracting for innovation under heterogeneity and ambiguity, simply to demonstrate how the ideas and techniques developed in the first chapter can be used beyond problems of insurance demand.

Genome wide studies have uncovered the existence of large-scale copy number variation (CNV) in the human genome. The human genome of different individuals was initially estimated to be 99.9% similar, but population studies on CNV have revealed that it is 12-16% copy number variable. Abnormal genomic CNVs are frequently found in subtelomeres of patients with mental retardation (MR) and other neurological disorders. Rearrangements of chromosome subtelomeric regions represent a high proportion of cytogenetic abnormalities and account for approximately 30% of pathogenic CNVs. Although DNA double strand breaks (DSBs) are implicated as a major factor in chromosomal rearrangements, the causes of chromosome breakage in subtelomeric regions have not been elucidated. But due to the presence of repetitive sequences in subtelomeres, we hypothesized that chromosomal rearrangements in these regions are not stochastic but driven by specific sequence motifs. In a collaborative effort with Dr. Rudd (Department of human genetics at Emory University), we characterized subtelomeric breakpoints on different chromosome ends in search of common motifs that cause double-strand breaks. Using a yeast-based gross chromosomal rearrangement (GCR) system, we have identified a subtelomeric breakage motif from chromosome 2 (2q SBM) with a GCR rate that is 340 fold higher than background levels. To determine if the fragility of 2q SBM was driven by the formation of secondary structures, the helicase activities of Sgs1 and Pif1 were disrupted. These helicases have been shown to destabilize DNA secondary structures such as G-quadruplex structures. Disruption of these helicases augmented chromosomal rearrangements induced by 2q SBM, indicating that these helicases are required for maintenance of this sequence. We also donwregulated replication fork components to determine if 2q SBM was imposing any problems to the replication fork machinery. Downregulation of replication fork components increased chromosomal rearrangements, indicating that intact replication fork was a critical determinant of 2q SBM fragility. Using a yeast-based functional assay, these experiments have linked human subtelomeric repetitive sequences to chromosomal breakage that could give rise to human CNV in subtelomeric regions.

The main motivation behind this thesis is the lack of belief subjectivity in problems of contracting, and especially in problems of demand for insurance. The idea that an underlying uncertainty in contracting problems (e.g. an insurable loss in problems of insurance demand) is a given random variable on some exogenously determined probability space is so engrained in the literature that one can easily forget that the notion of an objective uncertainty is only one possible approach to the formulation of uncertainty in economic theory. On the other hand, the subjectivist school led by De Finetti and Ramsey challenged the idea that uncertainty is totally objective, and advocated a personal view of probability (subjective probability). This ultimately led to Savage's approach to the theory of choice under uncertainty, where uncertainty is entirely subjective and it is only one's preferences that determine one's probabilistic assessment. It is the purpose of this thesis to revisit the "classical" insurance demand problem from a purely subjectivist perspective on uncertainty. To do so, we will first examine a general problem of contracting under heterogeneous subjective beliefs and provide conditions under which we can show the existence of a solution and then characterize that solution. One such condition will be called "vigilance". We will then specialize the study to the insurance framework, and characterize the solution in terms of what we will call a "generalized deductible contract". Subsequently, we will study some mathematical properties of collections of vigilant beliefs, in preparation for future work on the idea of vigilance. This and other envisaged future work will be discussed in the concluding chapter of this thesis. In the chapter preceding the concluding chapter, we will examine a model of contracting for innovation under heterogeneity and ambiguity, simply to demonstrate how the ideas and techniques developed in the first chapter can be used beyond problems of insurance demand.

This thesis is devoted to the study of mixed norm spaces that arise in connection with embeddings of Sobolev and Besov type spaces. We study different structural, integrability, and smoothness properties of functions satisfying certain mixed norm conditions. Conditions of this type are determined by the behaviour of linear sections of functions. The work in this direction originates in a paper due to Gagliardo (1958), and was further developed by Fournier (1988), by Blei and Fournier (1989), and by Kolyada (2005). Here we continue these studies. We obtain some refinements of known embeddings for certain mixed norm spaces introduced by Gagliardo, and we study general properties of these spaces. In connection with these results, we consider a scale of intermediate mixed norm spaces, and prove intrinsic embeddings in this scale. We also consider more general, fully anisotropic, mixed norm spaces. Our main theorem states an embedding of these spaces to Lorentz spaces. Applying this result, we obtain sharp embedding theorems for anisotropic Sobolev-Besov spaces, and anisotropic fractional Sobolev spaces. The methods used are based on non-increasing rearrangements, and on estimates of sections of functions and sections of sets. We also study limiting relations between embeddings of spaces of different type. More exactly, mixed norm estimates enable us to get embedding constants with sharp asymptotic behaviour. This gives an extension of the results obtained for isotropic Besov spaces by Bourgain, Brezis, and Mironescu, and for anisotropic Besov spaces by Kolyada. We study also some basic properties (in particular the approximation properties) of special weak type spaces that play an important role in the construction of mixed norm spaces, and in the description of Sobolev type embeddings. In the last chapter, we study mixed norm spaces consisting of functions that have smooth sections. We prove embeddings of these spaces to Lorentz spaces. From this result, known properties of Sobolev-Liouville spaces follow.

Typescript (Processed) / Errata slip inserted. / Spine title: Studies in collisional energy transfer of highly excited molecules. / Bibliography: leaves 143-167. / viii, 169 leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This thesis describes the studies made on several unimolecular reaction systems in order to obtain collisional energy transfer information on highly excited polyatomic molecules. Pressure-dependant very low-pressure pyrolysis (VLPP) and infrared multiphoton decomposition (IRMPD) experimental techniques are used. / Thesis (Ph.D.)--University of Adelaide, 1989

Thesis (Ph. D.)--Ohio State University, 2007. / Title from first page of PDF file. Includes bibliographical references (p. 440-459).

Thesis (Ph.D.)--McMaster University (Canada), 1994. / Source: Dissertation Abstracts International, Volume: 56-01, Section: B, page: 0240. Supervisor: M. J. McGlinchey.