Aquatic organisms in response to toxic insults from environmental pollutants activate defence systems including the aryl hydrocarbon receptor (AhR) in an attempt to metabolize and excrete these toxicants and their metabolites. These detoxification mechanisms however may come with certain energetic costs. I hypothesize that the activation of the AhR by β-Naphthoflavone (β-NF), a model AhR agonist, results in increased energetic costs requiring metabolic reorganization in rainbow trout hepatocytes. While the results obtained suggest that there are no significant energetic costs of AhR activation, analysis of enzyme activities suggests possible metabolic reorganization. This study also showed significant changes in cellular processes in hepatocytes over the incubation periods which previously were not reported. Furthermore, for the first time in fish hepatocytes, metabolic flux analysis (MFA) was used to examine intra-cellular metabolism, the applicability of which is discussed.

Bitumen recovery by the water-based extraction process produces waste streams known as tailings. When discharged into the tailing ponds, the coarse solids in the tailings stream settle out quickly, while the fine solids accumulate over years of settling to a solids content of 30-35% by weight. The formed fluid fine solids sludge, known as mature fine tailings (MFT), traps 1-3% by weight hydrocarbons within its stable slurry structure. The remediation of these mature fine tailings is one of the major challenges facing the oil sands industry. This study was intended to investigate the recovery of residual hydrocarbons in the MFT by froth flotation process. Using a laboratory Denver flotation cell operated in a batch mode, the effect of MFT dilution ratio by process water or tap water, the flotation hydrodynamics and aeration rate on hydrocarbon recovery kinetics was studied. It was found that at 1:2 dilution by weight of the MFT with process water, increasing aeration rate has a more favourable effect on recovering more than 85% of the hydrocarbons from the MFT. The hydrocarbon-rich froth produced was treated by naphtha and was found to produce a hydrocarbon product similar to diluted bitumen obtained in bitumen extraction process, suitable for upgrading. Similar approach was applied to the hydrocarbon-rich tailings from the Tailings Solvent Recovery Unit of paraffinic froth treatment. Satisfactory recovery of hydrocarbons from the MFT was obtained using a flotation column operated in a continuous mode, confirmed the results obtained from the batch tests. The tailings produced from the continuous flotation experiments were treated with polymer flocculants such as Magnafloc-1011 and Al-PAM to study the effect of hydrocarbon recovery on the remediation of the MFT. The results from initial tests showed that both flocculants were not as effective on flocculating MFT solids following the recovery of hydrocarbons by froth flotation. / in Chemical Engineering

A reliable estimate of the amount of oil or gas in a reservoir is required for development decisions. Uncertainty in reserve estimates affects resource/reserve classification, investment decisions, and development decisions. There is a need to make the best decisions with an appropriate level of technical analysis considering all available data. Current methods of estimating resource uncertainty use spreadsheets or Monte Carlo simulation software with specified probability distributions for each variable. 3-D models may be constructed, but they rarely consider uncertainty in all variables. This research develops an appropriate 2-D model of heterogeneity and uncertainty by integrating 2-D model methodology to account for parameter uncertainty in the mean, which is of primary importance in the input histograms. This research improves reserve evaluation in the presence of geologic uncertainty. Guidelines are developed to: a) select the best modeling scale for making decisions by comparing 2-D vs. 0-D and 3-D models, b) understand parameters that play a key role in reserve estimates, c) investigate how to reduce uncertainties, and d) show the importance of accounting for parameter uncertainty in reserves assessment to get fair global uncertainty by comparing results of Hydrocarbon Initially-in-Place (HIIP) with/without parameter uncertainty. The parameters addressed in this research are those required in the assessment of uncertainty including statistical and geological parameters. This research shows that fixed parameters seriously underestimate the actual uncertainty in resources. A complete setup of methodology for the assessment of uncertainty in the structural surfaces of a reservoir, fluid contacts levels, and petrophysical properties is developed with accounting for parameter uncertainty in order to get fair global uncertainty. Parameter uncertainty can be quantified by several approaches such as the conventional bootstrap (BS), spatial bootstrap (SBS), and conditional-finite-domain (CFD). Real data from a large North Sea reservoir dataset is used to compare those approaches. The CFD approach produced more realistic uncertainty in distributions of the HIIP than those obtained from the BS or SBS approaches. 0-D modeling was used for estimating uncertainty in HIIP with different source of thickness. 2-D is based on geological mapping and can be presented in 2-D maps and checked locally. / Petroleum Engineering

<p>The Bredasdorp Basin is one of the largest hydrocarbon producing blocks within Southern Africa. The E-M field is situated approximate 50 km west from the FA platform and was brought into commission due to the potential hydrocarbons it may hold. If this field is brought up to full producing capability it will extend the lifespan of the refining station in Mosselbay, situated on the south coast of South Africa, by approximately 8 to 10 years. An unexpected pressure drop within the E-M field caused the suite not to perform optimally and thus further analysis was imminent to assess and alleviate the predicament. The first step within the project was to determine what might have cause the pressure drop and thus we had to go back to cores drilled by Soekor now known as Petroleum South Africa, in the early 1980&rsquo / s.</p> <p><br> <br /> </br>Analyses of the cores exposed a high presence of granulation seams. The granulation seams were mainly subjected within sand units within the cores. This was caused by rolling of sand grains over one another rearranging themselves due to pressure exerted through compaction and faulting, creating seal like fractures within the sand. These fractures caused these sand units to compartmentalize and prohibit flow from one on block to the next. With advance inquiry it was discovered that there was a shale unit situated within the reservoir dividing the reservoir into two main compartments. At this point it was determined to use Petrel which is windows based software for 3D visualization with a user interface based on the Windows Microsoft standards. This is easy as well as user friendly software thus the choice to go with it. The software uses shared earth modeling tool bringing about reservoir disciplines trough common data modelling. This is one of the best modelling applications in the available and it was for this reason that it was chosen to apply within the given aspects of the project A lack of data was available to model the granulation seams but with the data acquired during the core analyses it was possible to model the shale unit and factor in the influences of the granulation seams to asses the extent of compartmentalization. The core revealed a thick shale layer dividing the reservoir within two sections which was not previously noted. This shale layer act as a buffer/barrier restricting flow from the bottom to the top halve of the reservoir. This layer is thickest at the crest of the 10km&sup2 / domal closure and thins toward the confines of the E-M suite. Small incisions, visible within the 3 dimensional models could serve as a guide for possible re-entry points for future drilling. These incisions which were formed through Lowstand and Highstand systems tracts with the rise and fall of the sea level. The Bredasdorp Basin consists mainly of tilting half graben structures that formed through rifting with the break-up of Gondwanaland. The model also revealed that these faults segregate the reservoir further creating bigger compartments. The reservoir is highly compartmentalized which will explain the pressure loss within the E-M suite. The production well was drilled within one of these compartments and when the confining pressure was relieved the pressure dropped and the production decrease. As recommendation, additional wells are required to appraise the E-M structure and determine to what extent the granulation seems has affected fluid flow as well as the degree of sedimentation that could impede fluid flow. There are areas still containing untapped resources thus the recommendation for extra wells.</p>

The primary objective of this study is to provide a greater understanding of the tectonic evolution of the Warburton, Cooper, Eromanga and Lake Eyre Basins in central Australia. However, this study additionally attempts to provide a greater understanding of lineaments. This study compares lineament data with a traditional tectonic analysis in order to evaluate lineaments and to best understand the tectonic evolution of the region.

The dioxin receptor (DR), a transcription factor with basic-helix-loop-helix/PERARNTSIM (bHLH/PAS) homology domains, is activated by toxic xenobiotic ligands leading to severe physiological disturbances most of which are due to deregulation of receptor’s central role in normal development. Activation mechanisms of DR in the presence of exogenous or endogenous ligands are poorly understood. Elucidation of factors involved in the activation of the receptor would assist not only in development of an optimal measure for risk assessment of levels of common environmental pollutants but also in providing novel targets for therapeutic interventions. Posttranslational modifications (PTMs) play an indispensable role in all major signal transduction pathways by increasing the inventory of chemical modifications beyond those already present in the side-chains of common amino acids. Thus, by simple on/off or complex patterns generated by these PTMs, they control a myriad of different biological outcomes. Numerous studies that have suggested an important role of posttranslational modifications in DR activation has prompted a search in this direction, however, apart from phosphorylations at Ser36 and Ser68 no other PTM sites are known. Advanced mass spectrometry (MS)-based characterisation of PTMs is an established technique that can comprehensively provide an accurate cast of all PTM variants and their locations on a protein. This thesis reports the first MS-based comprehensive characterisation of all PTM sites of the purified latent DR and preliminary analysis of identified PTM sites of the activated DR in response to developmental signals (suspension-activated DR) and signals leading to toxic outcomes (ligand-activated DR). The PTM map of the latent DR revealed from this study comprises of 25 phosphorylations, 4 monomethyl-lysines, 2 dimethyl-lysines, 1 O-acetyl-serine and 2 O-sulfono-serines. Most of the phosphorylations and other PTMs were present in the conserved regions of the protein. Investigation of the activated samples of the receptor revealed loss of the above repertoire of modifications and possible presence of some rarer modifications such as O-acetyl-serines in suspension-activated instead of O-sulfonations and pyrophosphorylation at Ser716 in both suspension- as well as ligand-activated DR. A comprehensive mutagenesis study is in progress to understand the functional consequence of each of these modification sites and unravel the functional posttranslational system in DR signalling.

This thesis is aimed to calculate the effective permeability tensor and to simulate the fluid flow in naturally fractured reservoirs. This requires an understanding of the mechanisms of fluid flow in naturally fractured reservoirs and the detailed properties of individual fractures and matrix porous media. This study has been carried out to address the issues and difficulties faced by previous methods; to establish possible answers to minimise the difficulties; and hence, to improve the efficiency of reservoir simulation through the use of properties of individual fractures. The methodology used in this study combines several mathematical and numerical techniques like the boundary element method, periodic boundary conditions, and the control volume mixed finite element method. This study has contributed to knowledge in the calculation of the effective permeability and simulation of fluid flow in naturally fractured reservoirs through the development of two algorithms. The first algorithm calculates the effective permeability tensor by use of properties of arbitrary oriented fractures (location, size and orientation). It includes all multi-scaled fractures and considers the appropriate method of analysis for each type of fracture (short, medium and long). In this study a characterisation module which provides the detail information for individual fractures is incorporated. The effective permeability algorithm accounts for fluid flows in the matrix, between the matrix and the fracture and disconnected fractures on effective permeability. It also accounts for the properties of individual fractures in calculation of the effective permeability tensor. The second algorithm simulates flow of single-phase fluid in naturally fractured reservoirs by use of the effective permeability tensor. This algorithm takes full advantage of the control volume discretisation technique and the mixed finite element method in calculation of pressure and fluid flow velocity in each grid block. It accounts for the continuity of flux between the neighbouring blocks and has the advantage of calculation of fluid velocity and pressure, directly from a system of first order equations (Darcy???s law and conservation of mass???s law). The application of the effective permeability tensor in the second algorithm allows us the simulation of fluid flow in naturally fractured reservoirs with large number of multi-scale fractures. The fluid pressure and velocity distributions obtained from this study are important and can considered for further studies in hydraulic fracturing and production optimization of NFRs.

The dioxin receptor (DR), a transcription factor with basic-helix-loop-helix/PERARNTSIM (bHLH/PAS) homology domains, is activated by toxic xenobiotic ligands leading to severe physiological disturbances most of which are due to deregulation of receptor’s central role in normal development. Activation mechanisms of DR in the presence of exogenous or endogenous ligands are poorly understood. Elucidation of factors involved in the activation of the receptor would assist not only in development of an optimal measure for risk assessment of levels of common environmental pollutants but also in providing novel targets for therapeutic interventions. Posttranslational modifications (PTMs) play an indispensable role in all major signal transduction pathways by increasing the inventory of chemical modifications beyond those already present in the side-chains of common amino acids. Thus, by simple on/off or complex patterns generated by these PTMs, they control a myriad of different biological outcomes. Numerous studies that have suggested an important role of posttranslational modifications in DR activation has prompted a search in this direction, however, apart from phosphorylations at Ser36 and Ser68 no other PTM sites are known. Advanced mass spectrometry (MS)-based characterisation of PTMs is an established technique that can comprehensively provide an accurate cast of all PTM variants and their locations on a protein. This thesis reports the first MS-based comprehensive characterisation of all PTM sites of the purified latent DR and preliminary analysis of identified PTM sites of the activated DR in response to developmental signals (suspension-activated DR) and signals leading to toxic outcomes (ligand-activated DR). The PTM map of the latent DR revealed from this study comprises of 25 phosphorylations, 4 monomethyl-lysines, 2 dimethyl-lysines, 1 O-acetyl-serine and 2 O-sulfono-serines. Most of the phosphorylations and other PTMs were present in the conserved regions of the protein. Investigation of the activated samples of the receptor revealed loss of the above repertoire of modifications and possible presence of some rarer modifications such as O-acetyl-serines in suspension-activated instead of O-sulfonations and pyrophosphorylation at Ser716 in both suspension- as well as ligand-activated DR. A comprehensive mutagenesis study is in progress to understand the functional consequence of each of these modification sites and unravel the functional posttranslational system in DR signalling.

Time-lapse seismic is a modern technology for monitoring production-induced changes in and around a hydrocarbon reservoir. Time-lapse (4D) seismic may help locate undrained areas, monitor pore fluid changes and identify reservoir compartmentalization. Despite several successful 4D projects, there are still many challenges related to time-lapse technology. Perhaps the most important are to perform quantitative time-lapse and to model and interpret time-lapse effects in thin layers. The former requires one to quantify saturation and pressure effects on rock elastic parameters. The latter requires an understanding of the combined response of time-lapse effects in thin layers and overcoming seismic vertical resolution limitation. / This thesis presents an integrated study of saturation and pressure effects on elastic properties. Despite the fact that Gassmann fluid substitution is standard practice to predict time-lapse saturation effects, its validity in the field environment rests upon a number of assumptions. The validity of Gassmann equations, ultimately, can only be tested in real geological environments. In this thesis I developed a workflow to test Gassmann fluid substitution by comparing saturated P-wave moduli computed from dry core measurements with those obtained from sonic and density logs. The workflow has been tested on a turbidite reservoir from the Campos Basin, offshore Brazil. The results show good statistical agreement between the P-wave elastic moduli computed from cores using the Gassmann equations and the corresponding moduli computed from log data. This confirms that all the assumptions of the Gassmann theory are adequate within the measurement error and natural variability of elastic properties. These results provide further justification for using the Gassmann theory to interpret time-lapse effects in this sandstone reservoir and in similar geological formations. / Pressure effects on elastic properties are usually obtained by laboratory measurements, which can be affected by core damage. I investigated the magnitude of this effect on compressional-wave velocities by comparing laboratory experiments and log measurements. I used Gassmann fluid substitution to obtain low-frequency saturated velocities from dry core measurements taken at reservoir pressure, thus mitigating the dispersion effects. The analysis is performed for an unusual densely cored well from which 43 cores were extracted over a 45 m thick turbidite reservoir. These computed velocities show very good agreement with the sonic-log measurements. This is encouraging because it implies that core damages that may occur while bringing the core samples to the surface are small and do not adversely affect the measurement of elastic properties on these core samples. Should core damage have affected our measurements, we would have expected a systematic difference between properties measured in situ and on the recovered. This confirms that, for this particular region, the effect of core damage on ultrasonic measurements is less than the measurement error. Consequently, stress sensitivity of elastic properties as obtained from ultrasonic measurements are adequate for quantitative interpretation of time-lapse seismic data. / In some circumstances, stress sensitivity may not be obtained by ultrasonic measurements. Cores may be affected by damage, bias in the plugging process and scale effects and therefore may not be representative of the in situ properties. Consequently it is desirable to obtain this dependence from an alternative method. This other approach ideally should provide the pressure - velocity dependence from an intact rock. Few methods can sample the in situ rock. Seismic, for instance, provides in situ information, but lacks vertical resolution. Well logs, on the other hand, can provide high vertical resolution information, but usually are not available before and after production changes. I propose a method to assess the in situ pressure - velocity dependence using well data. I apply this method to a reservoir made up of sandstone. I used 23 wells drilled and logged in different stages of development of a hydrocarbon field providing rock and fluid properties at different pressures. For each well logged at a specific time, pore pressure, velocity and porosity, among other properties, are known. Pore pressure is accessed from a Repeat Formation Tester (RFT). As a field depletes and new wells are drilled and logged, similar data sets related to different stages of depletion are available. I present an approach expanding Furre et al. (2009) study incorporating porosity and obtaining a three dimensional relationship with velocity and pressure. The idea is to help to capture rock property variability. / Quantitative time-lapse studies require precise knowledge of the response of rocks sampled by a seismic wave. Small-scale vertical changes in rock properties, such as those resulting from centimetre scale depositional layering, are usually undetectable in both seismic and standard borehole logs (Murphy et al., 1984). I present a methodology to assess rock properties by using X-ray computed tomography (CT) images along with laboratory velocity measurements and borehole logs. This methodology is applied to rocks extracted from around 2.8 km depth from offshore Brazil. This improved understanding of physical property variations may help to correlate stratigraphy between wells and to calibrate pressure effects on velocities, for seismic time-lapse studies. / Small scale intra-reservoir shales have a very different response from sands to fluid injection and depletion, and thus may have a strong effect on the equivalent properties of a heterogeneous sandstone reservoir. Since shales have very low permeability, an increase of pore pressure in the sand will cause an increase of confining pressure in the intra-reservoir shale. I present a methodology to compute the combined seismic response for depletion and injection scenarios as a function of net to gross (NTG or sand – shale fraction). This approach is appropriate for modelling time-lapse effects of thin layers of sandstones and shales in repeated seismic surveys when there is no time for pressure in shale and sand to equilibrate. I apply the developed methodology to analyse the sand - shale combined response to typical shale and sandstone stress sensitivities for an oil field located in Campos Basin, Brazil. For a typical NTG of 0.6, there is a difference of approximately 35% in reflection coefficient during reservoir depletion from the expected value if these shales are neglected. Consequently, not considering the small shales intra-reservoir may mislead quantitative 4D studies. / The results obtained in this research are aimed to quantify pressure and saturation effects on elastic properties. New methodologies and workflows have been proposed and tested using real data from South America (Campos Basin) datasets. The results of this study are expected to guide future time-lapse studies in this region. Further investigations using the proposed methodologies are necessary to verify their applicability in other regions.

The presence of complex mixtures of compounds in ambient air, many of which are either unknown or uncharacterised makes an assessment of risk associated with these exposures problematic. Bioanalytical methods can provide an integrative assessment of complex mixture potency for specific mechanisms of toxicity within these contexts. The aim of this study was to evaluate the suitability of monitoring ambient air exposures as sampled by (polyurethane foam) PUF passive air samplers (PAS) using effect based techniques (bioanalytical methods). Passive samplers have the advantage of offering a low-tech inexpensive monitoring strategy which can thereby increase sampling capacity across a broader range of scenarios simultaneously. One challenge posed by the application of passive samplers in particular for these assessments has been the expression of potency estimates in relatively non-comparable terms specific to a given dose of the sampler or for a specific deployment period. The project was therefore designed in order to address these aims and previously identified challenges by investigating the applicability of these techniques for: monitoring in both indoor and outdoor air, the determination of seasonal exposure gradients; the determination of exposure gradients in different locations (urban capitals, regional centres, background); and the application of in-situ calibration to provide comparable effect measurements in terms of equivalent reference compound air concentrations. Air sampled using PUF PAS was monitored for its capacity to induce biological responses which are mechanistically relevant to critical health endpoints in these scenarios. The mechanisms assessed included genotoxicity (DNA damage – umuC assay), Aryl hydrocarbon receptor (AhR) activity (CAFLUX assay), and estrogenicity (ESCREEN assay). The findings from this effect based monitoring revealed that the level of biological response measured changes with the exposure scenario (indoor vs. outdoor; summer vs. winter; urban capital cities vs. background locations). Estrogenicity for example assessed as estradiol equivalent air concentrations (E Eq BIO) averaged 54 pg.m-3 (1.5 - 185 pg.m-3) in indoor air, while samples from ambient air were found to be not estrogenic. Total aryl hydrocarbon receptor (AhR) activity assessed as 2,3,7,8-tetrachlorodibenzo-p-dioxin equivalent air concentrations (TCDD Eq BIO) averaged 4.1 pg.m-3 (1.3 – 7.2 pg.m-3) in indoor air while samples from ambient air averaged 15 pg.m-3 (1.5 – 46 pg.m-3)in summer and 53 pg.m-3 (2.2 – 251 pg.m-3) in winter. The relationship for both direct (-S9) and indirect (+S9) acting genotoxicity and AhR activity were found to be relatively consistent with respect to both season (elevated in winter) and location (elevated in urban capital cities). Overall suitable techniques were developed for combining passive sampling with multiple end-point toxicity testing and it was demonstrated that these techniques may be applied across different exposure scenarios. During the course of this method development and interpretation process a range of limitations were identified relating to: the use and application of effect based techniques to monitor environmental samples; the use of passive samplers within this context specifically; and also with the application of in-situ calibration techniques to passive samplers to improve the comparability of these assessments.