This thesis studies the prolyl-hydroxylase family of 2-oxoglutarate dependent oxygenases from structural, functional and evolutionary perspectives. The role of prolyl-hydroxylation was first identified in collagen, wherein hydroxyproline was found to stabilise the collagen triple helix. In the 1960s, the presence of hydroxyproline in collagen was found to be a result of enzyme catalysed protein modification. An enzyme, now known as collagen prolyl-4-hydroxylase (CP4H), was found to be completely dependent on Fe(II), 2-oxoglutarate (2OG) and molecular oxygen for catalysis, and was the inaugural member of enzyme family known as the Fe(II) and 2OG-dependent oxygenases (2OG oxygenases), the members of which have since expanded dramatically – more than 60 2OG oxygenases are predicted to exist in humans alone. It was not until the 21st century that hydroxyproline was found to play roles in human biology beyond its well-characterised role in collagen stabilisation. In animals, cells adapt to low oxygen conditions (hypoxia) via the upregulation of hundreds of target genes as governed by the hypoxia-inducible transcription factor (HIF). The mammalian hypoxic sensing system was discovered to be regulated by a conserved family of hypoxia-inducible factor prolyl-hydroxylases (PHDs or EGLNs), which catalyse the prolyl-4-hydroxylation of a conserved proline residue in HIF-α under normoxic conditions, so targeting HIF-α for proteasomal degradation via the von Hippel-Lindau (pVHL) E3 ubiquitin ligase pathway. As a result, the PHDs are current therapeutic targets for the treatment of anemia and ischemia-related diseases. Thus, hydroxyproline also plays a critical role in mammalian oxygen sensing. However, the discovery also raised the question of the evolutionary origin of these enzymes and what roles, if any, they may play in other organisms. This thesis begins by describing the identification and biochemical characterisation of the first homologue of the human PHDs in prokaryotes, specifically, in Pseudomonas species, which contains pathogens such as P. aeruginosa. Pseudomonas PHD (PPHD) was discovered to catalyse the prolyl-hydroxylation of a conserved region of elongation factor Tu (EF-Tu), a translational GTPase universally conserved in prokaryotes and known for its critical role in bacterial translation. A crystal structure of PPHD, the first of a prokaryotic prolyl-hydroxylase, was then determined, revealing a striking structural homology of PPHD to the human PHDs. The further determination of crystal structures of Pseudomonas EF-Tu and a PPHD:EF-Tu protein-protein complex, the first of any 2OG oxygenase in complex with its full-length protein substrate, provides important insights into the substrate recognition mechanisms of both the CP4Hs and the PHDs and reveals an evolutionarily conserved pathway of substrate recognition that extends to prokaryotes and will be useful in the design of selective inhibitors of the PHDs. Differences were investigated between the PHDs and a recently discovered subfamily of eukaryotic prolyl-3-hydroxylases, which catalyse the hydroxylation of a conserved proline residue in the small ribosomal subunit S23 (RPS23) and have been implicated in translation accuracy and the stress response. Crystal structures of the RPS23 hydroxylases human OGFOD1 and yeast Tpa1 in complex with 2OG-mimetic inhibitors provide insight into their evolutionary origins. Analyses of the structures will be useful for targeting either OGFOD1 or the PHDs for human therapy. The thesis then describes work on human CP4H, a 240 kDa α2β2 heterotetramer. A novel expression and purification protocol is described for the CP4H complex in addition to the first known reports of its crystallisation and diffraction. Further, the foundations of a high-throughput inhibition assay of the human CP4Hs is presented and will be of immediate interest for assaying inhibitors of the human PHDs in clinical trials, some of which are also predicted to inhibit the CP4Hs. In closing, the thesis attempts to synthesise the results presented in order to provide further insight into the question of the ancestral origins of the prolyl-hydroxylases, a family of enzymes whose range of functions and biological roles likely will continue to expand.

Nanotechnology is the science and technology of manipulating materials at atomic and molecular scale with properties different from bulk. Semiconductor QDs are important class of nanomaterials with unique physical and chemical properties owing to the quantum confinement effect. Size dependent optical properties make research on semiconductor QDs more attractive in the field of nanotechnology. Semiconductor QDs are usually composed of combination of elements from groups II–VI, III–V, or IV–VI of the periodic table. Group II-VI semiconductor QDs (ZnS, ZnSe, ZnO, CdSe, CdS) are most extensively studied systems, having bandgap which can be engineered through the variation of the material composition and size. Most common QDs are made of CdE (E=S, Se, Te) which are toxic. Recent environmental regulations restrict the use of toxic metals and therefore QDs containing nontoxic metals such as Zn are of great importance. The chemical synthesis of QDs involves different methods. Usually high temperature thermal decomposition of organometallic compounds in high boiling point organic solvents is used which needs long reaction time and involves complex synthesis procedures. New simpler and efficient synthetic routes with alternative solvents are required. Recently the synthesis of non-toxic QDs using green chemical routes is a promising approach receiving increasing attention. The aim of this Thesis is to develop novel routes for synthesis of semiconductor QDs employing green nanomaterial synthesis techniques. Therefore, in this work, we developed different green chemical routes mainly for the synthesis Zn-based QDs. Low temperature synthesis routes were developed for the synthesis of ZnS and ZnO QDs. Microwave irradiation was also used as efficient heating source which creates numerous nucleation sites in the solution, leading to the formation of homogeneous nanoparticles with small size and narrow size distribution. Different polar solvents with high MW absorption were used for synthesis of ZnS QDs. We also introduced ionic liquids as solvents in the synthesis of ZnS QDs using microwave heating. ILs are excellent reaction media for absorbing microwaves and are recognized as ‘green’ alternative to volatile and toxic organic solvents. For ZnS systems, the QDs produced by different methods were less than 5 nm in size as characterized by high-resolution transmission electron microscopy (HR-TEM). Selected area electron diffraction (SAED) patterns revealed that ZnS QDs synthesized by low temperature synthesis technique using conventional heating are of cubic crystalline phase while the QDs synthesized by using MW heating are of wurtzite phase. The optical properties were investigated by UV-Vis absorption spectrum and show a blue shift in absorption as compared to bulk due to quantum confinement effect. The photoluminescence (PL) spectra of ZnS QDs show different defect states related emission peaks and depend on different synthesis methods, high bandedge related emission is observed for ZnS QDs synthesized by using ionic liquids. ZnO QDs synthesized by low temperature route were found to be less than 4 nm in size and also show a blue shift in their absorption. The PL spectrum show bandedge related emission which is blue shifted compared with bulk with no emission originating from surface defect levels. The results show that QDs are of high crystalline quality with narrow size distribution. A comparative study of using conventional and MW heating in the synthesis of CdSe QDs was performed. The reactions involving microwave heating showed enhanced rates and higher yields. The developed methods involve all principles for green nanomaterials synthesis i.e. design of safer nanomaterials, reduced environmental impact, waste reduction, process safety, materials and energy efficiency. / <p>QC 20121115</p>

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La conception de systèmes embarqués modernes est de plus en plus complexe, car plus de fonctionnalités sont intégrées dans ces systèmes. En même temps, afin de répondre aux exigences de calcul tout en conservant une consommation d'énergie de faible niveau, MPSoCs sont apparus comme les principales solutions pour tels systèmes embarqués. En outre, les systèmes embarqués sont de plus en plus adaptatifs, comme l’adaptabilité peut apporter un certain nombre d'avantages, tels que la flexibilité du logiciel et l'efficacité énergétique. Cette thèse vise la conception sécuritaire de ces MPSoCs adaptatifs. Tout d'abord, chaque configuration de système doit être analysée en ce qui concerne ses propriétés fonctionnelles et non fonctionnelles. Nous présentons un cadre abstraite de conception et d’analyse qui permet des décisions d’implémentation plus rapide et plus rentable. Ce cadre est conçu comme un support de raisonnement intermédiaire pour les environnements de co-conception de logiciel / matériel au niveau de système. Il peut élaguer l'espace de conception à sa plus grande portée, et identifier les candidats de solutions de conception de manière rapide et efficace. Dans ce cadre, nous utilisons un codage basé sur l’horloge abstrait pour modéliser les comportements du système. Différents scénarios d'applications de mapping et de planification sur MPSoCs sont analysés via les traces d'horloge qui représentent les simulations du système. Les propriétés d'intérêt sont l’exactitude du comportement fonctionnel, la performance temporelle et la consommation d'énergie. Deuxièmement, la gestion de la reconfiguration de MPSoCs adaptatifs doit être abordée. Nous sommes particulièrement intéressés par les MPSoCs implémentés sur des architectures reconfigurables de hardware (ex. FPGA tissus) qui offrent une bonne flexibilité et une efficacité de calcul pour les MPSoCs adaptatifs. Nous proposons un cadre général de conception basésur la technique de la synthèse de contrôleurs discrets (SCD) pour résoudre ce problème. L’avantage principal de cette technique est qu'elle permet une synthèse d'un contrôleur automatique vis-à-vis d’une spécification donnée des objectifs de contrôle. Dans ce cadre, le comportement de reconfiguration du système est modélisé en termes d'automates synchrones en parallèle. Le problème de calcul de la gestion reconfiguration vis-à-vis de multiples objectifs concernant, par exemple, les usages des ressources, la performance et la consommation d’énergie est codé comme un problème de SCD . Le langage de programmation BZR existant et l’outil Sigali sont employés pour effectuer SCD et générer un contrôleur qui satisfait aux exigences du système. Finalement, nous étudions deux façons différentes de combiner les deux cadres de conception proposées pour MPSoCs adaptatifs. Tout d'abord, ils sont combinés pour construire un flot de conception complet pour MPSoCs adaptatifs. Deuxièmement, ils sont combinés pour présenter la façon dont le gestionnaire d'exécution conçu dans le second cadre peut être intégré dans le premier cadre de sorte que les simulations de haut niveau peuvent être effectuées pour évaluer le gestionnaire d'exécution. / The design of modern embedded systems is getting more and more complex, as more func- tionality is integrated into these systems. At the same time, in order to meet the compu- tational requirements while keeping a low level power consumption, MPSoCs have emerged as the main solutions for such embedded systems. Furthermore, embedded systems are be- coming more and more adaptive, as the adaptivity can bring a number of benefits, such as software flexibility and energy efficiency. This thesis targets the safe design of such adaptive MPSoCs. First, each system configuration must be analyzed concerning its functional and non- functional properties. We present an abstract design and analysis framework, which allows for faster and cost-effective implementation decisions. This framework is intended as an intermediate reasoning support for system level software/hardware co-design environments. It can prune the design space at its largest, and identify candidate design solutions in a fast and efficient way. In the framework, we use an abstract clock-based encoding to model system behaviors. Different mapping and scheduling scenarios of applications on MPSoCs are analyzed via clock traces representing system simulations. Among properties of interest are functional behavioral correctness, temporal performance and energy consumption. Second, the reconfiguration management of adaptive MPSoCs must be addressed. We are specially interested in MPSoCs implemented on reconfigurable hardware architectures (i.e., FPGA fabrics), which provide a good flexibility and computational efficiency for adap- tive MPSoCs. We propose a general design framework based on the discrete controller syn- thesis (DCS) technique to address this issue. The main advantage of this technique is that it allows the automatic controller synthesis w.r.t. a given specification of control objectives. In the framework, the system reconfiguration behavior is modeled in terms of synchronous parallel automata. The reconfiguration management computation problem w.r.t. multiple objectives regarding e.g., resource usages, performance and power consumption is encoded as a DCS problem. The existing BZR programming language and Sigali tool are employed to perform DCS and generate a controller that satisfies the system requirements. Finally, we investigate two different ways of combining the two proposed design frame- works for adaptive MPSoCs. Firstly, they are combined to construct a complete design flow for adaptive MPSoCs. Secondly, they are combined to present how the designed run-time manager by the second framework can be integrated into the first framework so that high level simulations can be performed to assess the run-time manager.