Performance is something that is always of concern when developing real-time 3D graphics applications. The way programs are made today with object-oriented programming has certain flaws that are rooted in the methodology itself. By exploring different programming paradigms we can eliminate some of these issues and find what is best for programming in different areas. Because real-time 3D applications need high performance the data-oriented design paradigm that makes the data the center of the application is experimented with. By using data-oriented design we can eliminate certain issues with object-oriented programming and deliver improved applications when it comes to performance, flexibility, and architecture. In this study, an experiment creating the same type of program with the help of different programming paradigms is made to compare the performance of the two. Some additional up- and downsides of the paradigms are also mentioned / <p>Det finns övrigt digitalt material (t.ex. film-, bild- eller ljudfiler) eller modeller/artefakter tillhörande examensarbetet som ska skickas till arkivet.</p>

Runtime performance is essential for real time games, the faster a game can run the more features designers can put into the game to accomplish their vision.A popular architecture for video games is the Entity Component System architecture aimed to improve both object composition and performance. There are many tests for how this architecture performs under its optimal linear execution.This thesis presents a performance comparison of how several popular open-source Entity Component System libraries perform when fetching data from other entities during iteration. An object-oriented test is also done to compare against and verify if the known drawbacks of object-orientation can still be seen within these test cases. Our results show that doing a random lookup during iteration can cause magnitudes worse performance for Entity Component Systems.

Denna studie jämför två olika 3D-ramverk i form av A-Frame med Entity component system och Babylon.js utan Entity component system för att undersöka hur arkitekturen i ramverket påverkar renderingstiden. För att mäta renderingstiden mäts frames per second på ett utvecklat tower defense spel per ramverk med 3D-grafik i webbläsaren Google Chrome. Detta är i form av ett tekniskt experiment för att utesluta utomstående variabler. Det utvecklades tre nivåer av komplexitet inom spelen för att undersöka hur komplexiteten påverkar renderingshastigheten men efter mätningarna visade det sig att de olika nivåerna av komplexitet i artefakterna hade ingen signifikant påverkan på resultatet. Dock fanns det en signifikant skillnad mellan de olika ramverken där A-Frame med Entity component system fick sämre resultat. För vidare arbeten behöver antalet webbläsare i experimentet utökas samt en högre nivå av komplexitet testas för att få mer verklighetstrogna resultat. / <p>Stavningsvarierade titlar på svenska och engelska:</p><p>Prestandajämförelse mellan webbaserade 3D-ramverk med olika arkitekturer</p><p>Performance comparison between web-based 3D frameworks using different architectures</p>

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Legionella pneumophila est un pathogène intracellulaire, agent de la Légionellose, et dont le réservoir dans l’environnement est constitué d’amibes aquatiques comme Acanthamoeba castellani. Mes objectifs de thèse étaient l’identification de mécanismes moléculaires contrôlant la virulence et la multi-résistance chez L. pneumophila, et en particulier l’exploration du rôle des protéines « GGDEF/EAL ». Les domaines GGDEF et EAL sont retrouvés dans des enzymes permettant respectivement de synthétiser (diguanylate cyclase, DGC) ou dégrader (phosphodiestérase, PDE) le di-GMP cyclique, un second messager spécifique des bactéries, qui participe au contrôle de fonctions clés comme la virulence ou la mobilité. L. pneumophila Lens possède 22 gènes codant des protéines GGDEF/EAL, et dont la plupart sont exprimés lorsqu’elle est dans sa phase virulente. L’activité enzymatique des 22 protéines « GGDEF/EAL » a été analysée in vitro : sur 10 protéines purifiées, 6 sont des DGC, dont 2 présentes une double activité DGC/PDE. L’inactivation de 5 gènes des 22 gènes et la surexpression de 2 autres entrainent une baisse de la virulence vis-à-vis d’A. castellanii. De plus, nous avons montré que l’activité DGC d’au moins 2 de ces protéines est requise lors du cycle infectieux. Enfin, nous avons décrit un système à deux composants original comprenant l’histidine kinase (HK) Lpl0330, capable de s’autophosphoryler sur un nouveau domaine HisKA, retrouvé dans 64 autres HK potentielles, et Lpl0329, le premier régulateur de réponse à double activité enzymatique caractérisé, dont la phosphorylation conduit à moduler le taux de di‐GMPc en favorisant une de ses deux activités (Levet-Paulo et al., 2011). / Legionella pneumophila is an intracellular pathogen found in aquatic environments where it replicates in protozoan hosts. My objectives were to identify molecular mechanisms that control virulence and multidrug resistance in L. pneumophila, and especially to explore the role of proteins “GGDEF/EAL” in virulence. GGDEF and EAL domains are found in enzymes able to synthesize (diguanylate cyclase, DGC) or degrade (phosphodiesterase, PDE) c-di-GMP, respectively. C-di-GMP is a bacterial second messenger which plays a key role in regulating main functions including motility, and virulence. L. pneumophila Lens contains 22 genes encoding GGDEF/EAL proteins and most of them are expressed simultaneously with genes encoding virulence factors. The enzymatic activities of the 22 GGDEF/EAL proteins of L. pneumophila Lens were assayed in vitro. Among the 10 proteins purified, 6 showed a DGC activity and 2 contained both activities. The role of the GGDEF/EAL proteins of L. pneumophila Lens on virulence was investigated. Inactivation of 5 genes and overexpression of 2 other genes led to a significant decrease in virulence. Moreover, DGC activity of at least two of these proteins is required for bacterial virulence. Finally, an original two-component system was identified comprising Lpl0330, a histidine kinase able to autophosphorylate on a new HisKA domain, and Lpl 0329, a protein with dual in vitro DGC/PDE activity. Phosphorylation of Lpl0329 led to a decrease in its DGC activity only, giving the first example of a bifunctional enzyme which modulates synthesis and turnover of c-di-GMP in response to phosphorylation (Levet-Paulo et al., 2011).

[pt] A implantação de aplicações baseadas em componentes distribuídos é composta por um conjunto de atividades geridas por uma Infraestrutura de Implantação. Aplicações atuais estão se tornando cada vez mais complexas, necessitando de um ambiente alvo dinâmico e multi-plataforma. Assim, a atividade de planejamento de uma implantação é o passo mais crítico, pois define a configuração da infraestrutura de execução de forma a atender os requisitos do ambiente alvo de uma aplicação. Por outro lado, o modelo de serviço na nuvem chamado Infraestrutura como Serviço(IaaS) oferece recursos computacionais sob demanda, com características dinâmicas, escaláveis e elásticas. Nesta dissertação nós estendemos a Infraestrutura de Implantação para componentes SCS de forma a permitir o uso de nuvens privadas ou públicas como o ambiente alvo de uma implantação, através do uso de uma cloud API e políticas flexíveis para especificar um ambiente alvo personalizado. Além disso, hospedamos a infraestrutura de implantação na nuvem. Isto permitiu-nos usar recursos computacionais sob demanda para instanciar os serviços da Infraestrutura de Implantação, produzindo uma Plataforma como Serviço(PaaS) experimental. / [en] Deployment of distributed component-based applications is composed of a set of activities managed by a Deployment Infrastructure. Current applications are becoming increasingly more complex, requiring a multi-platform and a dynamic target environment. Thus, the planning activity is the most critical step because it defines the configuration of the execution infrastructure in order to satisfy the requirements of the application’s target environment. On the other hand, the cloud service model called Infrastructure as a Service (IaaS) offers on-demand computational resources with dynamic, scalable, and elastic features. In this work we have extended the Deployment Infrastructure for SCS componentes to support private or public clouds as its target environment, through the use of a cloud API and flexible policies to specify a customized target environment. Additionally, we host the Deployment Infrastructure on the cloud, which allow us to use on-demand computational resources to instantiate Deployment Infrastructure services, creating an experimental Platform as a Service (PaaS).

Salmonella spp. sind fakultative intrazelluläre Pathogene, die gastrointestinale und systemische Erkrankungen in einem umfassenden Wirtsbereich, einschließlich Tier und Mensch, hervorrufen. Salmonella benötigt verschiedene Virulenzgene für die Infektion welche auf sogenannten Salmonella Pathogenitäts-Inseln (SPI) kodiert sind. Hinzu kommt, dass auch zahlreiche im Salmonella Genom verstreuten Gene an verschiedenen Aspekten von Virulenz und Pathogenese beteiligt sind. In der vorliegenden Studie wurde die Funktion eines zuvor nicht beschriebenen putativen transkriptionellen Regulators (STM0029) charakterisiert und definiert. Dieser scheint für die Abwehr von zellulären bakterizid wirkenden Verbindungen und das Überleben des Bakteriums innerhalb einer intrazellulären Nische von entscheidender Bedeutung zu sein. Die STM0029-deletierte Mutante wies eine gesteigerte Sensitivität gegenüber antimikrobiellen Peptiden und bakteriziden Verbindungen auf. Dazu zählten α-Defensin-1, β- Defensin-1, β-Defensin-2, LL-37 und Polymyxin B sowie Komponenten des Komplementsystems. Unerwartet war die Beobachtung, dass die Expression von STM0029 durch das PmrA/B Zwei Komponenten System reprimiert vorlag, während das PhoP/Q Zwei Komponenten System keinen Einfluss auf die Expression von STM0029 zu scheinen hat. Beide Komponent Systeme spielen bekanntlich eine entscheidende Rolle bei der Expressionsregulation von Genen die für das intrazelluläre Überleben von Salmonella wichtig sind. Bemerkenswert ist, dass ein Set von Genen welche an der Biosynthese und/oder der Modifikation für das LPS O-Antigen sowie des Peptidoglykans in der bakteriellen Zellwand beteiligt ist, im STM0029 Deletionshintergrund herab reguliert vorlag. Dieses Ergebnis deutet darauf hin, dass das STM0029 Genprodukt die Persistenz des Pathogen in Wirtszellen beeinflusst. Möglicherweise geschieht dies durch das Umgehen von wirtseigenen Abwehrmechanismen. / Salmonella spp. are facultative intracellular pathogens, which cause gastrointestinal and systemic diseases in a broad range of hosts including animals and humans. In addition to virulence genes clustered within pathogenicity islands, numerous additional genes scattered throughout the genome are also involved in various aspects of Salmoenlla virulence and pathogenesis. In this study, I identified a Salmonella putative transcriptional regulator encoded by a previously uncharacterized open reading frame designated STM0029. Deletion of STM0029 altered the expression of genes involved in both the resistance to host bactericidal challenges, and bacterial cell wall biosynthesis in S. Tyhpimurium. The ΔSTM0029 strain showed a defect in the resistance to host antimicrobial peptides, including α-defensin-1, β-defensin-1, β-defensin-2, LL-37, and polymyxin B as well as serum challenges compared to the wildtype. Unexpectedly, expression of STM0029 was found to be repressed by the PmrA/B two component system, but appeared to be independent of the PhoP/Q two component system, both of which are well-known regulatory systems involved in the regulation of expression of genes involved in Salmonella intracellular survival. Notably, the expression of a set of genes involved in bacterial LPS O-antigen and peptidoglycan biosyntheses and modifications showed decreases in the absence of STM0029. These experimental results indicate that the STM0029 gene product in S. Typhimurium contributes to resistance against host cell defense mechanisms, likely through regulation of genes involved in LPS O-antigen and peptidoglycan biosynthesis and modifications.

Bacillus subtilis is the model organism for low GC Gram-positive bacteria and is of great biotechnological interest. Protein phosphorylation is an important regulatory mechanism in bacteria and it has not been extensively studied yet. Recent site-specific phosphoproteomic studies identified a large number of novel serine/threonine phosphorylation sites in B. subtilis, including a) two transition phase global gene regulators DegS and AbrB and b) RecA, that plays a major role in double-strand break repair and DNA recombination. .B. subtilis disposes of several putative Ser/Thr kinases like PrkA, YbdM, YabT and a characterizd kinase PrkC, but very few physiological substrates for these have been defined so far. In vitro phosphorylation assays were used to identify which of these kinases were able to phosphorylate DegS, RecA and AbrB. DegS phosphorylation on serine 76 by the kinase YbdM influenced its activity towards DegU both in vitro and in vivo, and expression of DegS S76D( on replacing serine to aspartate) in B. subtilis perturbed cellular processes regulated by the DegS/DegU two component system. This suggests a link between DegS phosphorylation at serine 76 and the level of DegU phosphorylation, establishing this post-translational modification as an additional trigger for this two-component system. At the onset of sporulation, B. subtilis expresses an unusual serine/threonine kinase YabT, which exhibits a septal localization and is activated by non-sequence-specific DNA binding. Activated YabT phosphorylates RecA at the residue serine 2, which in turn promotes the formation of RecA foci at the onset of spore development. On the other hand, non-phosphorylatable RecA or inactivated YabT lead to reduced spore formation in the presence of DNA lesions . This suggests a functional similarity between B. subtilis developmental stage dependent RecA phosphorylation and its eukaryal homologous Rad51 phosphorylation, which leads to its recruitment to the lesion sites. We therefore proposed that RecA phosphorylation serves as an additional signal mechanism that promotes focus formation during spore development. AbrB is phosphorylated by YabT, YbdM and PrkC in vitro and AbrB phosphorylation leads to reduced affinity for its target DNA and abolished binding cooperativity in vitro and in vivo. Expression of the phosphomimetic AbrB-S86D or of the non-phosphorylatable AbrB-S86A mutant protein in B. subtilis disturbed some stationary phase phenomena such as exoprotease production, competence and the onset of sporulation, probably by deregulation of AbrB-target genes and operons. We therefore, proposed that AbrB phosphorylation as an additional regulatory mechanism needed to switch off this ambiactive gene regulator during the transition phase.

Les méthionines sulfoxyde réductases (Msr) sont impliquées dans la réparation des protéines. MsrA et MsrB sont ubiquitaires et réduisent les méthionines sulfoxydes en méthionines. Chez les bactéries, MsrA et MsrB sont localisées dans le cytoplasme et sont impliquées dans la résistance au stress oxydant. Durant ma thèse, j'ai étudié le rôle du système MsrA/B dans la physiologie d'Escherichia coli. Mon travail a porté sur l'étude de la recombinase A (RecA) comme cible du système MsrA/B. RecA joue un rôle central dans la réparation de l'ADN via ses fonctions principales : la recombinaison homologue, l'induction de la réponse SOS et l'induction de la mutagénèse SOS. J’ai pu établir un lien génétique entre le système MsrA/B et RecA. L'étude révèle que l'absence des Msr affecte la fonction de recombinaison homologue de RecA. J'ai montré que RecA oxydée perd sa capacité à former des filaments sur l’ADN, à hydrolyser de l’ATP et à effectuer l’échange de brin. De manière intéressante, la réparation de RecA oxydée par le système MsrA/B permet de restituer ses fonctions. D'autres analyses ont révélé que le résidu Met35 est important pour l’activité de RecA. Ces résultats m'ont permis de proposer un modèle dans lequel l'état d'oxydation des Met de RecA modulent son activité. Un autre pan de mon travail a permis la caractérisation d’une Msr périplasmique : MsrP. J'ai montré que MsrP est importante lors d’un stress HOCl et que son expression est induite lors d’un tel stress via le système à deux composantes YedVW. La kinase YedV possédant plusieurs Met au sein de son domaine senseur, j'ai proposé un modèle dans lequel l'activation de YedV se ferait via l'oxydation de ses Met. / Methionine sulfoxide reductase (Msr) are involved in proteins repair. MsrA and MsrB are ubiquitous enzymes which reduce methionine sulfoxide into methionine. In bacteria, MsrA and MsrB are localized in the cytoplasm and are involved in the resistance to oxidative stress. During my PhD, I investigated the role of the MsrA/B system in the physiology of the Escherichia coli. My work was devoted to the study of the recombinase A (RecA) as the target of MsrA/B system. RecA plays a central role in DNA repair via its main functions: homologous recombination, induction of the SOS response and the induction of the SOS mutagenesis. I was able to establish a genetic link between the MsrA/B system and RecA. My study shows that the absence of Msr affects the homologous recombination function of RecA. I have shown that RecA oxidized loses its ability to form filaments on DNA, to hydrolyze ATP and perform strand exchange process. Interestingly, repair RecA oxidized by MsrA/B system restores the functions of RecA. Further analysis revealed that the residue Met 35 is important for the activity of RecA. From these results, I proposed a model in which the oxidation of Met and repair MsrA/B is a dynamic system modulating the activity of RecA. Another part of my work allowed the characterization of periplasmic Msr of E. coli: MsrP. I have shown that MsrP is important under HOCl stress and its expression is induced during such stress via the YedVW two components system. The YedV kinase possessing multiple Met in its sensor domain, I proposed a model in which the activation of YedV would be by oxidation of its Met.