Graduate Theses & Dissertations

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role of Cln5 in autophagy, using a Dictyostelium discoideum model of Batten disease
This thesis investigated the role of the neuronal ceroid lipofuscinosis protein, Cln5, during autophagy. This was accomplished by performing well-established assays in a Dictyostelium cln5 knockout model (cln5-). In this study, cln5- cells displayed a reduced maximum cell density during growth and impaired cell proliferation in autophagy-stimulating media. cln5- cells had an increased number of autophagic puncta (autophagosomes and lysosomes), suggesting that autophagy is induced when cln5 is absent. cln5- cells displayed increased amounts of ubiquitin-positive proteins but had no change in proteasome protein abundance. During the development of cln5- cells, fruiting bodies developed precociously and cln5- slug size was reduced. Lastly, when cln5- cells were developed on water agar containing ammonium chloride (NH4Cl), a lysosomotropic agent, the formation of multicellular structures was impaired, and the small slug phenotype was exaggerated. In summary, these results indicate that Cln5 plays a role in autophagy in Dictyostelium. The cellular processes that regulate autophagy in Dictyostelium are similar to those that regulate the process in mammalian cells. Thus, this research provides insight into the undefined pathological mechanism of CLN5 disease and could identify cellular pathways for targeted therapeutics. Author Keywords: Autophagy, Batten disease, Cln5, Dictyostelium discoideum, NCL
Range dynamics of two closely related felids
Species ranges are changing and the rate at which the climate is warming is faster than anything previously seen in the past, consequently species will need to adapt quickly, track the climate or perish. Cold adapted terrestrial species are the most vulnerable, because they are limited by the availability of land at the cold edge of their range. This means that many alpine, boreal and polar species essentially have nowhere to go as the climate warms. Habitat generalists are widely distributed across the globe and are highly adaptable to anthropogenic change. Our future biodiversity may only consist of several habitat generalists. The Canada lynx (Lynx canadensis) is a boreal species that has limited range expansion potential at the cold end of its range and its range has already contracted by 40%. The lynx has nowhere to go as climate warming progresses in this current century. Therefore, understanding the causes of its range contraction could enlighten us on conservation and management strategies that we might undertake as climate warms. My analyses indicated that the Canada lynx seems to have tracked the habitat that it is adapted to in more northern homogenous boreal forests and the bobcat (Lynx rufus), a habitat generalist, has simply replaced it in the south. Author Keywords: Anthropogenic Change, Competition, Connectivity, Lynx canadensis, Lynx rufus, Range change
Breeding Phenology and Migration Habits of Whimbrel (Numenius phaeopus) in the Hudson Bay Lowlands, Canada
Understanding breeding and migration habits of Whimbrel (Numenius phaeopus) in the Hudson Bay Lowlands is important for the conservation of this population. I monitored Whimbrel at two breeding sites: the Churchill region of Manitoba and Burntpoint, Ontario. Annual average nest initiation timing was highly variable and successful nests were initiated significantly earlier than those that failed. Although nests were initiated significantly earlier at Burntpoint than Churchill, annual nest success quantified in program R MARK was similar across sites. Observed nest success rates were lower than historical records and most failure was due to predation. Annual nest survival varied widely and I used a generalized linear model to relate annual nest survival to annual average weather conditions. I observed weak relationships between annual nest survival and weather conditions in the northbound staging grounds. I tracked post-breeding migratory movements using the MOTUS radio telemetry system and observed consistent use of the mid-Atlantic coast of the United States during migration, especially among birds emerging from Churchill. In Burntpoint, I observed more variability in post-breeding migratory trajectories and significantly earlier post-breeding departure as compared to Churchill. The results of my study suggest differences in breeding and migration habits exist across nearby breeding populations, indicating that there is a need for population-specific conservation approaches for this declining species. Author Keywords: Migration, Movement Ecology, Nesting Ecology, Nest Success, Shorebird conservation, Whimbrel
Passage population size, demography, and timing of migration of Red Knots (Calidris canutus rufa) staging in southwestern James Bay
Many shorebirds rely on small numbers of staging sites during long annual migrations. Numerous species are declining and understanding the importance of staging sites is critical to successful conservation. We surveyed endangered rufa Red Knots staging in James Bay, Ontario during southbound migration from 2009 to 2018. We used an integrated population model to estimate passage population size in 2017 and 2018 and found that up to 27% of the total rufa population staged in James Bay. We also extended the model to incorporate age composition of the passage population. In future applications, this method could improve our understanding of the role of breeding success in population declines. We then estimated annual apparent survival from 2009 to 2018. Survival remained near constant, though lower than estimated elsewhere in the Red Knot range, which may reflect higher permanent emigration rates rather than truly lower survival. This work demonstrates that this northern region is a key staging site for endangered Red Knots and should be included in conservation planning. Author Keywords: integrated population model, mark-recapture, migratory stopover, shorebirds, species at risk, survival
Effects of Recycled Media on Culture Growth and Hormone Profiles in Heterotrophic Euglena gracilis
The rapid expansion of the worldwide population has caused an urgent need for the development of new, more environment-conscious, food sources. In this context, algae, such as Euglena, are of interest thanks to their capacity to naturally produce essential nutrients such as proteins and oils commonly found in animals and plant sources. While these processes are currently being investigated, underlying measures affecting growth of Euglena gracilis like hormonal influences and growth stress like nutrient deprivation are poorly understood. From this vantage point, this thesis seeks to understand the role of phytohormones cytokinin (CKs) and abscisic acid (ABA) in complex mechanisms underlying heterotrophic growth of Euglena gracilis under recycled, organic media conditions with no supplementation. Hormone profiles were quantified by HPLC-ESI-MS/MS and compared to culture growth dynamics of pH, weight accumulation, glucose content, cell count and morphology. It was expected that ABA acted as an inhibitory hormone and this was confirmed by its higher levels when CKs where low and vice versa. Contrastingly, it was expected that CKs stimulated growth, in which this was shown not to be the case. Interestingly, it was revealed that both hormone groups increase with increasing recycling. Other key findings include: E. gracilis synthesizes CKs via the tRNA-degradation pathway and is cZ and iP dominated, recycling E. gracilis medium is viable for growth, however, the percentage (25% or less) is crucial to cell viability and markedly no ABA was detected in E. gracilis pellet fractions from recycled media. Therefore, this data revealed that recycled media has a striking influence on physiological aspects of growth and illustrated unique changes in hormone profiles of which could be manipulated to help the food industry. Author Keywords: cytokinin, endogenous hormones, Euglena gracilis, heterotrophic, large scale microalgae cultivation, recycled medium
Forensic Epistemology
Forensic epistemology is the study of knowledge as it relates to forensic science and can be broken into four sources; intuitive, authoritative, logical and empirical. In a four-phase research approach, I explored reasoning skills (logical knowledge) used by crime scene experts and methods (empirical knowledge) for forensic case-specific experimentation. First, the reasoning skills of crime scene investigators (CSI) and bloodstain pattern analysts (BPA) were tested, correlated to demographics and reasoning categories were compared. Practitioner’s with graduate level education performed better on the reasoning test, however, significant differences were not found between test scores and years of experience. Similarly, there was no difference between test scores and employment status (specifically, police or civilian employees), for the CSI group nor within the BPA group. This information suggests that level of education plays the most important role in the development and use of reasoning skills, whereas experience and employment status are not as influential. Second, I investigate potential strategies in selecting data types for case-specific experimentation in pattern-interpretation disciplines within forensic science. I also examined the epistemic status of practitioner case experimentation in forensic science. Practitioners were more confident in a mixed-method approach when conducting case-specific experimentation. In addition, there is a knowledge gap in experimental design for some forensic practitioners. Third, is a reprint of the introductory section of my published book entitled The Scientific Method in Forensic Science: A Canadian Handbook that abridges knowledge gained from this dissertation with further evidence-based literature review and experiential examples. This phase summarizes the scientific method in forensic science and provides guidance for forensic science students and practitioners. The final phase merges the findings from the primary studies with a literature review; offering scientific evidence supporting suggested research and pedagogic strategies that can help increase the epistemic status of forensic science. Author Keywords: case-specific research, epistemology, forensic science, hypothetico-deductive reasoning, logic, research models
Wastewater Impacts on Freshwater Mussels and Water Quality in a Tributary of the Lower Grand River in Southwestern Ontario, Canada
The main goal of this thesis was to assess the potential impacts of discharges of treated effluent from a small facultative sewage lagoon serving approximately 300 residents of the Mississaugas of the Credit First Nation to freshwater mussel populations in Boston Creek, a small tributary of the lower Grand River. The current resident mussel populations inhabiting Boston Creek were assessed using semi-qualitative visual surveying methods. In addition to various population level observations, other possible point and non-point influences on water quality in Boston Creek were identified. Following this, Lasmigona costata mussels were deployed as biomonitoring organisms alongside passive samplers during the October 2017 lagoon discharge period. Time weighted average (TWA) concentrations of select Contaminants of Emerging Concern (CECs) and Polycyclic Aromatic Hydrocarbons (PAHs) were estimated from levels of these compounds accumulated on passive samplers to understand the influence of wastewater on water quality in Boston Creek. Finally, mussel tissues were analyzed for various biomarkers of exposure to contaminants. Population surveys indicated that Boston Creek supports a plentiful and diverse community of freshwater mussels and may be a refuge for the Species of Special Concern, Villosa iris. Passive sampling revealed that most PAHs measured were present at concentrations below detection limits, while CECs were typically detected at relatively low concentrations (ng/L) directly downstream of the lagoon discharge. Biomarker responses detected in Lasmigona costata generally could not be attributed to exposure to the lagoon effluent but these data may indicate response to other point and non-point sources of pollution that could be affecting resident freshwater mussel populations in Boston Creek. The mussels surveyed in Boston Creek may be displaying community level effects of exposure to other sources of pollution in the area. The results of this thesis will help in establishing water quality guidelines in the lower Grand River watershed that will assist in the recovery strategy for freshwater mussel species at risk in Ontario. Author Keywords: Biomarkers, Biomonitoring, CECs, First Nations, Freshwater Mussels, SAR
Environmental structure, morphology and spatial ecology of the five-lined skink (Plestiodon fasciatus) at high latitude range limits
Detecting relevant and meaningful patterns from the complex, interconnected network of relationships between organisms and their environment is a primary objective of ecology. Ecological patterns occur across multiple scales of space and time. In this dissertation, I examine aspects of environmental structure that influence a species’ distribution and are expressed in that species’ population dynamics. I compare the morphology of the five-lined skink (Plestiodon fasciatus) near its high latitude range limits with a lower latitude population and evaluate the economics of their behaviour in the context of its reproductive strategy. I tested the conformity of this species to biogeographical rules postulated by MacArthur, Bergmann, and Rensch. Spatial ecology was investigated in the context of the environmental potential for polygamy proposed by Emlen and Oring (1977) The five-lined skink, Plestiodon fasciatus, conformed to these biogeographic rules. Specifically, abiotic factors were the primary limiting factors affecting distribution at the high latitude range limits of the species; body size was larger in high latitude populations; and the degree of sexual size dimorphism was greater at high latitude than at low latitude. Spatial ecology at the individual scale was influenced by sites with suitable thermal conditions which facilitate the polygynandrous mating system documented in P. fasciatus in high latitude populations. My results confirm the importance of microsites with suitable thermal profiles as key habitat for ectothermic vertebrates at high latitudes. The influence of temperature as a limiting abiotic factor is expressed in population density, body size, spatial ecology, and reproductive strategy of P. fasciatus. Conservation and restoration of high latitude populations of ectothermic vertebrates should focus on ensuring thermal requirements of the species of concern are met before other factors are addressed, as temperature is likely the single most important limiting factor at high latitude range limits. Author Keywords: biogeography, lizard, Plestiodon fasciatus, range limits, sexual size dimorphism, spatial ecology
Potential for Greenhouse Gas Emissions from Sediments of Agricultural Streams and Lake Erie
This thesis examines how dissolved organic matter quantity and quality and nutrients influence the flux potential of greenhouse gases (GHG) from sediments collected from streams across southern Ontario as well as Lake Erie. Sediments were collected and incubated in a laboratory setting where headspace gases and interstitial waters were analyzed. Results demonstrated that nutrients (dissolved organic carbon (DOC), total dissolved phosphorous (TDP) and total dissolved nitrogen (TDN)) were commonly significant predictors of CO2, CH4, and N2O fluxes, but spatial discrepancies were observed for the significance of DOM quality and sedimentary characteristics. Land use was not found to be directly related to gas flux potential. Different relationships were observed between the streams and lake, and between the basins of Lake Erie. Overall, results from this study suggest that sediments from freshwater systems have the potential to be sources of GHG, the degree of which depends on nutrient concentrations and DOM structure from watershed inputs. Author Keywords: dissolved organic matter, greenhouse gases, Lake Erie, nutrients, sediment, streams
Disease ecology of ophidiomycosis in free-ranging snakes
Ophidiomycosis (snake fungal disease) is caused by the pathogen Ophidiomyces ophiodiicola. Infected snakes exhibit dermal lesions, occasional systemic infections, and, in some cases, mortality. We studied snakes at Rondeau Provincial Park, Ontario, Canada, to explore whether ophidiomycosis develops during brumation or year-round. Throughout their active season, we quantified the prevalence of clinical signs of the disease on snakes and conducted qPCR of skin swabs to determine the prevalence of O. ophiodiicola on snakes. Prevalence of O. ophiodiicola and disease symptoms were highest on eastern foxsnakes (Pantherophis vulpinus) and very rare on other snake species. In P. vulpinus, pathogen and clinical sign prevalence was highest, directly after emergence from overwintering, with the majority of P. vulpinus being able to resolve clinical signs of ophidiomycosis by the return of winter. When we analyzed the survivorship of P. vulpinus we determined that the likelihood of a snake dying with ophidiomycosis is similar to a snake dying without ophidiomycosis. Given that P. vulpinus were the most affected species at our study site, ophidiomycosis does not appear to pose an imminent threat to our study population of P. vulpinus under current conditions. Author Keywords: Eastern Foxsnake, Fitness, Ophidiomycosis, Pantherophis vulpinus, Seasonal trends, Snake fungal disease
Effects of wood ash addition on soil chemical properties and sugar maple (Acer saccharum, Marsh.) seedling growth in two northern hardwood forest sites in central Ontario
One possible solution to acidification and losses of base cations in central Ontario forest soils may be the application of wood ash. Wood ash is generally high in pH and contains large amounts of calcium (Ca) and other nutrients essential for ecosystem health, however it also contains trace metals. Understanding the chemistry of soils following ash application to forests is crucial for future policy recommendations and remediation efforts. In this study, soil and soil water chemistry was measured at two acidic forest sites in central Ontario. Sugar maple (Acer saccharum, Marsh.) seedling growth and chemistry, as well as understory vegetation composition, were also measured. At site one, plots (2 m x 2 m) were established with sugar maple, white pine (Pinus strobus L.) and yellow birch (Betula alleghaniensis Britt.) residential wood ash treatments and applied at rates of 0 and 6 Mg ha-1. The effects of residential wood ash on soil and understory vegetation were measured three- and 12-months following ash addition. At site two, plots (5 m x 5 m) were established with both fly and bottom industrial grade bark ash treatments of 0, 4 and 8 Mg ha-1 (n=4), and tension lysimeters were positioned in each plot at 30, 50, and 100 cm depths. The effects of industrial grade wood ash on soil, soil water and understory vegetation were measured four years following ash addition. Metal concentrations in the ashes were generally low but were higher in the fly ash and yellow birch ash types. At site one, significant increase in soil pH, and Ca and magnesium (Mg) concentrations were observed after three months, however changes varied by treatment. Some metal concentrations increased in the upper organic horizons, but metals were likely immobilized in the soil due to increases in soil pH, electrical conductivity (EC) and high organic matter content of the soil. After one year, changes to metal concentrations in soils could be seen in mineral horizons, and a few metals (aluminum (Al), zinc (Zn), copper (Cu), chromium (Cr), strontium (Sr)) increased in treatment plots. At site two, the effects of industrial-grade bark ashes on soil pH could still be seen after four years and soil water metal concentrations were not elevated relative to controls. Changes to understory vegetation composition following ash application were observed, but ash addition had no significant effect on sugar maple seedling growth (root:shoot ratio) and did not lead to significant increases in foliar metal concentrations. There were significant differences in root chemistry, suggesting metal translocation and uptake could be restricted. Mass balance estimates indicate that the organic horizon is a sink for all metals and simulated drought in this horizon led to a decrease in soil pH and increase in soil water metal concentration, but this occurred in all treatments including control. These results suggest that application of industrial and residential wood ash in moderate doses with trace metal concentrations below or near regulatory limits will increase soil pH and base cation concentrations, as well as increase seedling tissue nutrient concentrations in northern hardwood forest soils. However, depending on the parent material of the ash, increased metal availability can also occur. Author Keywords: Acer saccharum, calcium decline, forest soil amendment, Haliburton Forest and Wildlife Reserve, heavy metal, wood ash
Assessing basin storage
Water storage is a fundamental component of drainage basins, controlling the synchronization between precipitation input and streamflow output. The ability of a drainage basin to store water and regulate streamflow may mediate sensitivity to climate and land cover change. There is currently no agreement on the best way to quantify basin storage. This study compares results of a combined hydrometric and isotopic approach for characterizing inter-basin differences in storage across the Oak Ridges Moraine (ORM) in southern Ontario. The ratio of the standard deviation of the stable isotope signature of streamflow relative to that of precipitation has been shown to be inversely proportional to mean water transit times, with smaller ratios indicating longer water transit times and implying greater storage. Stable isotope standard deviation ratios were inversely related to baseflow index values. Basins demonstrating longer transit times were associated with hydrological characteristics that promote infiltration and recharge of storage. Author Keywords: baseflow, basin storage, climate change, mean transit time, Oak Ridges Moraine, stable isotopes

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