Flexible plastic liners are sometimes installed into new and existing oil and gas pipelines to prevent corrosion of the pipe wall. A practical difficulty of this method is that the plastic liners are permeable to gases, which can collect and form an annular space between the liner and the pipe. If the operating pressure in the pipe decreases then the collected gas can cause the liner to collapse and block the pipe. One method for overcoming this problem is to insert vents at intervals along the liner to allow the gas to escape into the pipe during depressurisation. However, there is concern that this arrangement might lead to excessive corrosion beneath the vent where the pipe wall is exposed. The rate of corrosion is expected to be controlled by the vent size but this principle needs to be confirmed by experiment. The work described in this thesis is aimed at investigating this corrosion by experiment for a range of conditions typical of oil and gas production. A novel crevice corrosion cell was designed, consisting of an X100 carbon steel plate and a sheet of transparent Perspex, separated by a thin gasket. A small hole in the Perspex simulated a liner vent and allowed carbon dioxide to reach the steel surface. Tests were carried out in 3.5% NaCl solutions saturated with carbon dioxide at 1 bar partial pressure. Corrosion rates along the length of the annular space were measured using the Linear Polarisation Resistance (LPR) technique on pairs of insulated X100 electrodes set into the plate. The corrosion rates within the annular space have been shown to be small compared to those in the bulk solution and to diminish rapidly with distance from the vent. Mathematical modelling, based on the transport of carbon dioxide, is described to explain these findings and support the experimental work. The effectiveness of the LinerVentTM, installed over the vent, in a turbulence pipeline was demonstrated. The benefit of applying cathodic protection within the annular space was also demonstrated. The results are discussed in terms of the fundamental corrosion principles and their practical implications

Le récepteur des oestrogènes (RE) peut moduler l’expression de gènes impliqués dans les processus de prolifération et d’apoptose cellulaires. Cette régulation est possible par le recrutement de complexes corégulateurs. Dans ces complexes, l’activité répressive s’explique essentiellement par la présence d’histones désacétylases (HDAC). Cette famille de protéines est composée de 18 membres classés en 4 groupes. Cette répartition est due aux similarités structurales et de fonctions de ces enzymes. Il y a la classe I (HDAC 1, -2, -3, -8), la classe II (HDAC 4, -5, -6, -7, -9, -10) et la classe IV (HDAC 11) qui ont une activité Zn2+ dépendante alors que la classe III (Sirt1-7) recense les HDAC avec une activité NAD+ dépendante. Des résultats récents du laboratoire ont montré, qu’au niveau ARNm, il y avait un important différentiel d’expression de HDAC9 entre les lignées cellulaires de cancer du sein RE positive et négative ou résistante au tamoxifène. Durant ma thèse, j’ai démontré que la régulation de HDAC9, au niveau de son expression, comme au niveau de ses fonctions, affecte la signalisation oestrogénique en modulant l’expression et l’activité transcriptionnelle de REα. De plus, de nombreuses études ont montré l’activité antiangiogénique d’inhibiteurs de HDAC (HDI) à large spectre comme la TSA (Tricostatin A). La conception et l’identification de HDI, potentiellement sélectifs, comme agents anti-tumoraux et/ou anti-métastatique représente une nouvelle approche de thérapie seule ou combinée avec les produits déjà utilisés dans le traitement du cancer. Ainsi, afin d’identifier et caractériser de nouveaux HDI, j’ai établi un outil bioluminescent pour la détection d’inhibiteurs sélectifs de HDAC. Plusieurs lignées cellulaires Gal4-VP16-HDAC ont été générées dans ce but / The estrogen receptor (ER) can modulate the gene expression with consequences in the cell proliferation, apoptosis. This modulation is possible by the recruitment of coactivator or corepressor complexes. The repression activity is in particular explained by the histones deacetylases (HDACs). This protein family is composed by eighteen members who have been classified in four groups. These HDACs are subdivided on structural and functional similarities. The class I isoforms (HDACs 1, 2, 3 and 8), class II (HDACs 4, 5, 6, 7, 9, 10) and class IV (HDAC11) are Zn-dependent enzymes, whereas class III HDACs (Sirtuins 1-7) are NAD+-dependent. Recent data from the laboratory have shown, at the mRNA level, there is an enormous expression differential of HDAC9 between breast cancer cell line ER positive and negative or OHT resistant cell line. During my thesis, I demonstrated that the regulations of the HDAC9 on the level of its expression as of its role in the various breast cancer cell lines were implicated in the estrogen signaling. This regulation takes place at the transcriptional level and in the ERet#945; activity.In addition, using broad spectrum HDAC inhibitors (HDIs) such as TSA (Tricostatin A), many studies have shown that these inhibitors had antiangiogenic activity. Thus, the design or the identification of selective and potent HDAC inhibitors as agents anti-tumoral and/or anti-metastatic can emerge in a novel opportunity used alone or in combination with the already existing agents for the treatment of cancers. In order to identify and characterize new HDIs, my thesis works consisted to establish bioluminescent cell lines for screening HDAC inhibitors. Different cell GAL4-VP16-HDACs chimeras' models were generated to determine the selectivity of HDIs for the different HDACs.

Hepatitis C is a serious disease that affects about 200 million people worldwide. No anti-HCV vaccine or specific anti-viral drugs are available today. Non-structural protein 3 (NS3) of HCV is a bifunctional serine protease/helicase, and the protease has become a prime target in the search for anti-HCV drugs. In this work, the complete HCV NS3 gene has been cloned and expressed, and the protein has been purified using affinity chromatography. An assay for measuring the protease activity of full-length NS3 protease has been developed and used for inhibition studies. A series of peptide-based inhibitors of NS3 protease varying in length, the composition of the side-chain and the N- and C-terminal groups have been studied. Potent tetra-, penta- and hexapeptide inhibitors of the NS3 protease were discovered. Hexapeptides with an acyl sulfonamide C-terminal residue were the most potent inhibitors of the NS3 protease, having nanomolar Ki-values. The selectivity of the inhibitors was assessed using other serine and cysteine proteases. NS3 protease inhibitors with electrophilic C-terminal groups were non-selective while those comprising a C-terminal carboxylate or acyl sulfonamide group were selective. All inhibitors with a small hydrophobic P1 side-chain residue were non-selective for the NS3 protease, being good inhibitors of human leukocyte elastase. This result highlights the importance of the P1 residue for inhibitor selectivity, which stems from the major role of this residue in determining substrate specificity of serine proteases. Electrophilic inhibitors often cause slow-binding inhibition of serine and cysteine proteases. This was observed with other proteases used in our work but not with NS3 protease, which indicates that mechanism of inhibition of NS3 protease by electrophilic inhibitors may not involve formation of a covalent bond. The structure-activity relationships obtained in this work can be used for improvement of peptide-based inhibitors of HCV NS3 protease towards higher inhibitory potency and selectivity.

Although extensive evidence suggests antidepressants are a non-effective treatment for the majority of depressive cases where they are prescribed and despite other developed countries taking steps to provide alternative treatments, Canada's prescription rates continue rising and no state action is being taken. The primary purpose of this study is to explore whether the media in English-speaking Canada, represented by its "newspaper of record," The Globe and Mail, has been performing its essential role in informing Canadians about the controversy surrounding antidepressants and the pharmaceutical system that that has made them central to treating depression. Data was collected in the form of newspaper articles from between 2000 and 2015 in order to analyze media coverage to ensure the essential facts were reported and to qualify to what degree a patient advocacy role challenging the norms of contemporary treatment has been adopted. / February 2017

Diffuse large B-cell lymphoma (DLBCL) is the most common form of non-Hodgkin lymphoma (NHL). The current standard of care is the combination of rituximab with cyclophosphamide, doxorubicin, vincristine and prednisone (R-CHOP), but this only results in a 60% over-all 5-year survival rate, thus highlighting a need for new therapeutic approaches. Histone deacetylase inhibitors (HDACi) are novel therapeutics that is being clinically evaluated for combination therapy. Rational selection of companion therapeutics for HDACi is difficult due to their poorly understood, cell-type specific mechanisms of action. To understand these mechanisms better, we developed a pre-clinical model system of response to the HDACi belinostat. Using this model system, we identified two major responses. Resistance, consisting of a reversible G1 cell cycle arrest with little induction of apoptosis; or sensitivity, consisting of mitotic arrest and high levels of apoptosis. In this dissertation, we determine that the induction of G1 cell cycle arrest is due to the increased expression of cyclin dependent kinase inhibitors (CDKi) that bind to and inhibit the cyclin E/CDK2 complex thereby blocking the final repressive phosphorylation steps of Rb protein. Repression of transcriptional elongation blocked CDKi upregulation and prevented G1 cell cycle arrest in belinostat-resistant cells. Additionally, we identified that belinostat arrests sensitive cells prior to metaphase and belinostat-resistant cells slow-down in mitosis but complete the process prior to arresting in G1. The combination of belinostat with the microtubule-targeting agent, vincristine resulted in strong synergistic induction of apoptosis by targeting mitotic progression. Furthermore, this combination prevents polyploidy, a key mechanism of resistance to microtubule targeting agents. Finally, we utilized selective class one HDAC inhibitors to identify the individual contributions of HDACs in the eliciting the responses observed with belinostat treatment. HDAC1&2 inhibition recapitulated the belinostat-resistant phenotype of G1 cell cycle arrest with little apoptosis, in both belinostat-resistant and sensitive cell lines. HDAC3 inhibition resulted in the induction of DNA damage, increased S phase and the induction of apoptosis in belinostat-resistant cells. Belinostat-resistant cells did not have observable effects to HDAC3 inhibitor alone but when combined with vincristine had significantly increased G2/M population at early time points. This suggests that HDAC3 maintains roles in DNA replication and also in mitotic progression. HDAC3 inhibition combined with vincristine resulted in a significant increase in polyploidy, suggesting that HDAC3 might not regulate the expression of apoptotic regulating factors as belinostat does.

Glucocorticoids (GC) are common components of many chemotherapeutic regimens for lymphoid malignancies. GC-induced apoptosis involves an intrinsic BCL-2 family-regulated pathway. It has been shown that BIM (BCL-2 interacting mediator of cell death), a BH3-only pro-apoptotic protein, is up-regulated by dexamethasone (Dex) treatment in acute lymphoblastic leukemia (ALL) cells. Furthermore, BIM is inactivated by extracellular signal-regulated kinase (ERK)-mediated phosphorylation. We therefore hypothesized co-treatment with Dex and MEK/ERK inhibitors would promote apoptosis in ALL cells through BIM up-regulation and activation. We show here that a MEK inhibitor, PD184352 synergistically enhances Dex lethality in CCRF-CEM (T-ALL) cells. Co-treatment with Dex and PD184352 results in BIM accumulation. Down-regulation of BIM by short-hairpin RNA in CCRF-CEM cells suppressed apoptosis by Dex/PD184352 co-treatment. In contrast, another BH3-only protein, BAD is dispensable. Thus, BIM is a critical molecule in this regimen, and targeting BIM by drugs combination could be effective on ALL and possibly other malignancies.

The goal of this escalating single-dose phase I research study was to determine the safety, tolerability, pharmacokinetics, pharmacodynamics as well as in vitro metabolism and plasma protein binding of MS-275, a novel histone deacetylase inhibitor, in patients with solid tumors and lymphomas. A validated LC/MS assay was developed to quantitate MS-275 in plasma, human liver microsomes and urine. The pharmacokinetic (PK) evaluation was done using a non-compartmental approach. In-vitro plasma protein binding profile of MS-275 was characterized by a validated micro-equilibrium dialysis method. In vitro phase I and phase II hepatic metabolism of MS-275 were evaluated using human liver microsomes. A correlative covariate analysis was performed in an effort to explain the wide inter-individual variability among patients.Results from the study demonstrate that the validated LC-MS assay is specific, accurate, precise and sensitive. MS-275 demonstrates a substantial inter-individual PK variability in systemic exposure and clearance; exposures increase in near-proportion, while peak concentrations increase more than-proportionally with an increase in dose. Mean apparent oral clearance (CL/F) is independent of dose and exhibits apparent dose-independent PK behavior over the studied dose range. Oral absorption is highly variable. MS-275 has a 50-fold longer half-life in humans compared to pre-clinical species. PK/PD analysis showed significant correlation between occurrence of DLT and higher systemic exposures. Although there was an increase in the acetylation of histone H3 and H4 over time, preliminary analysis showed no significant correlation between PK parameters and change in % histone acetylation after 24 hours. MS-275 is moderately bound to plasma proteins. Hepatic phase I and II metabolic pathways are only minor routes of elimination, and MS-275 is neither a substrate for liver-specific organic anion transporting proteins, OATP1B1 and OATP1B3, nor a substrate for gastrointestinal efflux transporters ABCB1 (P-gp) or ABCG2. No significant correlation was found between CL/F and demographic, body measures and other clinical covariates, and inter-patient variability in CL/F remained similar in magnitude even after correcting dose for body surface area (BSA) or other body measures. BSA is not a significant predictor of MS-275 PK, and flat-fixed dosing can be used in the future.

Phoslactomycin B (PLM-B), a potent and selective inhibitor of serine threonine phosphatase is of interest for its antitumor, antifungal and antiviral activity. The objective of this study was to evaluate the stability of phoslactomycin B at various pH and temperature conditions. Phoslactomycin B was produced from the mutant strain NP1 of Streptomyces sp.HK-803 and was purified by semi-preparative HPLC . A study of PLM-B degradation was carried out in the pH range of 2-10 at 30ºC and 50°C using HPLC. The PLM-B decomposition was observed to exhibit a U-shaped pH profile and demonstrated both acid and base-catalyzed decomposition. The decomposition could be described by the equation kOBS = kH x 10-pH + kOH x 10 pH- 14 (kH = 45±7 M-1 h-1; kOH = 448± 73 M-1 h-1). PLM-B was found to be most stable at pH 6.63. The degradation products in both acidic and basic pH have been collected and analyzed. Under basic condition, mass spectroscopic analysis revealed addition of water and NMR was consistent with the major products being formed due to lactone ring opening and/or a Micheal type addition reaction. Under acidic condition MS revealed loss of water for all three compounds. NMR analysis of one product (product 8) was consistant with C9- C11 phosphorinane derivative of PLM-B. The remaining compounds were shown to be mixture of various dehydration products. The degradation products despite containing small structural changes to PLM-B lost all detectable levels of antifungal activity.

Colorado potato beetle (Leptinotarsa decemlineata) is an economically important herbivorous pest. Cathepsin D-like aspartic peptidase (LdCD) plays an important role during protein degradation in the midgut of Colorado potato beetle. This work describes the preparation of two expression systems, namely in Escherichia coli and Pichia pastoris, for the production of recombinant LdCD. The protocol for refolding of denatured LdCD was designed and optimized. Activation of the inactive LdCD zymogen and cleavage of the propetide (activation peptide) were investigated. This process proceeds autocatalytically at acidic pH or with the assistance of the cysteine peptidase legumain. The proteolytic activity of LdCD was characterized using fluorogenic peptidic substrate and protein substrates, and kinetic parameters and pH optimum were determined. The inhibition specificity of LdCD was analyzed using a panel of peptidase inhibitors. LdCD was significantly inhibited by PDI (potato cathepsin D inhibitor), a protein inhibitor produced in potato leaves. This suggests that PDI is a natural defense protein, which is directed against LdCD in the midgut of Colorado potato beetle in order to block the digestion. The potential application of PDI in the construction of transgenic crops resistant against insects is discussed.

Gag polyprotein is the precursor of HIV-1 structural proteins, required for correct assembly, budding and maturation of viral particle within HIV-1 life cycle. The process of maturation into an infectious virion is dependent on Gag and GagPol cleavage at nine predefined sites by HIV-1 proteinase. Its disruption is one of the main targets of HIV treatment. HIV-1, however, develops resistance to the proteinase inhibitors by creating mutations in both the proteinase and the substrate. The Gag processing by HIV-1 proteinase is a highly sequential process, that happens in specific order and rate. Previous biochemical studies determined the kinetic data of these processes using oligopeptides representing naturally occuring cleavage sites. This thesis describes the cleavage of the Gag polyprotein itself, which is the natural substrate of HIV-1 proteinase. For this purpose, the full-length Gag polyprotein was recombinantly prepared in bacterial expression system. The cleavage was carried out and its products were analyzed via SDS-PAGE and Western blotting. The substrate specificity of the wild-type and mutant HIV-1 proteinase with respect to the full-length wild-type Gag polyprotein was compared. Substantial differences were observed between the rates of individual steps of cleavage by the wild-type and mutant...