Deep geological disposal is a method of managing high level, long-­‐lived nuclear waste. It is a concept that many countries are exploring for the possibility of managing nuclear waste generated from power production. For deep geological disposal to be viable then areas where problems may surface have to be explored. Bentonite clay has been proposed as the material to be used for the backfill of the repositories. Its swelling properties ensure that it will expand to plug the bore holes that will be made for the waste, its impermeable nature restricts contact between groundwater and the waste package and its stability on a geological timescale all make it desirable as a backfill material. This project looks at the role that colloids formed from the bentonite clay could have in facilitating radionuclide transport away from a nuclear waste repository. Several radionuclides (Eu(III), U(VI), Th(IV) and Am(III)) have been considered in this research, and information from these studies will be used in the BELBaR project’s outputs, which will eventually support a disposal safety case. Ternary systems of 152Eu(III), bulk bentonite and EDTA ([Eu] = 7.9 x 10-­‐10 M; pH = 6.0 – 7.0) have been studied. Without EDTA, there was slow uptake in a two-­‐stage process, with initial rapid sorption of Eu(III) (96%), followed by slower uptake of a smaller fraction (3.0 % over a period of 1 month). The reversibility of Eu(III) binding was tested by allowing Eu(III) to sorb to bentonite for 1 – 322 days. EDTA was added to the pre-­‐equilibrated Eu bentonite systems at 0.01 M. A dissociation rate constant of approximately 4.3 x 10-­‐8 s-­‐1 (values in the range 2.2 x 10-­‐8 – 1.0 x 10-­‐7 s-­‐1) for pre-­‐equilibration times ≥ 7 days was measured. Eventually, the amount of Eu(III) remaining bound to the bentonite was within error of that when EDTA was also present prior to contact (4.5 % ± 0.6). Eu interactions with colloidal bentonite were studied, and the dissociation rate constant measured by a resin competition method. A dissociation rate of 8.8 x 10-­‐7 s-­‐1 and a range of 7.7 x 10-­‐7 – 9.5 x 10-­‐7 s-­‐1 were measured. For both bulk and colloidal bentonite slow dissociation was observed for Eu(III), but there was no evidence for ‘irreversible’ binding. The interactions of 232U(VI) with bentonite colloids ([U] = 5.43 x 10-­‐10 M; pH = 8.8 ± 0.2) have been studied using a resin ion exchange competition technique. The reversibility of the interaction was studied by allowing U(VI) to sorb to bentonite colloids for periods from 1 – 35 days. A fraction of the U(VI) was removed from the solution instantaneously (28-­‐50 %), and after 3 days, the amount of U(VI) remaining on the bentonite colloids was 17-­‐ 25%. With time, the amount of U(VI) retained by the bentonite colloid is reduced further, with a first order dissociation rate constant of 5.6 x 10-­‐7 s-­‐1. Whilst the dissociating fraction was small (24% (+34; -­‐12 %)), complete dissociation was not observed. Although slow dissociation was observed for U(VI), there was no convincing evidence for ‘irreversible binding’ of the radionuclide by the colloid. The interactions of 228Th(IV) ([Th] = 3.79 x 10-­‐12 M; pH = 8.8 ± 0.2) and 241Am(III) ([Am] = 3.27 x 10-­‐9 M; pH = 8.8 ± 0.2), with bentonite colloids have been studied using an ion exchange competition technique. Th(IV) was not fully associated with the bentonite colloids, and filtration showed that the uptake after 1 week was 78.3% (± 2.7%). Am(III) was weakly associated to the bentonite colloids, the uptake after 1 week was 20.1 % (± 5.2 %). Cellulose phosphate was added to the radionuclide/bentonite colloid systems (1 g for Th(IV), 0.2 g for Am(III)), an amount that was sufficient to retain the radionuclide when no bentonite colloids are present. A fraction of the Th(IV) is initially removed by the Cellphos (75-­‐93 %), and after 7 days the amount of Th(IV) remaining on the colloids is 1 -­‐ 3 %. Over the time of the experiment, the amount of Th(IV) retained by the bentonite colloid appears to remain level and the amount bound to the bentonite colloid at the end of the experiment is 2.1 % ± 0.88 % which is within experimental error of the steady state equilibrium of the system. A fraction (48-­‐94 %) of the Am(III) is also initially removed by the Cellphos, after 7 days the8amount of Am(III) remaining on the colloids is 1.2 – 9.3 %. However, after 35 days of contact time with the cellulose phosphate it appears that Am(III) is released back into the system, preventing dissociation rates from being calculated in this case. Studies of the association of Eu(III) to the clay colloids and its subsequent dissociation in this thesis follow similar trends to those described elsewhere in the literature (Missana et al. (2008), Bouby et al. (2011)). The Eu/bentonite colloid dissociation rate calculated here (8.8 x 10-­‐7 s-­‐1 (± 9.1 x 10-­‐7 s-­‐1)) is within error of the dissociation rates for trivalent ions estimated by Wold (2010) (Am(III) 5.6 x 10-­‐7 s-­‐1 Cm(III) 1.7 x 10-­‐6 s-­‐1). The U(VI) studies in this thesis show a dissociation rate of 5.6 x 10-­‐7 s-­‐1 (± 4.2 × 10-­‐7) which is within error of the U(VI) dissociation rate estimated by Wold (2010) (8.3 X 10-­‐7 s-­‐1). Reliable dissociation rates could not be obtained from the Am(III) and the Th(IV) studies in this thesis, other studies (e.g. Bouby et al. (2011) showed signs of irreversible binding of Th(IV) to bentonite colloids, however, no irreversible binding was observed in this thesis. Am(III) did not appear to be a close analogue of Eu(III) in these systems. All of the isotopes studied in this thesis showed no evidence of irreversible binding to bentonite or bentonite colloids. As such, the role that bentonite colloids will have in the facilitated transport of radioisotopes away from a repository is likely to have only a limited impact, at most, on the environmental safety case.

Fatty Acid Amide Hydrolase (FAAH), a serine hydrolase family protein, hydrolyzes N-acylethanolamines (NAEs) by cleaving the amide bond linking the acyl group with ethanolamine to produce free fatty acids. Highly conserved ‘Amidase Signature (AS)’ sequence rich in serine, glycine and alanine residues characterize the protein. FAAH plays role in various physiological processes by regulating NAE levels, such as seedling growth, defense response. Understanding of the role of NAEs and FAAH has been however, limited to model plant Arabidopsis. Here, with interest to understand the role of FAAH in modulating NAE composition, tomato was chosen as a model system. Recently, SlFAAH1, an ortholog of AtFAAH1 was identified in tomato and was successfully expressed in prokaryotic expression system. Protein assay with lysate of cells expressing recombinant putative SlFAAH1 showed the ability to hydrolyze a polyunsaturated NAE (NAE20:4). Currently, additional assays are being carried out to determine optimal pH, temp, substrate specificity and associated enzyme kinetics. In parallel, the effect of exogenous NAEs on SlFAAH1 expression levels and during seedling development is being evaluated. Together, this study is expected to not only characterize a protein in tomato but also determine its role in mediating NAE metabolism and seedling development, and further allows for comparison with Arabidopsis and mammalian FAAH to determine its functional conservation.

Advanced combustion engine concepts require fuels which are meticulously designed to harness full potential of novel engine technologies. To develop such fuels, better understanding of fuel properties and their effect on combustion parameters is needed. The investigations reported in this work establishes relationships between several fuel properties and combustion parameters at engine relevant conditions. Further, these findings along with conclusions from other studies are utilized to synthesize fuels and surrogate fuels with tailored combustion properties. This approach of designing fuels relies on constrained non-linear optimization of several combustion properties simultaneously to design surrogate fuels for transportation fuels to enable combustion simulations. This scheme of fuel design has been devised and presented as Fuel Design Tool in Ahmed et al. Fuel 2015. Detailed investigations have been made to understand the effect of fuel properties on the ignition of fuels in Rapid compression machines utilizing a custom built multi-zone model. The study was further extended to explore fuel effects on engine combustion utilizing experiments and modelling to gather understanding of instances of engine knocking and pollutant formation. Bio-blended fuels allow mitigation of harmful pollutants and also enables engines to operate at higher efficiency. Ignition characteristics of two high octane bio-blended gasolines were studied experimentally in rapid compression machine and shock tube and detailed chemical kinetic analysis was conducted to understand how the presence of biofuels (i.e., ethanol) in gasoline influences the evolution of important radicals controlling ignition. Another set of biofuels namely methyl acetate and ethyl acetate were studied employing fundamental experimental and computational methods. The investigation involved development and analysis of combustion chemistry models, speciation studies in jet stirred reactors, ignition delay measurements and determination of laminar burning velocities. These fuels are found suited for high performance advanced spark ignition engines and the developed model and analysis will lead to optimization of combustion performance. The developed fuel design tool along with enhanced understanding of combustion chemistry and fuel properties enables a complete toolkit ready to be utilized to develop fuels with better suited properties for the advanced combustion modes.

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Increasingly stringent legislations call for more efficient and cleaner combustion technology as well as sustainable fuels. Chemical kinetic models are required in designing and optimizing novel engine concepts as well as selecting appropriate renewable fuels. Among the many reactions controlling fuel reactivity, OH + Fuel elementary reaction is one of the most important reactions that plays a critical role from low to high temperatures. In this thesis, OH + Fuel elementary reactions are studied for a wide spectrum of conventional and renewable fuels. The overall rate coefficients are measured in a shock tube using OH time-history profiles recorded with a UV laser diagnostic. Alkanes constitute important components of gasoline and diesel. Overall rate coefficients are measured for a series of large branched alkanes and the rate rules are derived based on the next-nearest-neighbor classification method. The strength of this method lies in the ability to predict the rate coefficients for large and/or highly-branched alkanes, where both experiments and theoretical calculations are hard to reach. Next, OH reactions with bio-derived fuels, methanol and cyclic-ketones, are studied. For OH + methanol reaction, site-specific contributions from different C-H bonds are quantified using deuterium kinetic isotopic effect, and the measured rate coefficients are found to improve the general behavior of a detailed methanol kinetic model. Reactions of cyclic ketones with OH radicals are found to exhibit similar reactivity as those of similar carbon length acyclic ketones + OH reactions. Acetaldehyde is one of the most abundant hazardous byproducts in the combustion of various fuels. Similar to methanol, OH + acetaldehyde reaction is 4 studied at the site-specific level and the importance of competing reaction channels are quantified at high temperatures. Finally, reactions of OH + cyclohexadienes and OH + trimethylbenzenes, relevant for the fate of polycyclic aromatics hydrocarbons, are investigated. A highly complex temperature dependence is observed for these molecules, a six-parameter Arrhenius expression is needed to describe the overall reactivity. The work reported in this thesis provides elementary reaction data that are highly valuable for increasing the fidelity and accuracy of predictive chemical kinetic models.

Protein kinase ASK1 (apoptosis signal-regulating kinase 1) is a member of the mitogen- activated protein kinase kinase kinase (MAP3K) family and plays a crucial role in immune and stress responses. Since the increased activity of ASK1 has been linked to the development of several diseases including cancer, cardiovascular and neurodegenerative diseases, this enzyme is a promising target for therapeutical intervention in these pathologies. The molecule of ASK1 consists of 1374 amino acid residues, but catalytic activity possesses only a kinase domain located approximately in the middle of the molecule. The activity of ASK1 is regulated by interactions with various proteins including the 14-3-3 protein. This protein recognizes a phosphorylated motif around Ser966 at the C-terminus of the catalytic domain of ASK1. This binding interaction inhibits ASK1 through unknown mechanism. ASK1 under stress conditions, such as oxidative stress, is dephosphorylated at Ser966 and the 14-3-3 protein dissociates. This dissociation is then one of the factors that lead to the activation of ASK1. The aim of this diploma thesis was to prepare a complex of the catalytic domain of ASK1 with the 14-3-3 protein for subsequent structural studies. Both proteins were expressed in E. coli cells and successfully purified. In...

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The primal aim of this thesis was to establish whether kinetic aspects of vitamin B6 metabolism predispose to earlier observed racial differences found in plasma pyridoxal-5'-phosphate (PLP). The active forms of vitamin B6 namely plasma PLP and pyridoxal (PL) as well as the three enzymes expressed in the erythrocyte involved in B6 metabolism, PL kinase, PLP phosphatase and pyridoxamine -5'- phosphate (pyridoxine -5'- phosphate) [PMP(PNP) ] oxidase were measured by high performance liquid chromatography. Phase one supported earlier experimental evidence and lower plasma PLP concentrations were found in blacks in a group of200 male volunteers recruited from the South African National Defence Force (SANDF). The respective enzyme activities involved in vitamin B6 metabolism, from the same test subjects, suggested similar PLP production from PMP and PL as well as PLP dephosphorylation which result in the release of PL into the circulating fluid. Since applied exclusion criteria eliminated the majority of biochemical, physiological, genetical - and disease related factors that influence vit B6 status, dietary factors and individual preferences regarding food intake, were most likely to be responsible for the significantly lower circulating plasma PLP encountered in blacks. Phase two compared pharmacokinetic parameters between 7 black - and 9 white test subjects recruited from the South African Police Services after a single 10 mg oral supplement ofpyridoxine hydrochloride. Statistical analysis of the parameters elimination half-life, elimination rate constant, clearance, volume of distribution, mean residence time, maximum peak concentration and time to maximum peak concentration failed to demonstrate any significant differences between the two groups. These results suggest consistent appearance rate, distribution and metabolism for the metabolites PLP and PL in the study population. A tendency in slower appearance rate, for both the metabolites PLP and PL, were observed in blacks and needs to be investigated further. The end product of vitamin B6 metabolism, 4-pyridoxic acid, which was expressed in terms of 24 hour urine volume, again failed to illustrate any significant differences between blacks and whites. These results suggested similar excretion properties in my population study. Furthermore, the pharmacokinetic parameters calculated for plasma PLP and PL respectively, were found to display one-compartment - and two-compartment pharmacokinetic model characteristics. This mono- and bi exponential elimination characteristics displayed by PLP and PL respectively could be of value in future research efforts in terms of sampling time. The distribution half-life can be determined by the calculation of two-compartment macro-rate constants. Fasting blood-samples should be collected when true baseline values are needed in the case of PL. Following vit B6 supplementation, one should allow at least 5 times the distribution half-life (5-6 hr in the case of PL) before blood-sampling in order to achieve true pharmacological response. Phase three of this study was conducted to illustrate the metabolic interplay ofthe enzymes PL kinase and PMP (PNP) oxidase involved in PLP production. The kinetic parameters, Michaelis- Menten constant and maximum velocity rate, at varying substrate concentrations, for the enzymes PL kinase and PMP (PNP) oxidase, were compared in 14 white - and 14 black male test subjects recruited from the SANDF. Both the average Michaelis-Menten constant and maximum velocity rate were higher in whites, but these differences were not statistically significant. The high individual variability for both parameters calculated, can possibly be ruled out if a crystalline enzyme form is used and should be investigated further. / Dissertation (MSc (Chemical Pathology))--University of Pretoria, 2001. / Chemical Pathology / unrestricted

Our purpose was to evaluate effects of cadence manipulation on plantar loading during running. Participants (n=38) ran on a treadmill at their preferred speed in 3 conditions: preferred, 5% increased, and 5% decreased while measured using in-shoe sensors. Data (contact time [CT], peak force [PF], force time integral [FTI], pressure time integral [PTI] and peak pressure [PP]) were recorded for 30 right footfalls. Multivariate analysis was performed to detect differences in loading between cadences in the total foot and 4 plantar regions. Differences in plantar loading occurred between cadence conditions. Total foot CT and PF were lower with a faster cadence, but no total foot PP differences were observed. Faster cadence reduced CT, pressure and force variables in both the heel and metatarsal regions. Increasing cadence did not elevate metatarsal loads; rather, total foot and all regions were reduced when healthy runners increased their cadence. If a 5% increase in cadence from preferred were maintained over each mile run the impulse at the heel would be reduced by an estimated 565 body weightss (BWs) and the metatarsals 140-170 BWs per mile run despite the increased steps taken. Increasing cadence may benefit overuse injuries associated with elevated plantar loading.

The kinetics of the oxidation of platinum metal have long been a topic of interest in the field of electrochemistry. Using a combination of cyclic voltammetry, potential step experiments, and sweep-hold experiments, this research studies the kinetics of the initial stages of oxide growth on Pt(100), Pt(111), and Pt(110) surfaces. By comparing the electrochemical results with surface X-ray diffraction (SXRD) experiments conducted at synchrotron facilities, it was found that the charge of the oxide peak is within 15 μC cm⁻² or about 0.1 ML for all three surfaces. This means that the amount of oxide formed on each surface is similar. It was also determined that the oxide formed on Pt(111) is a Pt(II) species, consistent with an oxide like PtO. From calculations from the potential step experiments, it was determined that on Pt(100) there are two distinct regions of current decay, but that double layer charging is not one of the two seen. Instead, it was determined that the oxidation is likely a two step process with the first step being an adsorption step and the second being a place exchange oxide formation step. It was also found that more charge is passed when conducting potential step experiments to the oxide region from potentials in the hydrogen underpotential deposition (HUPD) region than from potentials in the double layer region. Finally, the results of a sweep-hold experiment on Pt(100) show that the values for charge are similar when calculated via the data from a sweep-hold and potential step experiment from a potential in the double layer region. The results of this research help further the kinetic understanding of the platinum surface during its oxidation and reduction. / Graduate