Calcium phosphates are important compounds as they exist in natural aqueous systems such as rivers, lakes, ocean, and soil. These calcium phosphates are widely used to provide information on paleotemperatures as well as many anthropological features, such as paleodiets. One of the most ubiquitous forms of calcium phosphate is hydroxyapatite (Ca10(PO4)6(OH)2) which is a major component of hard tissue such as bones, fossils, and tooth enamel. The oxygen isotope systematics in the hydroxyapatite associated with carbonate-water system will provide further information to allow for the reconstruction of terrestrial and marine environments. For example, Fricke et al. (1998) used oxygen isotope analysis of the carbonate components of hydroxyapatite in tooth enamel of mammals to investigate changes in terrestrial climate. Therefore, the purpose of this research study was to examine the oxygen isotope systematics in inorganic carbonate-bearing hydroxyapatite and water at low temperatures. This Master’s thesis followed and modified the methods described in Lécuyer et al. (2010) in an attempt to synthesize hydroxyapatite crystals and carbonate-bearing hydroxyapatite. The crystals synthesized were characterized in terms of several conditions (i.e., influence of mixing rate and maturations, pH, and concentrations of NaHCO3). Methods to produce hydroxyapatite were developed and analyzed using X-Ray diffraction analysis. The results demonstrated a strong dependence of pH in the hydroxyapatite solutions. Moreover, the effect of concentrations of NaHCO3 was deemed to be essential in order to obtain the desired amount of structural carbonates in the hydroxyapatite crystals. Furthermore, this research evaluated the temperature dependence of oxygen isotopic fractionation between HAP-bound carbonate and water at 10, 25, and 40 oC. Our study is the first to assess the two mixing-rates experiments with different maturations (7 and 14 days) on the oxygen isotope effects and fractionation behaviour between HAP-bound carbonate and water. Both maturation time and the effect of initial concentration of NaHCO3 were found to be the most important in determining the equilibrium conditions in our experiments. / Dissertation / Master of Science (MSc)

Antibiotics and their corresponding resistance genes act as a tool to control bacterial survival. Antibiotic resistance is used to select for desired engineered cells, and study how pathogens acquire resistance to continue infection. Here, we develop tools to control the expression of antibiotic resistance genes using light. To accomplish this, we use optogenetics, the regulation of cellular behavior using light as a direct and programmable input for gene expression. We develop an optogenetic recombinase in Escherichia coli through split-protein engineering techniques, and characterize the behavior of our best candidate in detail: a split Cre recombinase that responds to blue light. We apply this optogenetic system to control the expression of resistance genes for four antibiotics: ampicillin/carbenicillin, kanamycin, chloramphenicol, and tetracycline. By varying the expression levels of these genes, we tune the concentrations at which bacteria can survive before and after light exposure. We then apply this system to improve production of fatty acids. Finally, we make progress toward characterizing the impact of resistance activation timing on bacterial survival. This work creates tools that are broadly useful for spatiotemporal control of bacterial survival, and enables precise studies on how bacterial resistance spreads at the single-cell level. / 2024-08-29T00:00:00Z

A novel approach to access N-Aryl nitrones via copper catalyzed coupling of benzyl alcohols with nitrosobenzenes is described. The results of mechanistic studies are conflicting but suggest this reaction proceeds through either redox process or a nucleophilic nitroso hydrate intermediate formed in situ, which was previously unprecedented. The unique electronics of this process allow access to nitrones with excellent step and atom economy, which are otherwise difficult to make using conventional methods. In this work, a total of 22 nitrones have been made. 15 of which from pure starting materials with yields ranging from 26 - 89 % and another 7 from two step, one pot reactions where the nitrosobenzenes were made in situ from commercially available anilines and reacted in a subsequent step to produce the nitrone in 8 - 46 % yield. In addition to the nitrone forming reaction occurring in the second step of a two-step sequence, we have also shown that subsequent reactions can be done on newly formed nitrones in one pot. This was demonstrated with a newly synthesized nitrone and a donor-acceptor cyclopropane in a [3+3] annulation reaction forming the cycloadduct in 90% yield. / Thesis / Master of Science (MSc) / With over 250 000 cases of resistant bacterial infections reported, and more than 5 400 directly causing Canadian deaths in 2018, we are currently facing an antibiotic crisis[67]. A particularly worrying class of resistance involves Gram-negative bacteria, as their highly impermeable outer membrane poses added complexity to their evolved resistance mechanisms[68]. The outer membrane restricts the chemical matter able to cross, making the bacteria intrinsically resistant to small molecule antibiotics and other compounds which may have intracellular targets[69],[70]. This barrier is therefore a major bottleneck for cellular mechanistic studies and compound mechanism of action, as these small molecules cannot gain entry to the cell. To circumvent this issue, outer membrane permeabilizing compounds must be discovered so that these systems can be more effectively studied. Commonly used membrane active compounds such as colistin and its derivatives, interact with both the outer and inner membranes of Gram-negative bacteria, and are toxic to cells[71]. Therefore, molecules that are outer membrane selective and nontoxic to Gram negative bacteria would be useful tools to expedite the study of biological systems.

The noise generated by jet engines represents a significant environmental concern that still needs to be addressed. Accurate and efficient numerical predictions are a key step towards reducing jet noise. The current standard in highidelity prediction of jet noise is large eddy simulation (LES), which resolves the large turbulent scales responsible for the low and medium frequency noise and models the smallest turbulent scales that correspond to the high frequency noise. While LES requires significant computational resources to produce an accurate solution, it fails to resolve the noise in the high frequency range, which cannot be simply ignored. To circumvent this, in this dissertation the Coupled LES-Synthetic Turbulent method (CLST) was developed to model the missing frequencies that relate to un-resolved sub-grid scale fluctuations in the flow. The CLST method combines the resolved, large-scale turbulent fluctuations from very large eddy simulations (VLES) with modeled, small-scale fluctuations from a synthetic turbulence model. The noise field is predicted using a formulation of the linearized Euler equations (LEE), where the acoustic waves are generated by source terms from the combined fluctuations of the VLES and the synthetic fields. This research investigates both a Fourier mode-based stochastic turbulence model and a synthetic eddy-based turbulence model in the CLST framework. The Fourier mode-based method is computationally less expensive than the synthetic eddy method but does not account for sweeping. Sweeping and straining of the synthetic fluctuations by large flow scales from VLES are accounted for in the synthetic eddy method. The two models are tested on a Mach 0.9 jet at a moderately-high Reynolds number and at a low Reynolds number. The CLST method is an efficient and viable alternative to high resolution LES or DNS because it can resolve the high frequency range in the acoustic noise spectrum at a reasonable expense.

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The concept of gamification is being increasingly explored and applied to offer new teaching or training tools to teachers, students or employees. The field of geology and geometallurgy wasn’t particularly discussed in the topic of gamification. With the objective of creating a synthetic geometallurgical database and a game structure for a gamified simulation of a metal mine, the eastern part of the Malmberget deposit in Sweden was simplified and modelled.The geological model was obtained with assumptions of continuity and proximity, and the lack of data was reconciled using targeted randomization and regular statistics to achieve a smoother and realistic result. A rule book was created to establish the framework that a geometallurgy game should follow,using a slightly adapted version of the Desing thinking framework by the Nielsen group, which consists of elaborating ideas and concepts, implementing them and testing the results before integrating feedbacks to the creation of future elements. The accent was put on obtaining an interactive experience where the player can try various things with a reasonable difficulty, and an accessibility to feedbacks.The purpose of this project is to elaborate a mining simulation game, that could be a valuable tool in the understanding of the interdisciplinary concept of geometallurgy, as well as raising the awareness about sustainable development and how mining can be a part of it. The starting point of this project is another attempt at gamifying geometallurgy by P. Lamberg. The simulation of mineral processing was done using the HSC Sim utilizing 8 different flowsheets that were designed to offer a variety and enable strategic choices. The events occurring at a real mine and beneficiation plant were translated into simple rules. The outcome is a realistic geological and processing model, which through the addition of mining, economics and market strategy, becomes a comprehensive geometallurgy database.