<p>Virulence in <em>Staphylococcus aureus </em>is mediated by the <em>accessory gene regulator </em>(agr) quorum sensing system. This regulatory system is activated by a secreted thiolactone peptide termed autoinducing peptide (AIP) and its receptor histidine kinase, AgrC. Interaction of extracellular AIP with a cognate AgrC receptor generates an intracellular signal that is transduced by conformational changes and phosphorylation events in a two-component sensor histidine kinase system. At the heart of the <em>agr</em> quorum-sensing cascade lies the two-component histidine kinase, AgrC, and the response regulator protein, AgrA. Interaction of AgrC and AgrA, and the resulting phosphotransfer event results in expression from the divergent promoters P2 and P3, inducing expression of the master quorum-sensing regulator RNAIII and upregulating the <em>agr</em> operon respectively. Signal transduction systems function as intracellular information-processing pathways that link sensation of external stimuli to specific adaptive processes. In <em>S. aureus</em> , these include the up-regulation of virulence factors and hemolysis production, biofilm formation, and colonization-based regulation of surface proteins and adhesion factors. As such, the interactions of these systems have become key targets in the design of small inhibitor compounds.</p> <p>Through the creation of a protein truncation series, we proposed the development of a small protein for the inhibition of key protein-protein interactions involved in <em>S. aureus</em> <em>agr</em> two-component signaling. Herein, we demonstrate the efficacy of these protein truncations as dominant negative inhibitors of AgrC:AgrA interactions, likely acting as a dominant phosphoacceptor in place of endogenous AgrA. We provide evidence of this function through <em>in vitro </em>hemolysis assays and phosphate-detection based gel electrophoresis.</p> / Master of Science (MSc)

The ability of fish to deform their bodies in steady swimming action is gaining from robotic designers. While bound by the same physical laws, fish have evolved to move in ways that often outperform artificial systems in critical measures such as efficiency, agility, and stealth through thousands of years of natural selection. As we expand our presence in the ocean with deep-sea exploration or offshore drilling for petroleum and natural gas, the demand for prolonging underwater operations is growing significantly. Therefore, it is critical for robotic designers to understand the physics of pisciform (fish-like) locomotion and learn how to effectively implement the propulsive mechanisms into their designs to create the next generation of aquatic robots. Aiming to assist this process, this thesis presents an experimental apparatus called Towed Biolocomotion Emulator (TBE), which is capable of imitating the undulating action of different fish species in steady swimming and can be quickly adapted to different configurations with modular modules. Using the TBE device, an experiment is performed to test its hydrodynamic performance and evaluate the effectiveness of the bio-inspired locomotion implemented on such a mechanical system. The analysis of hydrodynamic data collected from the experiment shows that there exists a small range of kinematic parameters where the undulating motion of the device produces the optimal performance. This result confirms the benefits of utilizing pisciform locomotion for small-scale underwater vehicles. In addition, this thesis also proposes a reduced-order flow model using the unsteady vortex lattice method (UVLM) to predict the hydrodynamic performance of such a system. The proposed model is then validated with the experimental data collected earlier. The tool developed can be employed to quickly explore the possible design space early in the conceptual design stage for such a bio-mimetic vehicle. / Master of Science / It is no surprise that through thousands of years of natural evolution, marine species possess incredible ability to navigate through water. As we expand our presence in the sea, more and more tasks require underwater operations such as ocean exploration, oil-rig maintenance, etc. Yet, most of the underwater robotic vehicles still utilize propellers as the primary propulsive mechanism. In many cases, the bio-inspired propulsion system that mimics the swimming action of fish offers many advantages in agility, maneuverability, and stealth. With the rising interest in the field, the works presented in this thesis aim to expand our understanding of how to implement the bio-inspired propulsive mechanism to robotic design. To achieve this, a mechanical device is designed to mimic the swimming action of different fish species. Then, an experiment is performed to subject the device to different fish-like motions and test their effectiveness. In addition, a reduced-ordered model is also introduced as an alternative method to predict the hydrodynamic performance of this propulsive mechanism. The works presented in this thesis help to expand the toolbox available for the engineer to design the next generation of the underwater robotic vehicle.

No / Previous studies in this laboratory have suggested that the isolated uterus from non-pregnant mice has a prostaglandin F and a thromboxane receptor population similar to that found in human myometrium. The aim of this study was to investigate any regional variation in myogenic activity ) and the and responsiveness to prostaglandin F(2alpha) (PGF(2alpha) thromboxane mimetic U46619 in the mouse uterus taken during different stages of the oestrous cycle and during pregnancy. Uterine samples from BKW mice were taken from different anatomical segments along the length of each uterine horn and set up for superfusion at 2 ml/min with Krebs solution (containing 1 microM indometacin) at 37 degrees C, and gassed with 95%O(2)/5%CO(2). Responses (area under the curve) are expressed as a percentage of the final contraction induced by hypotonic shock. Data are expressed as the means +/- s.e.m. of n=5-12 and were analysed using Student's paired t-test or two-way ANOVA with a Bonferroni post hoc test. Regional variation in myogenic activity was observed in all tissues studied except those taken during labour. These tissues displayed significantly greater myogenic activity than tissues taken at late gestation and at all stages of the oestrous cycle. Tissues from pregnant animals were generally more responsive to U46619 and PGF(2alpha) than tissues taken from non-pregnant animals. Tissues taken from the upper segment of the uterine horn were more responsive to both agonists during the oestrous cycle. The findings demonstrated that the hormonal milieu and site of excision are important for myogenic activity and responsiveness.

This thesis explores the implications of René Girard’s mimetic theory on Genesis 1 and 2 in the Old Testament. It tests the extent to which Genesis 1 and 2 are structured sacrificially or mythically as outlined by Girard. René Girard’s theory is summarized and clarified as to how the theory can be applied to biblical texts. In addition, Girard’s theory is explained in the context of theory-making in late modernity, and critiques of Girard from biblical, anthropological, sociological, and theological perspectives are addressed. A sacrificial structure is explored in Genesis and Exodus that informs the exegesis of Genesis 1 and 2. The critical elements in Girard’s scapegoat mechanism—acquisitive desire leading to rivalry, crisis, and ultimately to an expulsion—are examined in the expulsion of the Hebrews from Egypt (Exodus 1) and the expulsions of Abraham and Isaac in Genesis (Gen 12-21). A particular pattern takes shape that structures the narratives in the Pentateuch. An exegesis of Israel’s narrative of origins in Genesis 1 and 2 follows, incorporating Girard’s theoretical insights with higher critical methods conventionally employed to the Old Testament. The thesis discovers striking parallels with Israel’s narrative of origins. They are indeed sacrificially structured, but they also interrogate that structure and describe an alternative sacrificial response. The sacrifice that Yahweh instigates dismantles the mythical structure even as it moves through the sequence. The thesis concludes with a validation of Girard’s theory and explains how Girard’s theory can be useful to the current exegetical tasks. / Biblical and Ancient studies / D. Th. (Old Testament)

HIV-1 has evolved with a great deal of functional complexity contained within a very small genome by encoding small, but critical viral proteins within larger viral genes and dividing the replication cycle into early and late phases to differentially produce all proteins leading to efficient replication and virion release. Early replication is restricted by the host spliceosome that processes HIV-1 vRNA transcripts so only the small intragenomic proteins are produced, one of which is Rev (Regulator of Virion Expression). Rev in turn governs the transition from early to late replication by interacting with a highly structured region of vRNA termed the Rev Response Element (RRE). The binding of Rev to the RRE is believed to cause a change in the vRNA tertiary structure and inhibition of splicing of the vRNA. Once, a Rev:RRE complex is formed, a nuclear export signal within Rev facilitates the export of partially spliced and unspliced vRNA to the cytoplasm. During late replication the partially spliced and unspliced vRNA is translated to polyproteins and is packaged into a budding virion where the viral aspartyl protease (HIV-1 PR) autocatalytically excises itself from the larger polyprotein and processes the remaining polyproteins to release all viral structural and functional proteins to form a mature and infectious virion. Since the vRNA salvaged by Rev is translated to the polyproteins containing HIV-1 PR, the inhibition of Rev function will reduce the amount of HIV-1 PR available and thereby reduce the amount of HIV-1 PR therapeutics required to elicit a clinical effect. Therfore a combination approach to HIV-1 treatment using suitably developed therapeutics that inhibit Rev and HIV-1 PR function represents an attractive synergistic approach to treating HIV-1 infection in vivo. The work of this thesis was divided into two parts, the first part was concerned with HIV-1 PR structural biology and addressing problems encountered with inhibitor design. A bicyclic peptide (based on inhibitors of analogous structure) was co-crystallised with active HIV-1 PR to develop an enzyme-product (E-P) complex and with a catalytically inactive mutant HIV-1 PR to provide an analogy to the enzyme-substrate (E-S) complex. Both structures of the E-P and E-S complexes were solved to 1.6Å resolution and were compared to a hydroxyethylamine isostere enzyme-inhibitor complex (E-I), highlighting the similarity of binding mode for all ligands. The inhibitor in the E-I complex was translated towards the S1 - S3 pockets of the substrate binding cleft relative to the substrate in the E-S complex due to the increased length of the hydroxylethylamine isostere compared to the peptide backbone, although the inhibitor "puckered" the isostere linkage and maintains a binding mode similar to the substrate with very little overall differences in the position of the ligands and surrounding protein. The similarity of the E-S, E-I and E-P complexes was attributed to the macrocyclic ligands ordering the surrounding protein environment, especially the protein -strand "flap" structures that form a roof over the ligands in the active site but were not found to close more tightly in any of the trapped catalytic states. The new structures allowed refinement of details of the mechanism of peptide hydrolysis. The mechanism relies on the optimal nucleophilic attack of a water molecule on the scissile amide bond with concerted acid-base catalysis of the active site aspartyl residues intitiated by D125. The alignment and intrinsic position of the N-terminus of the bicyclic substrate was interpreted as being critical to facilitate efficient electron transfer with the bicyclic substrate. An N-terminal cyclic inhibitor, similar to the N-terminal portion of the bicyclic substrate, was used to address a major problem in HIV-1 PR drug design termed "cooperativity," where the sequential optimisation of an inhibitor (or substrate) to individual pockets of the substrate binding cleft, can negatively impact on adjacent and downfield subsites and thereby alter the binding mode of the "optimised" inhibitor. The technique referred to here as "templating" uses the N-terminal cycle to lock the binding mode into a known conformation, probing the S1' and S2' pockets. The structure activity relationship suggested that by viewing the S1' - S3' pockets as a single trough, bulky aromatic groups attached to an N-alkyl sulfonamide could be directed along the line of the trough without adverse interactions with the tops of the S1' and S3' pockets, providing very potent inhibitors. It was also found that specificity and potency of an inhibitor can be maintained with smaller functionalities that carry their bulk low and close to the inhibitor backbone in the S2' pocket, making the P2 functionalities more substrate-like. The second part of the thesis was concerned with establishing suitable surface plasmon resonance assays for testing potential inhibitors of Rev function. Recombinant Rev and its minimal RNA aptamer target (stem loop II of the RRE termed RBE3), were expressed, purified, and used to develop BIAcore-based assays and test potential inhibitors of their interaction. The system was applied to screening of aminoglycoside antibiotics and other small molecules in a competitive assay, and also to quantitative assay of Neomycin and moderate sized analytes: Rev and three peptidic analogues of the high-affinity binding site of Rev - the native peptide, succinylated form of the peptide and a form incorporating a novel helix-inducing cap. The peptide and protein assay was undertaken to test the proposition that helix induction of the high-affinity binding site of Rev can increase affinity for the biologically important RNA target and thereby form the basis of a new class of inhibitors. The screen of small molecule antagonists found that Neomycin was the best inhibitor of the Rev:RBE3 interaction and that efficacy of other aminoglycosides was due to the neamine-base structure presenting charge to bind to the RNA and blocking interaction with Rev. The quantitative assay was optimised to reduce non-specific interactions of Rev protein to allow reliable studies of the analytes with RBE3 by the sytematic testing of buffers and modifiers. It was found that mutliple analytes bound to the RBE3 aptamer and a comparison of the KD values found that the native and capped peptides had similar affinity for RBE3 RNA (native slightly greater at 21 ± 7nM cf capped 41 ± 10nM) that was greater than the Rev protein (101 ± 19nM), however the succinylated peptide exhibited stronger binding with a KD ≤8nM and Neomycin had the lowest affinity (KD 13 ± 3M). The similarity of the native and capped peptides may be due to the high concentration of salt in the assay buffers and was necessary for the stability of the Rev protein, but is sufficient to influence secondary structure of the peptides. Therefore, it could not be stated that the helix-inducing cap increased the affinity of the native peptide for the biologically important therapeutic target. The work conducted in this thesis firmly establishes foundations for the continued development of inhibitors against both Rev and HIV-1 PR that play key roles in the HIV-1 replication strategy. It is envisaged this work could lead to a novel synergistic therapeutic approach to treating HIV-1 infection.

This thesis explores the implications of René Girard’s mimetic theory on Genesis 1 and 2 in the Old Testament. It tests the extent to which Genesis 1 and 2 are structured sacrificially or mythically as outlined by Girard. René Girard’s theory is summarized and clarified as to how the theory can be applied to biblical texts. In addition, Girard’s theory is explained in the context of theory-making in late modernity, and critiques of Girard from biblical, anthropological, sociological, and theological perspectives are addressed. A sacrificial structure is explored in Genesis and Exodus that informs the exegesis of Genesis 1 and 2. The critical elements in Girard’s scapegoat mechanism—acquisitive desire leading to rivalry, crisis, and ultimately to an expulsion—are examined in the expulsion of the Hebrews from Egypt (Exodus 1) and the expulsions of Abraham and Isaac in Genesis (Gen 12-21). A particular pattern takes shape that structures the narratives in the Pentateuch. An exegesis of Israel’s narrative of origins in Genesis 1 and 2 follows, incorporating Girard’s theoretical insights with higher critical methods conventionally employed to the Old Testament. The thesis discovers striking parallels with Israel’s narrative of origins. They are indeed sacrificially structured, but they also interrogate that structure and describe an alternative sacrificial response. The sacrifice that Yahweh instigates dismantles the mythical structure even as it moves through the sequence. The thesis concludes with a validation of Girard’s theory and explains how Girard’s theory can be useful to the current exegetical tasks. / Biblical and Ancient studies / D. Th. (Old Testament)

La guerre et ses conséquences sont trop importantes pour que la réflexion philosophique ne s’y attarde pas. Pour comprendre ses fondements et ses mécanismes internes, il faut une pensée qui creuse au coeur même des comportements guerriers. C’est ce que Thomas Hobbes et Carl von Clausewitz ont chacun tenté de faire en réfléchissant sur la nature de la guerre. Ce mémoire vise entre autres à rendre compte de leur théorie respective sur la nature de la guerre et de voir les rapprochements possibles. L’analyse du concept d’état de guerre et de ses causes chez Hobbes, de même que la pensée de Clausewitz centrée sur la nature de la guerre, rendent compte d’une même dynamique où la relation de réciprocité qu’entretiennent les belligérants conduit à une montée de la violence. La notion de volonté est centrale chez nos auteurs, car elle explique autant cette montée continue de la violence que sa possible résolution vers la paix. Écartant la sphère de la morale et du droit pour penser le phénomène guerrier, leurs réflexions se veulent froides et sans illusion. En saisissant la dynamique relationnelle (et mimétique) qui conduit à un désir illimité de puissance, nos deux auteurs décortiquent l’essence de la guerre par une pensée fondamentalement orientée vers la paix. Ainsi nous donnent-ils des outils pour éviter le pire. / War and its consequences are too important for philosophy to ignore these. In order to understand its foundations and internal mechanisms, we must thought into the heart of war behaviors. That is what Thomas Hobbes and Carl von Clausewitz each tried to do in thinking about the nature of war. This dissertation aims among other things to understand their respective theory about the nature of war and to see how to put them together. The conceptual analysis of state of war and of its causes according to Hobbes, as well as Clausewitz’s thought centered on the nature of war, ascertain similar dynamism where the belligerents’ reciprocal relationship leads to a rise of violence. The notion of will is central to these authors because it explains as much this continued rise of violence as well a possible resolution towards peace. Moving aside the sphere of morality and law while thinking about the war phenomenon, their thoughts wish to be cold and without illusions. In grasping the relational (and mimetic) dynamic which leads to an unlimited desire for power, these two authors decorticate the essence of war through a thought fundamentally oriented towards peace. Thus they give us tools to avoid the worst.

Esta Tese é composta de projetos de intervenção realizados no período de 2004 a 2008. Os trabalhos de arte apresentados aqui são alterações na arquitetura de espaços de museus, galerias ou centros culturais. A natureza destes trabalhos é de uma resposta a estes contextos por meio de transformações operadas em sua luz ambiente. O uso de anteparos semi-transparentes que denomino filtros, cria um sistema temporário de dispositivos e efeitos que afetam o lugar e seus frequentadores. Esta tese aborda a qualidade mimética desta intervenções observando a estratégia comum a elas e também suas especificidades táticas. Os trabalhos são apresentados como \"máquinas de transformar\" que criam estados alterados do lugar. / This Thesis is constitued by intervention projects made from 2004 to 2008. The artworks presented here are alterations made in architectural spaces at museums, galleries, cultural centers, etc. The nature of these works is to respond to those contexts operating transformations in their ambient light. By using partially transparent surfaces that I define as filters, a temporary system of devices and effects is created to affect the place and its users. This thesis approaches the mimetic condition of these artworks, observing the strategy they have in common and also their tactical specificities. The artworks are presented as \"transformation machines\" that create altered states of the place.

Esta Tese é composta de projetos de intervenção realizados no período de 2004 a 2008. Os trabalhos de arte apresentados aqui são alterações na arquitetura de espaços de museus, galerias ou centros culturais. A natureza destes trabalhos é de uma resposta a estes contextos por meio de transformações operadas em sua luz ambiente. O uso de anteparos semi-transparentes que denomino filtros, cria um sistema temporário de dispositivos e efeitos que afetam o lugar e seus frequentadores. Esta tese aborda a qualidade mimética desta intervenções observando a estratégia comum a elas e também suas especificidades táticas. Os trabalhos são apresentados como \"máquinas de transformar\" que criam estados alterados do lugar. / This Thesis is constitued by intervention projects made from 2004 to 2008. The artworks presented here are alterations made in architectural spaces at museums, galleries, cultural centers, etc. The nature of these works is to respond to those contexts operating transformations in their ambient light. By using partially transparent surfaces that I define as filters, a temporary system of devices and effects is created to affect the place and its users. This thesis approaches the mimetic condition of these artworks, observing the strategy they have in common and also their tactical specificities. The artworks are presented as \"transformation machines\" that create altered states of the place.

<p>Rational conversion of biologically active peptides to nonpeptide compounds with retained activity is an appealing approach in drug development. One important objective of the work presented in this thesis was to use computational modeling to aid in such a conversion of the peptide angiotensin II (Ang II, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe). An equally important objective was to gain an understanding of the requirements for ligand binding to the Ang II receptors, with a focus on interactions with the AT₂ receptor.</p><p>The bioactive conformation of a peptide can provide important guidance in peptidomimetic design. By designing and introducing well-defined secondary structure mimetics into Ang II the bioactive conformation can be addressed. In this work, both γ- and β-turn mimetic scaffolds have been designed and characterized for incorporation into Ang II. Using conformational analysis and the pharmacophore recognition method DISCO, a model was derived of the binding mode of the pseudopeptide Ang II analogues. This model indicated that the positioning of the Arg side chain was important for AT₂ receptor binding, which was also supported when the structure–activity relationship of Ang II was investigated by performing a glycine scan.</p><p>To further examine ligand binding, a 3D model of the AT₂ receptor was constructed employing homology modeling. Using this receptor model in a docking study of the ligands, binding modes were identified that were in agreement with data from point-mutation studies of the AT₂ receptor.</p><p>By investigating truncated Ang II analogues, small pseudopeptides were developed that were structurally similar to nonpeptide AT₂ receptor ligands. For further guidance in ligand design of nonpeptide compounds, three-dimensional quantitative structure–activity relationship models for AT₁ and AT₂ receptor affinity as well as selectivity were derived. </p>