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<p>Viruses depend on their hosts for the production and spread of new virus particles. For efficient virus replication, the viral genes have adapted the strategy of being recognized and processed by the cellular biosynthetic machineries. Viruses therefore provide an important tool to study the cellular machinery regulating gene expression. In this thesis, we have used two model DNA viruses; herpes simplex virus (HSV) and adenovirus, to study RNA processing at the level of pre-mRNA splicing in mammalian cells. </p><p>During a lytic infection, HSV cause an almost complete shut-off of host cell gene expression. Importantly, HSV infection cause inhibition of pre-mRNA splicing which is possibly advantageous to the virus, as only four HSV genes contain introns. </p><p>The HSV immediate early protein, ICP27, has been shown to modulate several post-transcriptional processes such as polyadenylation and pre-mRNA splicing. We have studied the role of ICP27 as an inhibitor of pre-mRNA splicing.</p><p>We show that ICP27 inhibits pre-mRNA splicing <i>in vitro</i> in the absence of other HSV proteins. We further show that ICP27 inhibits splicing at the level of spliceosome assembly. Importantly, ICP27 induced inhibition of splicing can be reversed, either by the addition of purified SR proteins or by the addition of an SR protein specific kinase, SRPK1. We propose that SR proteins are prime candidates as mediators of the inhibitory effect of ICP27 on pre-mRNA splicing. </p><p>In order to learn more about how splicing is organized in the cell nucleus <i>in vivo</i>, we investigated how cellular splicing factors are recruited to sites of transcription and splicing in adenovirus infected cells using confocal microscopy. Our results showed that the SR proteins, ASF/SF2 and SC35, are efficiently recruited to sites in the nucleus where adenovirus genes are transcribed and the resulting pre-mRNAs are processed. Our results demonstrate that only one of the two RNA recognition motifs (RRMs) present in the ASF/SF2 protein is required for its recruitment to active sites of splicing. The arginine/serine rich (RS) domain in ASF/SF2 is redundant and insufficient for the translocation of the protein to active viral polymerase II genes in adenovirus infected cells.</p>

Transcription and DNA replication of herpes simplex virus type 1 (HSV-1) occur in nuclear domains adjacent to structures named ND10. The HSV-1 single-stranded DNA binding protein ICP8 localizes to these nuclear domains to direct the assembly of the pre- and replication compartments. Inhibition of cyclin dependent kinases with roscovitine inhibits HSV-1 DNA replication, even in the presence of all required HSV-1 proteins, at an unidentified step. Here I show that roscovitine inhibits the localization of pre-expressed ICP8 to new replication sites. Therefore, the inhibition of HSV-1 DNA replication occurs at a step prior to initiation. I next evaluated the mechanisms of inhibition of proper ICP8 localization. ICP8 was extracted at lower salt concentrations from roscovitine-treated than untreated cells, but the affinity of ICP8 for ssDNA in vitro was not affected. I propose that roscovitine inhibits HSV-1 DNA replication by inhibiting DNA accessibility. I also discuss alternative mechanisms.

Nous étudions, dans la première partie de notre thèse, les polysimplexes d’un espace euclidien de dimension quelconque, c’est-à-dire les objets consistant en une juxtaposition de simplexes réguliers (de tétraèdres si la dimension est 3) accolés le long de leurs faces. Nous étudions principalement le groupe des symétries de ces polysimplexes. Nous présentons une façon de représenter un polysimplexe à l’aide d’un diagramme. Ceci fournit une classification complète des polysimplexes à similitude près. De plus, le groupe des symétries se déduit du groupe des automorphismes du diagramme. Il découle en particulier de notre étude qu’en dimension supérieure à 2, une telle structure ne possède jamais deux faces parallèles et ne contient jamais de circuit fermé de simplexes. Dans la seconde partie de notre thèse, nous abordons un problème classique de combinatoire : l’énumération des pavages d’un rectangle mxn à l’aide de dominos. Klarner et Pollack ont montré qu’en fixant m la suite obtenue vérifie une relation de récurrence linéaire à coefficients constants. Nous établissons une nouvelle méthode nous permettant d’obtenir la fonction génératrice correspondante et la calculons pour m <= 16, alors qu’elle n’était connue que pour m <= 10.

Die Dissertation untersucht die Entwicklung der prosodischen Struktur von Simplizia und Komposita im Deutschen. Ausgewertet werden langzeitlich erhobene Produktionsdaten von vier monolingualen Kindern im Alter von 12 bis 26 Monaten. Es werden vier Entwicklungsstufen angenommen, in denen jedoch keine einheitlichen Outputs produziert werden. Die Asymmetrien zwischen den verschiedenen Wörtern werden systematisch auf die Struktur des Zielwortes zurückgeführt. In einer optimalitätstheoretischen Analyse wird gezeigt, dass sich die Entwicklungsstufen aus der Umordnung von Constraints ergeben und dass dasselbe Ranking die Variation zwischen den Worttypen zu einer bestimmten Entwicklungsstufe vorhersagt. / The thesis investigates the development of the word-prosodic structure in child German. The database consists of longitudinal production data of four monolingal children aged between 12 and 26 months. It is argued in the thesis that the children pass through four developmental stages which are characterized by non-uniform outputs. The asymmetries in the output pattern are attributed to the proosdic shape of the target word. The thesis provides an optimality-theoretic analysis showing that a single ranking of constraints accounts for the variation in the output at a given stage.

Viruses depend on their hosts for the production and spread of new virus particles. For efficient virus replication, the viral genes have adapted the strategy of being recognized and processed by the cellular biosynthetic machineries. Viruses therefore provide an important tool to study the cellular machinery regulating gene expression. In this thesis, we have used two model DNA viruses; herpes simplex virus (HSV) and adenovirus, to study RNA processing at the level of pre-mRNA splicing in mammalian cells. During a lytic infection, HSV cause an almost complete shut-off of host cell gene expression. Importantly, HSV infection cause inhibition of pre-mRNA splicing which is possibly advantageous to the virus, as only four HSV genes contain introns. The HSV immediate early protein, ICP27, has been shown to modulate several post-transcriptional processes such as polyadenylation and pre-mRNA splicing. We have studied the role of ICP27 as an inhibitor of pre-mRNA splicing. We show that ICP27 inhibits pre-mRNA splicing in vitro in the absence of other HSV proteins. We further show that ICP27 inhibits splicing at the level of spliceosome assembly. Importantly, ICP27 induced inhibition of splicing can be reversed, either by the addition of purified SR proteins or by the addition of an SR protein specific kinase, SRPK1. We propose that SR proteins are prime candidates as mediators of the inhibitory effect of ICP27 on pre-mRNA splicing. In order to learn more about how splicing is organized in the cell nucleus in vivo, we investigated how cellular splicing factors are recruited to sites of transcription and splicing in adenovirus infected cells using confocal microscopy. Our results showed that the SR proteins, ASF/SF2 and SC35, are efficiently recruited to sites in the nucleus where adenovirus genes are transcribed and the resulting pre-mRNAs are processed. Our results demonstrate that only one of the two RNA recognition motifs (RRMs) present in the ASF/SF2 protein is required for its recruitment to active sites of splicing. The arginine/serine rich (RS) domain in ASF/SF2 is redundant and insufficient for the translocation of the protein to active viral polymerase II genes in adenovirus infected cells.

L'encéphalite herpétique (EH), causée par l'herpès simplex virus-1 (HSV-1), peut résulter de défauts monogéniques de l'immunité médiée par TLR3. L'induction d'interférons (IFNs)-α/β ou -λ via TLR3 est cruciale à la protection après infection primaire avec HSV-1 dans le système nerveux central (SNC). Nous décrivons deux enfants avec l'EH portant différentes mutations hétérozygotes (D50A et G159A) dans TBK1, encodant TANK-Binding Kinase 1, une kinase aux carrefours de multiples voies de signalisation induisant des IFNs. Les deux allèles mutants de TBK1 sont perte-de-fonction par des mécanismes différents: instabilité de la protéine (D50A) ou perte d'activité kinase (G159A). Ces allèles sont associés à un trait autosomal dominant (AD) par des mécanismes différents: haplotype-insuffisance (D50A) ou dominance négative (G159A). Un défaut de réponses à poly(I:C) par TLR3 est observable dans les fibroblastes hétérozygotes pour G159A, et non pour D50A TBK1. Néanmoins, la réplication virale et la mortalité cellulaire après infection par deux virus dépendants de TLR3 (HSV-1 et VSV) étaient élevées dans les fibroblastes des deux patients. Ces phénotypes peuvent être sauvés par IFN-α2b. De plus, la production d'IFNs en réponse à des agonistes et virus indépendants de TLR3 est maintenue dans les PBMCs et fibroblastes des patients. Le phénotype cellulaire restreint, partiel représente ainsi le phénotype clinique de ces patients, limité à l'EH. Ces données identifient la déficience partielle AD de TBK1 comme une nouvelle étiologie génétique de l'EH de l'enfance, et indiquent que TBK1 est essentiel pour le contrôle de HSV-1 dans le SNC, médié par TLR3 et dépendant des IFNs

Fracture repair is a regenerative event that involves the precise coordination of a variety of cells for successful healing process. Within the microstructure hierarchy of bone repair, the predominant cells involved include the chondrocytes, osteocytes, osteoblasts, and osteoclasts. Although the role of osteoblasts during fracture healing has been previously shown, their role during the initiation phase of endochondral fracture repair remains unclear. In order to study the role of osteoblasts during fracture repair, we used a transgenic mouse model expressing the herpes simplex virus thymidine kinase gene in early differentiating osteoblasts, which allows conditional ablation of cells in osteoblastic lineage upon treatment with the Gancicolvir drug. Results from this study suggest that not only are osteoblasts required in later stages of fracture repair as the medium for bone synthesis, and osteoclast activation during bone remodelling, but could also be required for the initiation and advancement of the endochondral ossification process.

This thesis studies the Reach Control Problem (RCP) for affine systems defined on simplices. The thesis focuses on cases when it is known that the problem is not solvable by continuous state feedback. Previous work has proposed (discontinuous) piecewise affine feedback to resolve the gap between solvability by open-loop controls and solvability by feedbacks. The first results on solvability by time-varying feedback are presented. Time-varying feedback has the advantage to be more robust to measurement errors circumventing problems of discontinuous controllers. The results are theoretically appealing in light of the strong analogies with the theory of stabilization for linear control systems. The method is shown to solve RCP for all cases in the literature where continuous state feedback fails, provided it is solvable by open loop control. Textbook examples are provided. The motivation for studying RCP and its relevance to complex control specifications is illustrated using a material transfer system.

Fracture repair is a regenerative event that involves the precise coordination of a variety of cells for successful healing process. Within the microstructure hierarchy of bone repair, the predominant cells involved include the chondrocytes, osteocytes, osteoblasts, and osteoclasts. Although the role of osteoblasts during fracture healing has been previously shown, their role during the initiation phase of endochondral fracture repair remains unclear. In order to study the role of osteoblasts during fracture repair, we used a transgenic mouse model expressing the herpes simplex virus thymidine kinase gene in early differentiating osteoblasts, which allows conditional ablation of cells in osteoblastic lineage upon treatment with the Gancicolvir drug. Results from this study suggest that not only are osteoblasts required in later stages of fracture repair as the medium for bone synthesis, and osteoclast activation during bone remodelling, but could also be required for the initiation and advancement of the endochondral ossification process.