Understanding the stratigraphic architecture of geologically complex reservoirs, such as the heavy oil deposits of Western Canada, is essential to achieve an efficient hydrocarbon recovery. Borehole and 3-D seismic data were integrated to define the stratigraphic architecture and generate 3-dimensional geological models of the Mannville Group in Saskatchewan. The Mannville is a stratigraphically complex unit formed of fluvial to marine deposits. Two areas in west-central and southern Saskatchewan were examined in this study. In west-central Saskatchewan, the area corresponds to a stratigraphically controlled heavy oil reservoir with production from the undifferentiated Dina-Cummings Members of the Lower Cretaceous Mannville Group. The southern area, although non-prospective for hydrocarbons, shares many similarities with time-equivalent strata in areas of heavy oil production. Seismic sequence stratigraphic principles together with log signatures permitted the subdivision of the Mannville into different packages. An initial geological model was generated integrating seismic and well-log data Multiattribute analysis and neural networks were used to generate a pseudo-lithology or gamma-ray volume. The incorporation of borehole core data to the model and the subsequent integration with the lithological prediction were crucial to capture the distribution of reservoir and non-reservoir deposits in the study area. The ability to visualize the 3-D seismic data in a variety of ways, including arbitrary lines and stratal or horizon slicing techniques helped the definition of stratigraphic features such as channels and scroll bars that affect fluid flow in hydrocarbon producing areas. Small-scale heterogeneities in the reservoir were not resolved due to the resolution of the seismic data. Although not undertaken in this study, the resulting stratigraphic framework could be used to help construct a static reservoir model. Because of the small size of the 3-D seismic surveys, horizontal slices through the data volume generally imaged only small portions of the paleogeomorphologic features thought to be present in this area. As such, it was only through the integration of datasets that the geological models were established.

TiPARP is a PARP-like mART that is induced by and negatively regulates AHR transactivation. Despite these insights, not much is known about TiPARP. This study aimed to characterize the regulation of TiPARP by AHR, PDGFR, and ERα, and investigate potential receptor interplay. Gene expression studies revealed that coactivation of AHR and PDGFR can enhance TiPARP expression after 3 h relative to activation of either receptor pathway alone. Gene expression and ChIP studies demonstrated that while co-activation of AHR and ER enhanced AHR, ARNT, and ERα recruitment to the regulatory region of TiPARP, TiPARP mRNA levels were not potentiated by co-activation relative to activation of either pathway. Dissection of the 5’ regulatory region of TiPARP using reporter gene assays revealed that a putative AHRE cluster and an ERE half-site were functional. Lastly, overexpression of TiPARP with an estrogen-responsive reporter revealed that TiPARP can repress ERα signalling and requires its catalytic activity.

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There is a strong association between estrogen exposure and breast cancer risk. Estrogen can activate estrogen receptor alpha (ERalpha) to increase cell proliferation. Estrogen can also be metabolized into genotoxic compounds to induce DNA damage and mutations. Activation of the aryl hydrocarbon receptor (AHR) and nuclear factor erythroid-2 like 2 (NFE2L2; NRF2) can alter the production of genotoxic estrogen. The present thesis investigated the signalling mechanisms of ERalpha, AHR, and NRF2 and how their interaction might modulate breast cancer risk. In Chapter 2, genome-wide, but promoter-focused analysis of ERalpha binding sites in T-47D breast cancer cells identified potential cell line specific differences in estrogen signalling between T-47D and the commonly used MCF-7 breast cancer cells. CYP2B6 was identified to be an ERalpha target gene in T-47D cells but not MCF-7 cells, supporting cell line dependent effect in estrogen signalling. In Chapter 3 and 4, genome-wide analyses of AHR binding sites were performed to investigate the molecular criteria governing genomic AHR transactivation in vivo in mouse and in vitro in MCF-7 breast cancer cells. Our analysis identified 1) the previously established aryl hydrocarbon response element to be an important, but not an absolute requirement in AHR transactivation and 2) key epigenetic modifications that modulate AHR-dependent gene regulation. Lastly, in Chapter 5, interaction among ERalpha, AHR, and NRF2 was presented at the regulatory region of two NRF2 target genes, NADPH Quinone Oxidoreductase 1 (NQO1) and Heme Oxygenase 1 (HMOX1). ERalpha repressed, whereas AHR enhanced NRF2-dependent NQO1 and HMOX1 mRNA expression through altered p300 recruitment and Histone H3 Lysine 9 acetylation. Collectively, this thesis examined novel molecular mechanisms that might alter breast cancer development/progression by modulating ER, AHR, and NRF2 activity.

There is a strong association between estrogen exposure and breast cancer risk. Estrogen can activate estrogen receptor alpha (ERalpha) to increase cell proliferation. Estrogen can also be metabolized into genotoxic compounds to induce DNA damage and mutations. Activation of the aryl hydrocarbon receptor (AHR) and nuclear factor erythroid-2 like 2 (NFE2L2; NRF2) can alter the production of genotoxic estrogen. The present thesis investigated the signalling mechanisms of ERalpha, AHR, and NRF2 and how their interaction might modulate breast cancer risk. In Chapter 2, genome-wide, but promoter-focused analysis of ERalpha binding sites in T-47D breast cancer cells identified potential cell line specific differences in estrogen signalling between T-47D and the commonly used MCF-7 breast cancer cells. CYP2B6 was identified to be an ERalpha target gene in T-47D cells but not MCF-7 cells, supporting cell line dependent effect in estrogen signalling. In Chapter 3 and 4, genome-wide analyses of AHR binding sites were performed to investigate the molecular criteria governing genomic AHR transactivation in vivo in mouse and in vitro in MCF-7 breast cancer cells. Our analysis identified 1) the previously established aryl hydrocarbon response element to be an important, but not an absolute requirement in AHR transactivation and 2) key epigenetic modifications that modulate AHR-dependent gene regulation. Lastly, in Chapter 5, interaction among ERalpha, AHR, and NRF2 was presented at the regulatory region of two NRF2 target genes, NADPH Quinone Oxidoreductase 1 (NQO1) and Heme Oxygenase 1 (HMOX1). ERalpha repressed, whereas AHR enhanced NRF2-dependent NQO1 and HMOX1 mRNA expression through altered p300 recruitment and Histone H3 Lysine 9 acetylation. Collectively, this thesis examined novel molecular mechanisms that might alter breast cancer development/progression by modulating ER, AHR, and NRF2 activity.

TiPARP is a PARP-like mART that is induced by and negatively regulates AHR transactivation. Despite these insights, not much is known about TiPARP. This study aimed to characterize the regulation of TiPARP by AHR, PDGFR, and ERα, and investigate potential receptor interplay. Gene expression studies revealed that coactivation of AHR and PDGFR can enhance TiPARP expression after 3 h relative to activation of either receptor pathway alone. Gene expression and ChIP studies demonstrated that while co-activation of AHR and ER enhanced AHR, ARNT, and ERα recruitment to the regulatory region of TiPARP, TiPARP mRNA levels were not potentiated by co-activation relative to activation of either pathway. Dissection of the 5’ regulatory region of TiPARP using reporter gene assays revealed that a putative AHRE cluster and an ERE half-site were functional. Lastly, overexpression of TiPARP with an estrogen-responsive reporter revealed that TiPARP can repress ERα signalling and requires its catalytic activity.

Transition metal-aromatic hydrocarbon complexes were generated in a supersonic jet and studied by zero electron kinetic energy (ZEKE) photoelectron spectroscopy and theoretical calculations. The target metal complexes were identified using time-of-flight mass spectrometry, and their ionization thresholds were located via photoionization efficiency spectroscopy. ZEKE spectroscopy was used to measure the ionization energies and vibrational frequencies of the metal complexes. Their electronic states and corresponding molecular structures were determined by comparing the experimental spectra to quantum chemical calculations and Franck-Condon simulations. In this dissertation, the metal complexes of four different aromatic hydrocarbon ligands were studied: benzene (bz), naphthalene (np), biphenyl (bp) and 1-phenyl naphthalene (phnp). In these complexes, the metal atom or ion was determined to bind to either one or two -rings. Three different bonding schemes were observed in these complexes. A twofold bonding scheme was observed in M+/M-np (M = Sc, Y, Ti, Zr, Hf), while a sixfold bonding scheme was observed in Sc+/Sc-bz and M+/M-bz2 (M = Sc, Ti, V, Cr, Mo, W). In the metal-polyphenyl complexes (i.e. Sc-, La-, and Ti-bp and Sc-phnp), twelve-fold metal-ligand bonding occurred, sixfold to two -rings of the ligand. This twelve-fold bonding mechanism requires rotation of the -rings by ~ 42 o and bending of the -rings by 40 to 57 o to clamp the metal atom or ion between the two -surfaces. Although the ground state spin multiplicities of the bare metal atoms and ions varied quite extensively, the multiplicities of the metal complexes were determined to be either singlet or doublet, except for Sc+/Sc-bz, V+-bz2, Ti-np, and Zr-np, where the triplet or quartet spin multiplicities were favored. The low spin and relatively narrower range of electron-spin multiplicities in the complexes were the result of d orbital splitting, where the degeneracy of the d orbitals was broken. Thus, the valence electrons were paired in each metal d-based molecular orbital of the complex to form low-spin singlet or doublet spin states. Some complexes favored triplet and quartet multiplicities, because the energy difference between the two highest occupied molecular orbitals was smaller than the electron pairing energy.

Inflammatory Bowel Diseases, Crohn's Disease and Ulcerative colitis, are idiopathic chronic conditions with multifactorial determinants. In general, terms, intestinal inflammation results from abnormal host-microbe interactions. Alterations in homeostasis involve host genetic factors, environmental cues and unique luminal microbial niches. We have examined the coordinated expressions of several molecular targets relevant to the mucosal immune system and identified signature biomarkers of IBD. Qualitative and quantitative changes in the composition of microbiota can be related to unique immuno-phenotypes. This in turn can have more systemic effects that involve energy metabolism. Adiponectin, an adipose tissue derived adipokine, can restore cellular ATP levels and fulfills innate immune functions. We have concluded that IBD might represent a state of adiponectin resistance relating to chronic inflammation and obesity status. Lastly we hypothesized that activation of xenobiotic pathway (AHR-aryl hydrocarbon receptor) can further modulate host immune and metabolic responses, and thus contribute to IBD phenotypes. We found that IBD is associated with robust mucosal, aryl hydrocarbon receptor pathway and related to proinflammatory cytokine secretion. We conclude that IBD heterogeneity is reflected through distinct immunophenotypes. Furthermore, environmental cues that involve the AhR receptor and adipose tissue derived adiponectin are important regulators of the inflammatory process in IBD.

Microbes fulfill important ecosystem functions by contributing as drivers of global nutrient cycles. Their distribution patterns are mainly controlled by environmental heterogeneities. So far, little is known about the mode of action of particular environmental drivers on the microbiota, particularly in low productivity habitats. The aim of this thesis was to investigate the relationships between local environmental drivers and the microbial responses at the level of communities, individuals and realized function, using three structurally different model habitats sharing the feature of overall low productivity. Using a hypothesis-based approach and extensive 16S rRNA amplicon mapping of bacterioplankton colonizing the polar Southern Ocean, I identified how the seasonal formation of open-water polynyas and coupled phytoplankton production affected the diversity of surface bacterial communities and resulted in a cascading effect influencing the underlying dark polar water masses. Additional laboratory experiments, with cultures exposed to light, resulted in reduction in alpha diversity and promoted opportunistic populations with most bacterial populations thriving in the cultures typically reflected the dominants in situ. Furthermore it was experimentally tested how induced cyclic water table fluctuations shaping environmental heterogeneity in a constructed wetland on temporal scale, by directly affecting redox conditions. Twelve months of water table fluctuations resulted in enhanced microbial biomass, however a shift in community composition did not lead to a significant increase in pollutant removal efficiency when compared to a static control wetland. I detected phyla that have previously been proposed as key players in anaerobic benzene break-down using a protocol that was developed for single cell activity screening using isotope-substrate uptake and microautoradiography combined with taxonomic identification based on fluorescent in situ hybridization targeting the 16S rRNA. Eventually, I provide an example of how anthropogenic pollution with polyaromatic hydrocarbons induced a strong environmental filtering on intrinsic microbial communities in lake sediments. In conclusion, my studies reveal that microorganisms residing in low productivity habitats are greatly influenced by environmental heterogeneity across both spatial and temporal scales. However, such variation in community composition or overall abundance does not always translate to altered community function.