Constraint-based models of metabolism seldom incorporate capacity constraints on intracellular fluxes due to the lack of experimental data. This can sometimes lead to inaccurate growth phenotype predictions. Meanwhile, other forms of data such as fitness profiling data from growth competition experiments have been demonstrated to contain valuable information for elucidating key aspects of the underlying metabolic network. Hence, the optimal capacity constraint identification (OCCI) algorithm is developed to reconcile constraint-based models of metabolism with fitness profiling data by identifying a set of flux capacity constraints that optimally fits a wide array of strains. OCCI is able to identify capacity constraints with considerable accuracy by matching 1,155 in silico-generated growth rates using a simplified model of Escherichia coli central carbon metabolism. Capacity constraints identified using experimental fitness profiles with OCCI generated novel hypotheses, while integrating thermodynamics-based metabolic flux analysis allowed prediction of metabolite concentrations.

Remediation of trace element-contaminated sites must consider both the nature of the contaminants and environmental surroundings. This thesis examined treatments for two contamination scenarios. The first study characterized chromium dynamics during the redox-sorption treatment of aqueous hexavalent chromium with the reducing agent sodium dithionite and two iron oxides. Results showed that chromium was successfully removed from solution by precipitation and sorption. The iron oxide derived from ferric chloride had a greater sorption capacity for hexavalent chromium than the oxide derived from ferrous chloride. The second study examined the phytoextraction treatment of soils contaminated with multiple trace elements. Deschampsia caespitosa plants had better early growth in the contaminated high-organic matter soil than three Brassica species. However, D. caespitosa plants did not take up sufficient amounts of trace elements during the study to be considered useful for short-term phytoextraction. These findings are applicable to the development of effective trace element remediation methods.

Constraint-based models of metabolism seldom incorporate capacity constraints on intracellular fluxes due to the lack of experimental data. This can sometimes lead to inaccurate growth phenotype predictions. Meanwhile, other forms of data such as fitness profiling data from growth competition experiments have been demonstrated to contain valuable information for elucidating key aspects of the underlying metabolic network. Hence, the optimal capacity constraint identification (OCCI) algorithm is developed to reconcile constraint-based models of metabolism with fitness profiling data by identifying a set of flux capacity constraints that optimally fits a wide array of strains. OCCI is able to identify capacity constraints with considerable accuracy by matching 1,155 in silico-generated growth rates using a simplified model of Escherichia coli central carbon metabolism. Capacity constraints identified using experimental fitness profiles with OCCI generated novel hypotheses, while integrating thermodynamics-based metabolic flux analysis allowed prediction of metabolite concentrations.

The tumor suppressor p53 has a close relation with reactive oxygen species (ROS). As an indispensable component of the cellular redox system, ROS not only have been established to be involved in p53-dependent apoptosis, but also regulate p53 activity. Recent studies revealed several novel actions of p53, such as transactivation of antioxidative proteins, mitochondria translocation and inhibition of glycolysis. The fate of cells where p53 signaling pathways are initiated is either survival or death. In this review, we examine the hypothesis that ROS regulate cell fate through p53, in a way that physiological ROS levels trigger the protective pathways, while p53 behaves more like a cell killer under cytotoxic oxidative stress.

In cellular respiration, electron transfer from the breakdown of foodstuff is coupled to the formation of an electrochemical proton gradient. This is accomplished through proton translocation by respiratory complexes, and the proton gradient is subsequently used e.g. to drive ATP production. Consequently, proton- and electron-transfer reactions through the hydrophobic interior of membrane proteins are central to cellular respiration. In this thesis, proton- and electron transfer through an aa3-type terminal oxidase, cytochrome c oxidase (CytcO) from Rhodobacter sphaeroides, have been studied with the aim of understanding the molecular proton-transfer machinery of this proton pump. In the catalytic site of CytcO the electrons combine with protons and the terminal electron acceptor O2 to form water in an exergonic reaction that drives proton pumping. Therefore, CytcO must transfer both protons that are pumped and protons for the oxygen chemistry through its interior. This is done through its two proton-transfer pathways, termed the D pathway and the K pathway. Our studies have shown that the protons pumped during oxidation of CytcO are taken through the D pathway, and that this process does not require a functional K pathway. Furthermore, our data suggests that the K pathway is used for charge compensation of electron transfer to the catalytic site, but only in the A2 → P3 state transition. Our data also show that the water molecules identified in the crystal structures of CytcO play an important role in proton transfer through the D pathway. Finally, the effects of liposome reconstitution of CytcO on D-pathway proton transfer were investigated. The results suggest that the membrane modulates the rates of proton transfer through the D pathway, and also influences the extent of electron transfer between redox-active sites CuA and heme a.

Remediation of trace element-contaminated sites must consider both the nature of the contaminants and environmental surroundings. This thesis examined treatments for two contamination scenarios. The first study characterized chromium dynamics during the redox-sorption treatment of aqueous hexavalent chromium with the reducing agent sodium dithionite and two iron oxides. Results showed that chromium was successfully removed from solution by precipitation and sorption. The iron oxide derived from ferric chloride had a greater sorption capacity for hexavalent chromium than the oxide derived from ferrous chloride. The second study examined the phytoextraction treatment of soils contaminated with multiple trace elements. Deschampsia caespitosa plants had better early growth in the contaminated high-organic matter soil than three Brassica species. However, D. caespitosa plants did not take up sufficient amounts of trace elements during the study to be considered useful for short-term phytoextraction. These findings are applicable to the development of effective trace element remediation methods.

Ligand design plays an important role in the development and control of new coordination compounds. A new ligand architecture, Nindigo, has previously been reported and this study represents an expansion of that research to gain better insights into the attributes of this multifunctional ligand family. Mono- and bis-palladium chelates of Nindigo have been synthesized with resulting electrochemical measurements allowing for the reversible redox-active nature of the ligand set to be identified. The electronic absorption properties of these complexes were also studied. The presence of the palladium centre was found to drastically perturb the ligand centered π-π* transition resulting in significant red shifts in the absorption spectra with respect to free Nindigo. The main group coordination chemistry of Nindigo was explored by generating mono- and bis-BF2 Nindigo chelates. The electrochemical and spectral properties of these compounds were investigated with both families displaying weak emission in the NIR region. The bis-BF2 chelates were found to be sensitive in nature and decompose to the mono-BF2 chelates. In addition, heteroleptic complexes of mono-BF2 Nindigo chelates with palladium were also synthesized. The redox chemistry as well as the electronic absorption characteristics of these compounds provides a conceptual bridge between the two homologues. Homoleptic zinc and copper complexes of mono-BF2 Nindigo chelates have been synthesized. The zinc derivative serves as an “innocent” system where all redox and spectral properties are ligand centered and the oxidation states of both the metal and surrounding ligands can be assigned. The copper complexes exhibit more diverse chemistry with the redox and electronic absorption properties differing dramatically from the zinc system. A combination of EPR, XPS and computational analysis suggests the copper systems to be non-innocent in nature. In addition to the bis-bidentate anionic Nindigo ligand system, the fully oxidized neutral analogue has also been synthesized. DehydroNindigo exhibits significantly different chemical behaviour from Nindigo. Bridged ruthenium dimers have been synthesized that are obtained as two isomers, cis and trans (with respect to the bridging ligand). Both isomers exhibit rich electrochemical behaviour. The mixed valence states of both species are found, electrochemically, to be extremely stable with respect to disproportionation. / Graduate / 0485 / 0488 / gnawn@uvic.ca

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This dissertation focuses on understanding the complex interactions between hydrological and geochemical processes, and specifically how these interactions are affected by subsurface heterogeneity across scales. Heterogeneity in the form of macropores and fractures provide preferential flowpaths and affect contaminant transport. Biogeochemical processes are also strongly affected by such heterogeneities. Any lithological layering or interface (e.g. plume fringe, wetland-aquifer boundary, etc.) increases biogeochemical activity around that interface. Hydrologic conditions, rainfall events, drainage patterns, and pH variations are also dominant controls on redox processes and thereby affect contaminant distribution and migration. An inherent limitation of modeling fate and transport of contaminants in the subsurface is that the interactions among biogeochemical processes are complex and non-linear. Therefore, this research investigates the effect of hydrological variations and physical heterogeneity on coupled biogeochemical processes across column and landfill scales. Structural heterogeneity in the form of macropore distributions (no macropore, single macropore, and multiple macropores) in experimental soil columns is investigated to accurately model preferential flow and tracer transport. This research is crucial to agricultural systems where soil and crop management practices modify soil structure and alter macropore densities. The comparison between deterministic and stochastic approaches for simulating preferential flow improved the characterization of interface parameters of the dual permeability model, and outlined the need for efficient sampling algorithms or additional datasets to yield unique (equifinal) soil hydraulic parameters. To evaluate the effect of heterogeneity on redox processes, repacked soil columns with homogeneous and heterogeneous (layered) profiles from soil cores collected at the Norman Landfill site, Oklahoma, USA were employed. Results indicate that heterogeneity in the form of textural layering is paramount in controlling redox processes in the layered column. To evaluate the effect of hydrologic conditions on redox processes, temporal data at the Norman landfill site was used. Results indicate that seasonal hydrologic variations exert dominant control over redox-sensitive concentrations. An integrated MCMC algorithm was devised to upscale linked biogeochemical processes from the column to the field scale. Results indicate that heterogeneity and hydrologic processes are paramount in controlling effective redox concentrations at the Norman landfill site.

Along with an increasing understanding of the harmful effects on the environment of a wide range of pollutants has come the need for more sensitive, faster and less expensive detection methods of identification and quantitation. Many environmental pollutants occur in low levels and often in complex matrices thus analysis can be difficult, time consuming and costly. Because of the availability and easy cultivation of the microorganisms with potentially high specificity, there is considerable interest in the use of living microorganisms as the analytical component (the biocomponent) of sensors for pollutants. While a number of biosensors using bacteria have been developed, yeast has been comparatively rarely used as the biocomponent. Yeast are attractive because they are easy to culture and they are eukaryotes which means their biochemistry is in many respects closer to that of higher organisms. This thesis describes the development of whole cell bioassays that use yeast cells as a sensing element and redox mediators to probe the intracellular redox reactions to monitor the catabolic activity of the yeast resulting from the external substrate, steady-state voltammetry is utilised as the electrochemical detection technique. The isogenic differential enzyme analysis (IDEA) concept of Lincoln Ventures Limited, lead NERF funded research consortium uses bacteria that have been cultured using specific organic pollutants as the carbon source which are the biocomponent in sensors. The use of wild type yeast Arxula adeninivorans that has the ability to use a very wide variety of substrates as sources of carbon and nitrogen was used as an alternative to bacteria to validate the “IDEA” concept. Naphthalene and di-butyl phthalate were chosen as model target contaminant molecules. The performance, detection limits and the usefulness of yeast based biosensor applications for environmental analysis are discussed. This thesis also describes the development and optimisation of a simple, cost effective in vivo estrogens bioassay for the detection of estrogens using either genetically modified or a wild type yeast Saccharomyces cerevisiae. In this study, catabolic repression by glucose was exploited to achieve specificity to estrogens in complex environmental samples that eliminates the requirement for conventional sample preparation. This is the first time that the use of wild type yeast to quantify estrogens has been reported. The attractive features of the bioassay are its use of a non-GMO organism, its speed, its high specificity and sensitivity with a detection limit of 10-15 M. The similarity of binding affinities for major estrogens to those of human estrogens receptors makes this in vivo estrogen bioassay very useful for analytical/screening procedures. The electrochemical detection method also makes it easy to interface with a variety of electronic devices.