Graduate Theses & Dissertations

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SARS-CoV-2 Protein-based Detection Using Localized Surface Plasmon Resonance
During the COVID-19 pandemic, nucleic acid and antibody-based testing methods were heavily relied upon, but can be costly, time-consuming and exhibit high false -negative and -positive rates. Thus, alternative strategies are needed. Viral antigens such as the SARS-CoV-2 spike (S) glycoprotein are critical in the function of the virus and useful as diagnostic biomarkers for viral infections. For biosensing applications, aptamers are suitable high-affinity and cost-effective binding partners for their specific targets. Using localized surface plasmon resonance (LSPR), real-time, rapid acquisition of results can be achieved, essential for improving the efficacy of a sensor. Herein, LSPR aptamer sensors were fabricated for the detection of the SARS-CoV-2 protein. Data indicate that the best performing aptasensor was the streptavidin-biotin sensor, while the current gold aptasensor exhibited lower sensitivity and the fabrication of the carboxyl aptasensor was unsuccessful. The S1 aptamer selectively bound the S1 protein with high binding affinity. Excellent shelf-life stability, reusability, and high recovery in complex matrices was also maintained. Additionally, a receptor binding domain (RBD) functionalized sensor was fabricated to examine the interactions with angiotensin converting enzyme 2 (ACE2), for future assessment of inhibitors used in drug therapies. Overall, LSPR has been demonstrated as a viable tool for measuring SARS-CoV-2 related aptamer-protein and protein-protein interactions, and this strategy may be applied to other viral or non-viral antigen targets. Author Keywords: Antigen-based Detection, Coronavirus, COVID-19, Inhibition, Localized Surface Plasmon Resonance, SARS-CoV-2
The Relations Between Identity Developmental Processes, Study Habits, and Academic Performance
Adolescence is a time when young people focus their attention on setting and pursuing long-term goals. Contemporary approaches of identity development focus on three pivotal processes underlying the identity formation process and the maintenance of one’s identity (e.g., core values, etc.). These processes are commitment (commitments to a goal), in-depth exploration (exploration of choices and options), and reconsideration of commitment (feelings of uncertainty about current commitments). The primary purpose of the current study was to examine the relations between identity processes, study habits, and academic performance in 45 female undergraduate students (M age = 21.00). Utilizing a self-report measure, findings suggested a significant positive relation between educational and relational commitment, as well as reconsideration of commitments in the educational domain and reconsideration of commitments in the relational domain. In terms of identity processes and grades, a regression analysis revealed that educational reconsideration of commitments predicted academic performance. Further, for those employing poor study habit skills, educational reconsideration of commitment predicted academic performance. The present study offers insight on the importance of assessing adolescent’s uncertainty of educational and relational commitments, while also highlighting the protective factor of maintaining good study habit strategies. Author Keywords: academic performance, adolescence, educational, identity, relational, study habits
Exploring the Role of Natural Antisense Transcripts in the Stress Response of Ustilago maydis
Fungal pathogens adapt to environmental changes faster than their hosts, due in part to their adaptive mechanisms exhibited in response to stress. Ustilago maydis was used to investigate potential natural antisense transcript (NAT) RNA-mediated mechanisms that enhance fungal adaptation to stress. Of the 349 NATs conserved amongst U. maydis and two related smut fungi, five NATs were identified as having altered transcript levels in response to multiple stress conditions. Subsequently, antisense transcript expression vectors were created for select NATs and transformed into U. maydis haploid cells. When exposed to stress conditions, two antisense expressing mutant strains exhibited alterations in growth. RT-qPCR analysis of mRNA complementary to expressed NATs revealed no significant change in mRNA levels, which suggests NAT expression may influence stress response through dsRNA formation or other RNA mediated mechanisms. These results establish a basis for further investigations into the connection between NATs and the stress response of fungi. Author Keywords: natural antisense transcripts, non-coding RNAs, stress response, Ustilago maydis
Ê-NITONAHK MIYO-PIMÂTISIWIN (SEEKING THE GOOD LIFE) THROUGH INDIGENOUS DANCE
This thesis is about the ways in which Indigenous dance serves as a social determinant of Indigenous health and well-being. Utilizing both contemporary and traditional versions of the Medicine Wheel for the framework, analysis and organization of the thesis allows for a holistic perspective which includes the spiritual, physical, emotional and mental aspects. The importance of Indigenous dance for Indigenous health and well-being is confirmed through: existing literature; interviews with Indigenous choreographers, dancers, theatre artists, and performers; Indigenous exponents of the forms; and Indigenous Elders. In order to contextualize current practices of Indigenous dance, the history of Indigenous dance in relation to colonization is presented. The research and experiences of co-researchers show the need for Indigenous dance and culture to be supported as a social determinant of health and well-being. Author Keywords:
Gene flow directionality and functional genetic variation among Ontario, Canada Ursus americanus populations.
Rapidly changing landscapes introduce challenges for wildlife management, particularly for large mammal populations with long generation times and extensive spatial requirements. Understanding how these populations interact with heterogeneous landscapes aids in predicting responses to further environmental change. In this thesis, I profile American black bears using microsatellite loci and pooled whole-genome sequencing. These data characterize gene flow directionality and functional genetic variation to understand patterns of dispersal and local adaptation; processes key to understanding vulnerability to environmental change. I show dispersal is positively density-dependent, male biased, and influenced by food productivity gradients suggestive of source-sink dynamics. Genomic comparison of bears inhabiting different climate and forest zones identified variation in genes related to the cellular response to starvation and cold. My thesis demonstrates source-sink dynamics and local adaption in black bears. Population management must balance dispersal to sustain declining populations against the risk of maladaptation under future scenarios of environmental change. Author Keywords: American black bear, Dispersal, Functional Genetic Variation, Gene Flow Directionality, Genomics, Local Adaptation
Functional Variation within Middle Paleolithic Ground Stone Tools
In the southern Levant, ground stone tools (GST) provide insight into early plant food exploitation, butchery, and cognition. Outside of these examples, GST evidence is scarce, particularly for the Middle Paleolithic. An extensive assemblage of GST recovered from Nesher Ramla, an open-air hunting camp in Israel, presents the unique opportunity to study the role of GST within Middle Paleolithic behaviour. Use-wear and residue analysis, together with replication experiments are employed to investigate GST function within a specific period of site use by focusing on GST from the Upper Sequence (Units I-II) which reflects a trend of decreasing site-use intensity. The results indicate that GST were employed for bone breaking and knapping during the final phases of occupation while comparison with Unit V suggests longer occupations involved more diverse and extensive use of GST. GST at open-air sites are also proposed to represent a strategy for intensive exploitation of location-specific resources. Author Keywords: Ground Stone Tools, Hammerstones, Middle Paleolithic, Residue Analysis, southern Levant, Use-Wear Analysis
Heteronormativity in Virtual World Design
The purpose of this research is to highlight the limitations and opportunities for playful expression of gender identity in character creation systems of virtual worlds, and how these might work to reinforce, or disrupt, the heteronormative imperative. The primary sites considered in this analysis are the video game World of Warcraft and the live action role-playing game Amtgard. I provide evidence that while the World of Warcraft’s character creation system is sexist and works to reinforce heteronormative ideology, Amtgard’s relatively ambiguous design provides opportunity for disruption of these norms. Participant research with Amtgard players demonstrates actual instances of Amtgard’s more flexible character creation system being utilized in expression and exploration of gender identity which resists the heteronormative imperative. Based on this, I call on game developers to reject designs which necessitate selection of gender from within the traditional binary and embrace more ambiguous design in development of character creation systems. Author Keywords: Avatars, Game Design, Games, Gender, Identity, Virtual Worlds
Interseeded Cover Crops in Ontario Grain Corn Systems
Ontario grain corn is highly valuable, accounting for 60% of Canada’s total corn output. Grain producers are increasingly interested in including cover crops (CCs) in their cropping systems, but they have concerns regarding successful CC establishment and potential adverse competitive effects on corn yield and nutrient status. One option to improve the success of CC establishment is the interseeding in corn at the V4 -V6 stages. Interseeding improves the chances of good CC establishment, with potential benefits for soil health, weed control, and plant productivity. This thesis research was conducted to evaluate the short-term effectiveness of interseeding annual ryegrass (AR), red clover (RC), and their mixture (MIX) in grain corn at three locations in central and southwestern Ontario. Cover crop and corn yields, and their nitrogen (N) uptake, residual soil N, soil biological parameters, weed biomass, and residue decomposition rates were measured. CC biomass was highly variable (range: 0 - 1.6 Mg ha-1), influenced by climatic conditions, location, and CC type. Total carbon (C) and N contributions from CCs were similarly influenced by site-year and CC type. Regression analyses showed significant influence of corn biomass on CC establishment. Red clover had a significantly lower C/N ratio (11.8) than AR (18.2) and MIX (15.6). Strikingly, the amount of CC biomass accumulated in early spring reduced weeds by 50%. Moreover, CCs did not reduce corn grain or stover yield, nor N uptake, and soil mineral N in either fall or spring. Soil metabolic activity measured by BIOLOG Ecoplates was significantly greater in plots with AR than RC, MIX or NOCC. Soil biological parameters showed no CC effect. Results of residue decomposition i.e., C and N mineralization showed negligible CC residue effects on corn stover decomposition or N immobilization. The findings from this research suggest the need for assessing a more diverse range of CCs over longer durations to establish more specific CC niches for improving soil health in Ontario corn systems. Author Keywords: CLPP, cover crops, grain corn, nitrogen uptake, residue decomposition, soil health
Abundance and Distribution of Microplastics in Lake Scugog Catchment, Ontario
Plastic pollution is a growing concern, owing to its durability, ubiquity, and potential health impacts. The overall objective of this study was to assess the abundance and distribution of microplastics within Lake Scugog catchment, Ontario. This was fulfilled through two tasks (i) the development of a microplastic particle budget for the lake catchment, and (ii) the determination of the dry deposition of atmospheric microplastics in Port Perry, Ontario. The total input of microplastics into Lake Scugog (atmospheric deposition and stream inflow) was 2491 x106 mp/day, while the output (lake outflow and sedimentation) was 1761 x106 mp/day, suggesting that 29% of inputs were retained in the lake. The dry deposition of microplastics in Port Perry was 1257 mp/m2/day, which was high when compared to bulk deposition (37 mp/m2/day) in the same area. By quantifying the major pathways of microplastics better management techniques can be implemented. Author Keywords: Catchment, Dry Deposition, Microplastics, Ontario, Particle Budget, Plastic pollution
Nutrigenomics of Daphnia
Organismal nutrition lies at the interface between biotic and abiotic factors in an ecosystem, dictating the transfer of energy and nutrients across trophic levels. Our ability to detect nutritional limitation in consumers is reliant on a priori knowledge of dietary history due to our inability to differentiate nutrient stress based on body-wide responses. Molecular physiological responses are increasingly being used to measure physiological stress with high levels of specificity due to the specific modes of action ecological stressors have on organismal molecular physiology. Because animal consumers respond to varying nutrient supplies by up- and down-regulating nutrient-specific metabolic pathways, we can quantify nutritional status by quantifying the expression of those pathways. Here I present an investigation into the use of transcriptomics to detect nutritional stress in the keystone aquatic herbivore, Daphnia pulex, I use RNAseq and quantitative PCR (qPCR) identify nutritional indicator genes. I found that nutritional status could be determined with 100% accuracy with just ten genes. Additionally, the functional annotation of those genes uncovered previously unidentified responses to dietary stress. Further testing and validation of the selected indicator genes is required however these findings have the potential to revolutionize our ability to measure and monitor consumer nutritional stress. Author Keywords: Biomarkers, Daphnia, Gene expression, Nutrigenomics, Nutritional ecology, RNAseq
Islands, ungulates, and ice
Central to wildlife conservation and management is the need for refined, spatially explicit knowledge on the diversity and distribution of species and the factors that drive those patterns. This is especially vital as anthropogenic disturbance threatens rapid large-scale change, even in the most remote areas of the planet. My dissertation examines theinfluence of land- and sea-scape heterogeneity on patterns of genetic differentiation, diversity, and broad-scale distributions of island-dwelling ungulates in the Arctic Archipelago. First, I investigated genetic differentiation among island populations of Peary caribou (Rangifer tarandus pearyi) in contrast to continental migratory caribou (Rangifer tarandus) and evaluated whether genetic exchange among Peary caribou island populations was limited by the availability of sea ice – both now and in the future. Differentiation among both groups was best explained by geodesic distance, revealing sea ice as an effective platform for Peary caribou movement and gene flow. With future climate warming, substantial reductions in sea ice extent were forecast which significantly increased resistance to caribou movement, particularly in summer and fall. Second, I assessed genetic population structure and diversity of northern caribou and deciphered how Island Biogeography Theory (IBT) and Central Marginal Hypothesis (CMH) could act in an archipelago where isolation is highly variable due to the dynamics of sea ice. Genetic differentiation among continental and island populations was low to moderate. In keeping with IBT and CMH, island-dwelling caribou displayed lower genetic diversity compared to mainland and mainland migratory herds; the size of islands (or population range) positively influenced genetic diversity, while distance-to-mainland and fall ice-free coastlines negatively influenced genetic diversity. Hierarchical structure analysis revealed multiple units of caribou diversity below the species level. Third, I shifted my focus to the terrestrial landscape and explored the elements governing species-environment relationships. Using species distribution models, I tested the response of caribou and muskoxen to abiotic versus abiotic + biotic predictors, and included distance to heterospecifics as a proxy for competitive interactions. Models that included biotic predictors outperformed models with abiotic predictors alone, and biotic predictors were most important when identifying habitat suitability for both ungulates. Further, areas of high habitat suitability for caribou and muskoxen were largely disjunct, limited in extent, and mainly outside protected areas. Finally, I modelled functional connectivity for two genetically and spatially disjunct groups of island-dwelling caribou. For High Arctic caribou, natural and anthropogenic features impeded gene flow (isolation-by-resistance); for Baffin Island caribou we found panmixia with absence of isolation-by-distance. Overall, my dissertation demonstrates the varying influences of contemporary land- and sea-scape heterogeneity on the distribution, diversity and differentiation of Arctic ungulates and it highlights the vulnerability of island-dwelling caribou to a rapidly changing Arctic environment. Author Keywords: Circuitscape, connectivity, Island Biogeography, landscape genetics, population structure, species distribution models
Particulate Matter Component Analyses in Relation to Public Health in Canada
This thesis explores the shot-term relationship between exposure to ambient air pollution and human health through metrics such as mortality and hospitalization in Canada. We begin by detailing the organization and interpolation of air pollution data from its partially quality-controlled source form. Analyses of seasonal, regional and temporal trends of all major components of PM2.5, was performed, showing a seasonal variation across most regions and validating the dataset. A one-pollutant statistical Generalized Additive Model was applied to the data, estimating the health risk associated with exposure to thirteen different components of PM2.5. The selected components were based on those that compromised the majority of the mass and included: sulphate, nitrate, zinc, silicon, iron, nickel, vanadium, potassium, organic carbon, organic matter, elemental carbon, total carbon. Trends based on annual estimates of the association for PM2.5, and its constituents,were compared, showing that carbonaceous compounds, sulphate and nitrate had similar estimates of association. Many estimates, as is common in population ecologic epidemiology, had association estimates statistically indistinguishable from zero, but with clear features of interest, including evident differences between cold and warm season associations in Canada's temperate climate. A method to model two correlated pollutants (in this case, PM2.5 and O3) was developed using thin plate splines. In this approach, the location of the response surface (after accounting for the temperature, a smooth function of time and day of week) that corresponds to the average pollutant concentration and the average plus one unit was used as the estimate of the joint contribution of pollutants due to a unit increase. The estimates from the thin plate spline (TPS) approach were compared to the single pollutant models, with large increases and decreases in PM2.5 and O3 being captured in the TPS estimates. However, this approach indicated significantly larger error in the estimates than would be expected, indicating a possible future area for refinement. Author Keywords: Air pollution, Environmental Epidemiology, Generalized Additive Models, Human Health, Multivariate Models, Thin Plate Splines

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1973 - 2033
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Format: 2023/01/28