Inhibiting therapeutically important protein-protein interactions has been a tremendous challenge for medicinal chemists. The folded 3D structures of peptides and proteins, mainly comprise secondary structural elements i.e α-helices and β-sheet have created an opportunity to design small molecules and peptidomimetic inhibitors of protein-protein interaction (PPI). Hence, information about the formation and stabilization of these secondary structures is vital for designing future drugs. In this dissertation, several cyclic beta-hairpin peptidomimetics that mimic the recognition surface have been designed and synthesized as inhibitors for different targets such as integrin mediated extracellular matrix -cell adhesion in multiple myeloma, p53-MDM2 PPI, amyloid beta fibrillogenesis inhibitor. Cyclization of linear peptides to restrict the number of conformations available to the linear peptide can increase its affinity for the target as well as increase its proteolytic resistance. In this study, different beta turn promoters that increase the propensity of cyclic peptides to adopt beta-sheet structures have been designed and synthesized. Chapter two discusses the design and synthesis of several cyclic III (Integrin Interaction Inhibitor) peptides that block adhesion of integrins to extracellular matrix components in Multiple Myeloma tumor cells. These cyclic peptides, as assayed by TOPRO 3 assay were more potent than the parent linear peptide with a bio-activity of 1.08 μM. We have also studied structure activity relationships (SAR) of these cyclic III peptide analogs to increase the potency and bioavailability of these peptides. Chapter three describes the application of cyclic beta-hairpin peptidomimetics to inhibit abeta fibrillogenesis that is responsible for Alzheimer’s disease. We have successfully designed and synthesized cyclic peptides that target the hydrophobic region (17-21) of abeta fibril which is believed to cause self aggregation and plaque formation. We have also successfully explored these cyclic beta-hairpin peptides to disrupt p53-MDM2 interactions. Chapter five discusses the design and synthesis of novel cysteine based Peptide Nucleic Acid (PNA) monomers that are aimed to increase cellular uptake by introducing positively charged species attached to the cysteine side chain. We have successfully synthesized CPNA monomers and made efforts to make PNA oligomers.

The term ???Integral Abutment Bridges??? is used broadly all over the world these days. While the expansion joints used in bridges were once a scientifically proved cure to the problem of natural expansion and contraction, there are the excessive maintenance costs being accumulated annually due to the deterioration of essential functions from deicing chemicals and debris. This drawback triggered the advent of Integral Abutment Bridges. The performance of Integral Abutment Bridges at almost no extra costs in seasonal and daily cyclic contraction and expansion can be assessed as a monumental landmark of civil engineering technologies with respect to the massive budget reductions. However, since Integral Abutment Bridges are destined to expand or contract under the laws of nature, the bridge design became more complicated and sophisticated in order to complement the removal of expansion joints. That is why numerous researchers are attracted to Integral Abutment Bridges with deep interests. Accordingly, in designing the piled abutments of Integral bridges, it is essential to precisely predict the bridge???s behavior in advance. Researchers have been broadly carried out during the last several decades on the behavior of piled bridge abutments. However, most of the studies have been analyzed with focus on structural elements or soils, respectively for the static and dynamic loads such as thermal variations and earthquake loads. This presented research developed 3D numerical models with 3 m, 4 m, 5 m, 6 m, 7 m, and 8 m-tall abutments in the bridge using the finite element analysis software MIDAS CIVIL that simulate the behaviors of Integral Abutment Bridges to study the soil-structure interaction mechanism. In addition, this work evaluated and validated the suitability to the limit of the abutment height in Ontario???s recommendations for Integral Abutment Bridges by a parametric study under the combined static loading conditions. In order to be a balanced research in terms of a multidisciplinary study, this research analyzed key facts and issues related to soil-structure interaction mechanisms with both structural and geotechnical concerns. Moreover, the study established an explanatory diagram on soil-structure interaction mechanisms by cyclic thermal movements in Integral Abutment Bridges.

Thesis (Ph. D.)--University of Washington, 1997. / Vita. Includes bibliographical references (leaves [115]-133).

Neste trabalho, usamos uma abordagem de anéis de grupo para caracterizar códigos cíclicos sobre anéis de cadeia, seus duais e algumas condições sobre códigos auto-duais. Caracterizamos também os códigos cíclicos livres sobre anéis de cadeia e por fim exibimos uma fórmula para o peso de qualquer código cíclico sobre anéis de cadeia de comprimento e p^n 2p^n. / In this thesis, we use an approach of group rings to characterize cyclic codes over chain rings, their duals and some conditions on self-dual codes. It also features free cyclic codes over chain rings and finally we show a formula for the weight of any cyclic code over chain rings of length p^n and 2p^n.

Les anévrysmes se développant au niveau des fistules artério-veineuses (FAV), représentent une complication rare mais potentiellement mortelle dont la physiopathologie reste inexplorée. Jusqu’à présent la pratique courante était de les remplacer par un segment prothétique. Nous avons proposé un nouveau traitement chirurgical consistant en une anévrysmorraphie veineuse renforcée extérieurement par une exoprothèse. Notre premier objectif a été de rapporter les résultats à un an de cette nouvelle technique. Dans un second temps nous avons perfusé ex vivo des veines saphènes humaines renforcées par la même exoprothèse dans des conditions hémodynamiques de shear stress (SS) artériel en faisant varier la pression. L’analyse morphologique a montré le développement d’une hyperplasie intimale dans la veine sans et avec exoprothèse à haute pression. L’analyse des gènes et des protéines impliqués dans le remodelage vasculaire n’a pas montré de différence entre la veine nue et la veine renforcée mais nous a permis de mieux caractériser le rôle du SS et de la pression dans le mécanisme de l’artérialisation veineuse. Notre troisième objectif a été de décrire le remodelage anévrysmal des FAV. A partir d’une tissuthèque constituée d’échantillons de veines prélevées chez les patients opérés, nous avons comparé la veine artérialisée anévrysmale à la veine non artérialisée non anévrysmale. Les métalloprotéinases et leurs inhibiteurs participent activement à ce remodelage. Les anévrysmes régulièrement ponctionnés ont un profil inflammatoire qui influence la nature de ce remodelage. / Aneurysm complicating arteriovenous fistula (AVF) is a rare but potentially life-threatening complication. To date, its pathobiology remains unexplored and prosthetic replacement constitutes the conventionnal treatment. We have proposed a new surgical technique consisting in a venous aneurysmorraphy reinforced by an exoprosthesis. Our first goal was to evaluate the one-year results in terms of patency and aneurysm recurrence. Secondly, we have studied the impact of the exoprosthesis on human saphenous veins perfused ex vivo and submitted to different flow conditions consisting in an arterial shear stress (SS) in association with a low or a high pressure setting. Morphological analysis revealed an intimal hyperplasia in veins with and without exoprosthesis under high pressure. Analysis of the proteins and genes involved in the vascular remodeling did not showed an exoprosthesis effect but allowed us to better decipher the selective role played by SS and pressure in the arterialization process. Thirdly, we have collected tissue samples from patients operated and compared aneurysmal arterialized veins to non-aneurysmal non-arterialized veins. Metalloproteinases and their inhibitors actively participate in the remodeling. In aneurysms frequently cannulated inflammation influence the remodeling process.

No description available.

No description available.

A large number of evolutionarily conserved genes have been identified by comparative genomics approaches. However, a considerable fraction of these genes lack functional characterization despite the availability of several bioinformatics approaches for prediction of protein function. Moreover, with the advent of genome sequencing efforts, numerous disease associated genes have been identified. While high throughput approaches aid in identification of genes, studying individual genes is important to understand their cellular roles. During studies on cyclic AMP metabolism in mycobacteria conducted in the laboratory, a Class III cyclic nucleotide phosphodiesterase, Rv0805 was identified from Mycobacterium tuberculosis. Interestingly, additional bioinformatics analysis identified orthologs were in higher eukaryotes. These were members of the metallophosphoesterase-domain-containing protein 1 (MPPED1) and metallophosphoesterase-domain-containing protein 2 (MPPED2) family. Class III cyclic nucleotide phosphodiesterases were previously reported only in prokaryotes and are distinct from Class I cyclic nucleotide phosphodiesterases generally found in eukaryotes. Thus MPPED1 and MPPED2 proteins were the first identified eukaryotic Class III cyclic nucleotide phosphodiesterases. In humans, MPPED2 is located on chromosome 11 in the region p13-14 that has been associated with WAGR (Wilms’ tumor, aniridia, genitourinary anomalies, and mental retardation) syndrome. Inspection of this region across sequenced mammalian genomes has revealed a shared synteny. Most interestingly, a stretch of 200 bp within the coding sequence of MPPED2 is identified to be one of 481 ultra conserved regions within the human genome. Furthermore, orthologs of MPPED2 can be traced all the way back to Drosophila melanogaster and Caenorhabditis elegans. All of these observations indicate that MPPED2 is highly conserved and hints at its likely importance in many organisms. MPPED1 and MPPED2 have been reported to be expressed in adult and fetal brain respectively and have been annotated as metallophosphoesterases. Metallophosphoesterases are a superfamily of proteins that show wide phyletic distribution and exhibit diversity in their substrate utilization and function. Previous studies from the laboratory have shown that MPPED1 and MPPED2 are indeed metallophosphoesterases and demonstrate cyclic nucleotide phosphodiesterase activity. The crystal structure of MPPED2 was obtained in collaboration with Dr. Marjetka Podobnik (National Institute of Chemistry, Slovenia). Interestingly, the crystal structure of MPPED2 revealed the presence of bound 5’GMP molecule at the active site, and this finding was investigated further in this thesis. MPPED2 bound 5’GMP and 5’AMP with high affinity (IC50 of ~70 nM) which inhibited the activity of MPPED2. Key residues involved in stabilising the 5’ nucleotide have been identified by structure guided mutational analysis. The MPPED2-G252H mutant, generated to mimic the active site of MPPED1, also bound 5’GMP or 5’AMP but with much lower affinity. Given the high affinity of MPPED2 towards 5’GMP/5’AMP, it can be speculated that MPPED2 may show poor phosphodiesterase activity in the cell, and could function in a catalytically-independent manner, perhaps as a scaffolding protein. MPPED1 on the other hand may have a catalytic role that could be regulated by intracellular levels of 5’AMP, 5’GMP and their respective cyclic nucleotides. In order to investigate the biological role of the MPPED1/MPPED2 family of proteins, Drosophila melanogaster was chosen as a model organism owing to the presence of a single ortholog, CG16717, in its genome. Biochemical characterization of CG16717 revealed that the protein was in fact a metallophosphodiesterase capable of hydrolysing cyclic AMP and cyclic GMP, albeit poorly. CG16717 could be inhibited by 5’ nucleotides at high concentrations that may seldom be achieved in-vivo, suggesting that CG16717 may have roles in the organism that depend on its catalytic activity. CG16717 has not been functionally characterized previously. In this thesis, a detailed analysis of CG16717 expression pattern has been performed. CG16717 was found to be expressed in all stages of the fly lifecycle. In adult female flies, levels of CG16717 increased across age. Moreover, CG16717 was not differentially regulated under conditions of starvation, paraquat-induced oxidative stress or in the presence of heavy metals. Spatial expression analysis revealed that CG16717 was expressed in all adult tissues tested, with maximal expression in the brain, suggesting that neuronal expression of CG16717 may be important for its function. Attempts to identify specific cells expressing CG16717 using an enhancer-promoter analysis were not successful. In order to elucidate the physiological role of CG16717, and after having ruled out options of using a P-element insertion mutant and RNA interference approaches, a targeted knock-out of CG16717 was generated using homologous recombination based genomic engineering. CG16717KO flies generated were homozygous viable suggesting that CG16717 was dispensable for fly survival at least under normal laboratory conditions. In line with high expression of CG16717 in the brain and in-vitro ability of CG16717 to hydrolyse cAMP and cGMP, CG16717KO flies showed two to three-fold higher levels of cyclic nucleotides in the head fraction than wild-type flies. C25E10.12, one of the three C. elegans orthologs of CG16717 has been identified to be a target of the transcription factor daf-16 (FOXO) that is inhibited by active insulin signalling. Moreover, knock-down of C25E10.12 reduced the lifespan of age-1 (PI3K) mutant worms. In contrast to this, CG16717 was not found to be differentially regulated in dFOXO null flies. CG16717KO flies however, showed median lifespan that was shorter than control wild-type flies even in the presence of functional PI3K. Various genetic approaches were employed to verify if reduced lifespan was indeed a consequence of loss of CG16717. In the first approach, a wild-type copy of CG16717 was re-introduced at the genomic locus of CG16717 in the CG16717KO flies using attP-attB recombination. However, this approach could not rescue the reduced lifespan of CG16717KO flies, probably due to very low expression of CG16717. In the second approach, CG16717 was reconstituted using genomic constructs containing a copy of CG16717. Finally, CG16717 was expressed ubiquitously using the bipartite Gal4/UAS system. Both the genomic construct and the expression of CG16717 using the Gal4/UAS approach were able to restore the lifespan of CG16717KO flies. More importantly, overexpression of CG16717 in an otherwise wild-type fly led to enhanced lifespan over and above that of control flies. All of these together suggested that CG16717 plays a critical role in regulating lifespan. Mutants of the insulin and target of rapamycin (TOR) signalling pathways have previously been reported to show lifespan extension. Moreover, these mutants have also been associated with reduced growth, increased stress resistance and reduced fecundity. Given the reduction in lifespan of CG16717KO flies, the other insulin/TOR signalling associated phenotypes were tested. While CG16717KO flies showed no difference in terms of developmental growth, and resistance to starvation or paraquat induced oxidative stress, CG16717KO flies were less fecund compared to wild-type controls. Multiple approaches were adopted even in the case of reduced fecundity to verify if the observed phenotype was a consequence of loss of CG16717. However, neither reconstitution of CG16717 using the genomic construct nor ubiquitous expression of CG16717 using the bipartite Gal4/UAS system were able to rescue the reduced fecundity phenotype of CG16717KO flies. This suggested that reduced fecundity in CG16717KO flies was probably not linked to CG16717 and was a consequence of a second mutation at a site distinct from CG16717. Two other approaches were employed to confirm these observations. When CG16717KO/Deficiency lines were tested, these showed fecundity comparable to wild-type control flies despite the lack of CG16717. CG16717KO flies were extensively out-crossed in an attempt to segregate the second site mutation from the CG16717 locus and their fecundity was tested. However, these flies which retained the deletion of CG16717, showed fecundity comparable to wild-type control flies, reiterating that reduced fecundity was not linked to loss of CG16717. In an attempt to find possible links between reduced longevity of CG16717KO flies and the well-established insulin/TOR pathways, transcript levels of key players of these pathways were measured by qRT-PCR. The translational repressor 4EBP was found to be upregulated in CG16717KO flies compared to wild-type control flies. Interestingly, increased 4EBP levels have been associated with enhanced lifespan but in this case despite higher levels of 4EBP, CG16717KO flies showed reduced lifespan. Phosphorylation status of 4EBP and other players involved in the insulin/TOR phosphokinase signalling cascade would shed light on the activity of these pathways. In summary, this thesis has attempted to understand the biochemistry and physiological functions of an evolutionarily conserved metallophosphoesterase. Its apparent role in regulating life span in the fly suggests that the functions of this protein are likely to impinge on a number of diverse and important pathways involved in basic physiological processes in the organism. Further investigation would shed light on the molecular basis by which CG16717 affects lifespan, and opens up new avenues to understanding the contributions of CG16717 in regulating lifespan and diverse neurological functions.

Le travail s’intéresse aux effets d’un pré-écrouissage cyclique axial ou en torsion sur le comportement cyclique et la durée de vie en fatigue sous sollicitation axiale à température ambiante d’un acier inoxydable austénitique 304L. Les essais cycliques séquentiels à amplitude de déformation croissante ou décroissante montrent que la courbe cyclique du 304L est non-unique. Cette caractéristique est liée à la persistance de l’état microstructural généré pendant les cycles d’amplitude de déformation maximale de la première séquence. En augmentant le nombre des séquences, l’acier 304L montre une tendance vers une courbe cyclique asymptotique, l’écrouissage semble se stabiliser. Des essais de fatigue sous chargement axial ont été réalisés sur des éprouvettes vierges ou pré-écrouies en traction-compression ou en torsion. Les durées de vie ont été sensiblement réduites pour les éprouvettes pré-écrouies. Ce phénomène est lié à la formation de structures de dislocations denses héritées de la phase de pré-écrouissage. Cependant, l’augmentation de l’amplitude de déformation en fatigue réduit l’effet du pré-écrouissage. / This study investigates the effects of loading history on the cyclic stress-strain curve and fatigue behavior of 304L stainless steel at room temperature. Tension-compression tests were performed ont the same specimen under controlled strain, using several loading sequences of increasing or decreasing amplitude. The results showed that fatigue life is significantly reduced by the previous loading history. A previously developed method for determining the effect of prehardening was evaluated. Microstructural analyses were also performed; the microstructures after preloading and their evolution during the fatigue cycles were characterized by TEM. The results of these analyses improve our understanding of the macroscopic properties of 304L stainless steel and can help us identify the causes of failure and lifetime reduction.

The purpose of this study was to examine the effect of partial and total immersion in sodium hypochlorite on nickel-titanium rotary files and to determine whether resistance to fracture was influenced by the immersion time. One hundred K3™ and 100 ProFile® rotary files were either partially or totally immersed in 5.25% sodium hypochlorite for zero, one, five, thirty, or sixty minutes. After immersion, files were subjected to cyclic fatigue testing. Time to fracture was recorded and analyzed by a two-way ANOVA. Tukey's honest significant difference was used to identify any differences in immersion times. Within all ProFile groups and partial immersion K3 groups, there was no significant decrease in time to fracture with increased immersion time in sodium hypochlorite. Only the K3 total immersion groups revealed a significant decrease in time to fracture with increased immersion time in sodium hypochlorite.