Graduate Theses & Dissertations


Mfsd8 regulates growth and multicellular development in Dictyostelium discoideum
The neuronal ceroid lipofuscinoses (NCLs), commonly known as Batten disease, are a family of inherited neurodegenerative lysosomal storage disorders. CLN7 disease is a subtype of NCL that is caused by mutations in the MFSD8 gene. MFSD8 encodes a lysosomal transmembrane protein that is predicted to play a role in transporting small substrates across membranes. However, little is known about its role and substrate specificity. Previous work identified an ortholog of human MFSD8 in the social amoeba Dictyostelium discoideum and reported its localization to endocytic compartments. In this study, the effects of mfsd8 loss during Dictyostelium growth and multicellular development were further characterized. Dictyostelium mfsd8- cells displayed increased rates of proliferation and pinocytosis in liquid media. During growth, loss of mfsd8 altered lysosomal enzymatic activities and reduced the intracellular and extracellular levels of autocrine proliferation repressor A. mfsd8- cells grown on a lawn of bacteria formed plaques in a shorter period of time compared to WT cells, providing additional support for the enhanced growth of mfsd8- cells. Upon starvation, the aggregation of mfsd8- cells was delayed, and mfsd8- cells formed more mounds that were smaller in size, which may be attributed to the reduced cell-substrate adhesion and altered lysosomal enzymatic activities observed for mfsd8- cells. Following aggregation, tipped mound formation was delayed, however, loss of mfsd8 did not affect the timing of slug/finger and fruiting body formation. Additionally, slug migration was reduced in mfsd8- cells. These aberrant phenotypes, excluding fruiting body formation, were effectively or partially rescued when Mfsd8-GFP was introduced into mfsd8- cells. Overall, these results show that Mfsd8 plays a role in regulating growth and developmental processes in Dictyostelium via lysosomal-associated functions. Author Keywords: CLN7, Dictyostelium discoideum, Lysosomes, MFSD8, Neuronal Ceroid Lipofuscinoses
Molecular Architectures for Improved Biomaterials Derived from Vegetable Oils – Application to Energy Storage and Lubricants
The replacement of petroleum with renewable feedstock for energy and materials has become a priority because of concerns over the environment and finite nature of petroleum. The structures of the available natural biomass feedstocks fall short in delivering key functionality required in materials such as lubricants and phase change energy storage materials (PCMs). The approach taken in this thesis was to combine select functional groups with vegetable oil derivatives to create novel PCMs and lubricantswhich deliver desired functionality. One series of diester PCMs were prepared with terephthalic acid and fatty alcohols to address known shortcomings of esters. The second class of PCMs are sulfones prepared from oxidation of fatty sulfides to improve thermal energy storage. Overall, the new PCMs presented narrow phase change temperature ranges, high transition temperature (between 67 to 110℃), high transition enthalpy (210 to 266J/g), minimal supercooling and congruent phase transitions unaffected by cooling rates. They also demonstrated higher thermal degradation stability with onset of degradation from 290 to 310℃. The series of lubricants studied consists of sulfide and sulfonyl functional groups attached to the unsaturation sites of oleyl oleate as pendant groups to improve the thermal and flow properties. The new lubricants present subzero crystallization temperatures, very low crystallization enthalpy and dynamic viscosity as high as 180mPas. Furthermore, they also presented high onset of degradation (up to 322℃) and oxidation (up to 298℃). The PCMs and lubricants of the present thesis demonstrate that select functional groups can be used with common structural elements of vegetable oil such as fatty acids, ester groups and unsaturation sites to make a variety of molecular structures capable of delivering desired properties Author Keywords: Crystal Structure, Lubricant, Phase Change Material, Renewable, Structure-Property Relationships, Vegetable Oil
Assessing habitat suitability and connectivity for an endangered salamander complex
Habitat loss and fragmentation have significantly contributed to amphibian population declines, globally. Evaluating the state of remaining habitat patches can prove to be beneficial in identifying areas to prioritize in conservation efforts. Pelee Island, Ontario is home to a complex of salamanders including small-mouthed salamanders (Ambystoma texanum), blue-spotted salamanders (A. laterale) and unisexual Ambystoma (small-mouthed salamander dependent population). These populations have declined from intense landscape changes since the late 1800s, particularly from the historical drainage of wetlands. In this thesis, I evaluated the suitability and connectivity of habitat patches occupied by these salamanders to assess the size of, and dispersal capabilities between, remaining habitat patches. I found that there was a low amount of suitable terrestrial habitat available for this complex of salamanders, and existing habitat patches were small and isolated. Forested areas and non-breeding wetlands were considered to be suitable habitat when adjacent to existing breeding locations, suggesting that these habitats should be a focus for conservation efforts. Notably, intervention may be necessary to maintain this amphibian complex as many assemblages are isolated from one another and potential corridors currently consist of primarily unsuitable habitat. Given that much of the salamander complex is reliant on one species for reproduction, the long-term viability of this population of Ambystoma salamanders may rely on the enhancement of suitable habitat near current breeding sites by conservation organizations and local stakeholders. Ultimately, the approach used in this thesis emphasizes the value of evaluating habitat within a fragmented landscape to focus conservation efforts on imperilled species. Author Keywords: amphibians, connectivity, habitat suitability, landscape fragmentation, landscape resistance, unisexual
Impacts of Cover Crops on Soil Health, Soil Nitrogen Dynamics, and Cytokinin Profiles
In Ontario, the dominant cash crop rotations consist of soybean (SB), which is a leguminous crop grown in rotation with maize (MZ) and winter wheat (WW). In addition to these crops, some farmers integrate cover crops (CC) into crop rotation, especially during the fallow period and winter seasons, to reduce nitrogen (N) losses via nitrate (NO3-) leaching and emission of N2 and the greenhouse gas nitrous oxide (N2O). This thesis focused on understanding the impact of crop phases in a MZ-(SB-WW)-CC rotation on the abundance of N-cycling bacterial communities that mediate nitrification and denitrification pathways. In addition, the influence of CCs on soil cytokinin (CK) profiles, which are plant growth-promoting hormones, were studied in a greenhouse trial to assess their potential impacts when integrating CCs into crop rotations. In particular, the relationship between traditional soil health parameters and the soil CK profiles was studied to understand how CKs might reflect biotic interactions and soil vitality. Results indicate N fertilizer application mono ammonium phosphate (MAP) and starter N:P: K (24:6:24) during WW planting in fall largely supported nitrifying bacterial communities (amoA) and potentially contributed to NO3- leaching. Management of MZ, which included spring-applied MAP resulted in larger denitrifying (nirK) bacterial communities, increasing the potential risk of N-loss via emission of dinitrogen gas (N2) and greenhouse gas N2O. However, CC soils had significantly lower nirK than MZ, reflecting the importance of strong and deep root systems of CCs, which have a higher ability to scavenge the substrates for denitrifying communities (NO3-). This highlights the importance of growing CCs in reducing the potential risk for N-loss via leaching and denitrification. Additionally, in the greenhouse trial, the ability of CCs to affect CK was detected, highlighting the importance of integrating CC in crop rotations. This is particularly noteworthy, given that total CK profiles showed strong associations with traditional soil health parameters such as labile or active carbon and soil microbial community diversity. It was concluded that total soil CK can be used as a novel and dynamic soil health measure. Future research on quantifying N2O fluxes and levels of NO3- in leachates would provide a more precise understanding of the impact of different crop rotation phases on N-dynamics in these fields. Further studies on single or combined measures of soil CKs are warranted to develop its potential as a practical and effective soil health parameter. Author Keywords: Cover crops, Crop rotations, Cytokinin hormone, Nitrogen Cycle, qPCR, Soil health
Effect of Attending a Virtual Oncology Camp on Childhood Cancer Patient's Pyshcosocial Functioning and Parental Stress - A Pilot Study
Objectives/purpose: The current study examined whether attending a 1-month virtual oncology camp (VOC) improved resilience and hope in childhood cancer patients and parental/caregiver stress. Methods:Childhood cancer patients/survivors and their parent/caregivers enrolled for VOC, participated in an online anonymous survey: before, after and 3-months after VOC. The survey included the Child and Youth Resilience Measure (CYRM) and the Snyder’s Children’s Hope Scale (CHS) for the childhood cancer patients/survivors and the Pediatric Inventory for Parents (PIP) for parent/caregivers. Results:CYRM scores increased from T1 to T2 (d=0.86). Compared to T1, at T2 CHS scores also increased (d=1.33). Both CHS and CYRM scores remained higher at T3 compared with T1 (d=1.34; d=0.86). There were no changes in PIP scores between any time points. Conclusion and significance: Our study demonstrated that participation in a VOC improved children’s resilience and hope but did not change parental stress. Highlighting the clinical significance of these VOCs and the impacts they have on childhood cancer patients/survivors. Author Keywords: cancer, children, hope, parental stress, resilience, virtual oncology camp
Organic Matter and Total Mercury in Acid-Sensitive Lakes in Ireland
The following study measured dissolved organic carbon (DOC) and total mercury (THg) concentrations in acid sensitive lakes in the Republic of Ireland. Sixty-eight upland lakes and 48 lowland lakes were sampled for DOC; the upland lakes were additionally sampled for THg. Spatial variability of DOC was explained by regional precipitation and soil organic matter. A subset of lakes was tested for long-term trends and in contrast to reports of rising DOC in European surface waters, changes in DOC were minor. Spatial variability in THg was explained by DOC and organic matter aromaticity. Long-term THg concentrations increased, likely caused by inputs of terrestrial THg. A subset of lakes was sampled for sediment and soil and the results suggested soils drove THg variation in lake water and sediment. Lake water and sediment THg was low and consistent with background regions, while soil THg was relatively high due to high organic content. Author Keywords: Dissolved Organic Carbon, Lakes, Organic Matter, Soil, Total Mercury, Water
Active layer thermal regime in subarctic wetlands at the southern edge of continuous permafrost in Canada
The fine-scale controls of active layer dynamics in the subarctic at the southern edge of continuous permafrost are currently poorly understood. The goal of this thesis was to understand how environmental conditions associated with upland tundra heath, open graminoid fen, and palsas/peat plateaus affected active layer thermal regime in a subarctic peatland in northern Canada. Indices of active layer thermal regime were derived from in-situ measurements of ground temperature and related to local measurements of air temperature, snow depth, and surface soil moisture. Active layer thaw patterns differed among landforms, with palsas and tundra heath having the least and greatest amount of thaw, respectively. Tundra heath thaw patterns were influenced by the presence of gravel and sandy soils, which had higher thermal conductivity than the mineral and organic soils of fens and palsas. Vegetation also influenced thaw patterns; the lichen cover of palsas better protected the landform from incoming solar radiation than the moss, lichen, and low-lying shrub cover of upland tundra heath, thus allowing for cooler ground temperatures. Air temperature was the most significant predictor of active layer thermal regime. Surface soil moisture varied among landforms and greater surface soil moisture reduced the amount of active layer thaw. These findings improved understanding of how landform and climate can interact to affect the active layer. Author Keywords: Active layer thermal regime, Active layer thickness, Climate change, Peatland, Permafrost, Subarctic
Linking large scale monitoring and spatially explicit capture–recapture models to identify factors shaping large carnivore densities
Understanding the spatial ecology of large carnivores in increasingly complex, multi-use landscapes is critical for effective conservation and management. Complementary to this need are robust monitoring and statistical techniques to understand the effect of bottom-up and top-down processes on wildlife population densities. However, for wide-ranging species, such knowledge is often hindered by difficulties in conducting studies over large spatial extents to fully capture the range of processes influencing populations. This thesis addresses research gaps in the above themes in the context of the American black bear (Ursus americanus) in the multi-use landscape of Ontario, Canada. First, I assess the performance of a widely adopted statistical modelling technique – spatially explicit capture-recapture (SECR) – for estimating densities of large carnivores (Chapter 2). Using simulations, I demonstrate that while SECR models are generally robust to unmodeled spatial and sex-based variation in populations, ignoring high levels of this variation can lead to bias with consequences for management and conservation. In Chapter 3, I investigate fine-scale drivers of black bear population density within study areas and forest regions by applying SECR models to a large-scale, multi-year black bear spatial capture-recapture dataset. To identify more generalizable patterns, in Chapter 4 I then assess patterns of black bear density across the province and within forest regions as a function of coarse landscape-level factors using the same datasets and assess the trade-offs between three different modeling techniques. Environmental variables were important drivers of black bear density across the province, while anthropogenic variables were more important in structuring finer-scale space use within study areas. Within forest regions these variables acted as both bottom-up and top-down processes that were consistent with ecological influences on black bear foods and intensity of human influences on the species’ avoidance of developed habitats. Collectively, this thesis highlights the opportunities and challenges of working across multiple scales and over expansive landscapes within a SECR framework. Specifically, the multi-scale approach of this thesis allows for robust inference of the mechanisms structuring fine and broad scale patterns in black bear densities and offers insight to the relative influence of top-down and bottom-up forces in driving these patterns. Taken together, this thesis provides an approach for monitoring large carnivore population dynamics that can be leveraged for the species conservation and management in increasingly human-modified landscapes. Author Keywords: animal abundance, black bear, capture-recapture, density estimation, statistical ecology, wildlife management
Land Cover Effects on Hydrologic Regime within Mixed Land Use Watersheds of East-Central Ontario
Land cover change has the potential to alter the hydrologic regime from its natural state. Southern Ontario contains the largest and fastest growing urban population in Canada as well as the majority of prime (Class I) agricultural land. Expansions in urban cover at the expense of agricultural land and resultant ‘agricultural intensification’, including expansion of tile drainage, have unknown effects on watershed hydrology. To investigate this, several streams with a range of landcovers and physiographic characteristics were monitored for two years to compare differences of flashiness and variability of streamflow using several hydrologic metrics. Urban watersheds were usually the flashiest while agriculture had moderate flashiness and natural watersheds were the least flashy across all seasons, signifying that landcover effects were consistent across seasons. Tile drainage increased stream flashiness during wet periods, but minimized the stream response to an extreme rain event in the summer, perhaps due to increases in soil moisture storage. A sixty-year flow analysis showed that flashiness and streamflow increased (p < 0.05) above a development threshold of ~10% of watershed area. Flashiness was also greater in wetter years suggesting that climate shifts may enhance stream variability in developed watersheds. Author Keywords: Agriculture, Flashiness, Hydrologic Metrics, Hydrologic Regime, Landcover Change, Urban
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
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
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


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