Graduate Theses & Dissertations


silicon sol-gel approach to the development of forensic blood substitutes
The research and development of synthetic blood substitutes is a reported need within the forensic community. This work contributes to the growing body of knowledge in bloodstain pattern analysis by offering a materials science approach to designing, producing and testing synthetic forensic blood substitutes. A key deliverable from this research is the creation of a robust silicon-based material using the solution-gelation technique that has been validated for controlled passive drip and spatter simulation. The work investigates the physical properties (viscosity, surface tension and density) of forensic blood substitute formulations and describes the similarity in the spreading dynamics of the optimized material to whole human blood. It then explores how blood and other fluids behave in impact simulation using high-speed video analysis and supports the use of the optimized material for spatter simulation. Finally, the work highlights the practical value of the material as an educational tool for both basic and advanced bloodstain experimentation and training. Author Keywords: bloodstain pattern analysis, forensic blood substitutes, high-speed video analysis, silicon solution-gelation chemistry, thin-film deposition, training and education
effects of particulate matter on the fate and toxicity of silver nanoparticles
As an emerging contaminant, the antimicrobial agent silver nanoparticles (AgNPs) have been receiving considerable attention to determine their potential effects to aquatic ecosystems. However, estimates of aquatic consumer survivorship and other toxicological endpoints vary considerably among experiments, largely due to the environment in which the test takes place. Throughout this thesis I aim to understand which natural environmental variables impact toxicity to the common aquatic consumer Daphnia. I focus on the effects of particulate matter as it may play a role in animal nutrition as well as interact with AgNPs. I explore particulate matter’s effect on survival in the complex matrices including other natural variables that could impact toxicity. I conduct a series of complimentary field and laboratory studies to understand how particles impact AgNP toxicity and how those interactions vary within whole lake ecosystems. Using laboratory studies, I establish that algal particles mitigate the toxic effects of AgNPs on Daphnia survival through removing Ag from the water column and that phosphorus increases this effect. Using wild Daphnia and lake water, I demonstrate the ability of particulate matter to mitigate toxicity in complex natural settings. It was also one of the major predictors of AgNP toxicity to Daphnia along with dissolved organic carbon and daphnid seasonal health. Finally, using a whole lake AgNP addition experiment, I demonstrate that particles and AgNPs interact variably in the lake. Silver from AgNPs binds to particles and is removed to the sediments through the actions of settling particles without impacting the dynamics of living communities. Overall, I am able to demonstrate that the natural components of lake ecosystems, especially particulate matter, are able to mitigate the effects of AgNPs in lake ecosystems to a point where they likely will be never pose a threat to the survivorship of aquatic consumers such as Daphnia. Author Keywords: Daphnia, ecotoxicity, particulate matter, Silver nanoparticles, whole lake experiment
Interactome Study of Giardia Intestinalis Cytochromes B5
Giardia intestinalis is an anaerobic protozoan that lacks common eukaryotic heme-dependent respiratory complexes and does not encode any proteins involved in heme biosynthesis. Nevertheless, the parasite encodes several hemeproteins, including three members of the Type II cytochrome b5 sub-group of electron transport proteins found in anaerobic protist and amitochondriate organisms. Unlike the more well-characterized cytochrome b5s of animals, no function has been ascribed to any of the Type II proteins. To explore the functions of these Giardia cytochromes (gCYTB5s), I used bioinformatics, immunofluorescence microscopy (IFM) and co-immunoprecipitation assays. The protein-protein interaction in silico prediction tool, STRING, failed to identify relevant interacting partners for any of the Type II cytochromes b5 from Giardia or other organisms. Differential cellular localization of the gCYTB5s was detected by IFM: gCYTB5-I in the perinuclear space; gCYTB5-II in the cytoplasm with a staining pattern similar to peripheral vacuole-associated protein; and gCYTB5-III in the nucleus. Co-immunoprecipitation with the gCYTB5s as bait identified potential interacting proteins for each isotype. The most promising candidate is the uncharacterized protein GL50803_9861, which was identified in the immunoprecipitate of both gCYTB5-I and II, and which co-localizes with both. Structural analysis of GL50803_9861 using Swiss Model, Phyre2, I-TASSER and RaptorX predicts the presence of a nucleotide-binding domain, which is consistent with a potential redox role involving nicotinamide or flavin-containing cofactors. Finally, the protein GL50803_7204 which contains a RNA/DNA binding domain was identified a potential partner of gCYTB5-III. These findings represent the first steps in the discovery of the roles played by these proteins in Giardia. Author Keywords: Cytochrome b5, Giardia intestinalis, Heme, Interactome, Protein structure prediction
Stress Axis Function and Regulation in New World Flying Squirrels
Across vertebrate taxa, the hypothalamic-pituitary-adrenal axis (or the stress axis) is highly conserved, and is central to vertebrate survival because it allows appropriate responses to psychological stressors. Habitat shapes successful physiological and ecological strategies, and to appreciate how individual species respond to stressors in their environment, it is essential to have a thorough knowledge of the basic stress physiology of each species. In this dissertation, I studied the functioning and evolution of the stress physiology of New World flying squirrels. I showed that baseline, circulating cortisol levels in northern (Glaucomys sabrinus) and southern (G. volans) flying squirrels are some of the highest ever reported for mammals, indicating that their stress axes operate at a higher set point than most other species. I also assessed other aspects of their acute stress response, including free fatty acid and blood glucose levels, and indices of immune function, and showed that the flying squirrels’ physiological reaction to stressors may differ from that of other mammals. Using immunoblotting, I found that corticosteroid-binding globulin (CBG) expression levels in flying squirrels appeared to be higher than previously reported using alternative methods. I also concluded however, that these levels did not appear to be high enough to provide their tissues with the protective CBG-bound buffer from their high circulating cortisol concentrations experienced by the majority of vertebrates. Thus, this arm of cortisol regulation within the flying squirrel stress axes may be weak or non-existent. Following this, I focused on southern flying squirrels and showed evidence that the second arm of cortisol regulation — the negative feedback mechanism at the level of the brain — functions effectively, but that this species is glucocorticoid resistant. Their tissue receptors appear to have a reduced affinity for cortisol, and this affinity may change seasonally to allow for the onset of other biological processes required for survival and reproduction. Due to their distinctive stress physiology, northern and southern flying squirrels may provide comparative physiologists with model systems for further probing of the function and evolution of the stress axis among vertebrates. Author Keywords: corticosteroid-binding globulin, flying squirrel, Glaucomys, glucocorticoids, physiological ecology, stress physiology
Reproductive Fitness of Smallmouth Bass (Micropterus dolomieu) Under Heterogeneous Environmental Conditions
Identifying the biotic and abiotic factors that influence individual reproductive fitness under natural conditions is essential for understanding important aspects of a species’ evolutionary biology and ecology, population dynamics, and life-history evolution. Using next generation sequencing technology, I developed five microsatellite multiplex reactions suitable for conducting large scale parentage analysis of smallmouth bass, Micropterus dolomieu, and used molecular pedigree reconstruction techniques to characterize the genetic mating system and mate selection in adult smallmouth bass nesting in Lake Opeongo, Ontario, Canada. I used multivariate spatial autocorrelation analysis to indirectly infer the occurrence and extent of natal philopatry among spawning adults, to assess the strength and direction of sex-bias in natal dispersal patterns, and to evaluate the degree of nest site fidelity and breeding dispersal of spawning adults. I also evaluated how differences in littoral zone water temperature caused by wind-induced seiche events influence the relative reproductive success of spawning adults. Lastly, I provide a synopsis of potential future research aimed at further exploring factors that influence the reproductive fitness of smallmouth bass in Lake Opeongo. This information will contribute to our understanding of the factors regulating smallmouth bass populations, and provide insight into the factors controlling the variance in individual reproductive success and thus recruitment dynamics in this species. Author Keywords: Dispersal, Fitness, Mate selection, Mating systems, Philopatry
successful invader in expansion
Researchers have shown increasing interest in biological invasions for the associated ecological and economic impacts as well as for the opportunities they offer to study the mechanisms that induce range expansion in novel environments. I investigated the strategies exhibited by invasive species that facilitate range expansion. Invasive populations exhibit shifts in life-history strategy that may enable appropriate responses to novel biotic and abiotic factors encountered during range expansion. The spatio-temporal scales at which these shifts occur are largely unexplored. Furthermore, it is not known whether the observed dynamic shifts represent a consistent biological response of a given species to range shifts, or whether the shifts are affected by the abiotic characteristics of the new systems. I examined the life-history responses of female round gobies Neogobius melanastomus across fine and coarser spatial scales behind the expansion front and investigated whether invasive populations encountering different environmental conditions (Ontario vs France) exhibited similar life-history shifts. In both study systems, I found an increase in reproductive investment at invasion fronts compared to longer established areas at coarse and fine scales. The results suggest a similar response to range shifts, or a common invasion strategy independent of environmental conditions experienced, and highlight the dynamic nature of an invasive population’s life history behind the invasion front. The second part of my research focused on the development of an appropriate eDNA method for detecting invasive species at early stages of invasion to enable early detection and rapid management response. I developed a simple, inexpensive device for collecting water samples at selected depths for eDNA analysis, including near the substrate where eDNA concentration of benthic species is likely elevated. I also developed a protocol to optimise DNA extraction from water samples that contain elevated concentration of inhibiters, in particular near-bottom samples. Paired testing of eDNA and conventional surveys was used to monitor round goby expansion along its invasion pathway. Round gobies were detected in more sites with eDNA, permitting earlier, more accurate, upstream detection of the expansion front. My study demonstrated the accuracy and the power of using eDNA survey method to locate invasion fronts. Author Keywords: Age-specific reproductive investment, DNA extraction, Energy allocation, Fecundity, Invasion front, Range expansion
Linking Inuit and Scientific Knowledge and Observations to Better Understand Arctic Char (Salvelinus alpinus (L.)) Community Monitoring
Arctic Char (Salvelinus alpinus (L.)) have been, and remain, an important subsistence resource for the Inuvialuit, the Inuit of the western Canadian Arctic. The effects of climate variability and change (CVC) in this region have been noticeably increasing over the past three decades. There are concerns as to how CVC will affect Arctic Char and the Inuvialuit who rely on this resource as they will have to adapt to changes in the fishery. Community-based monitoring, is an important tool for managing Arctic Char. Therefore, my dissertation focused on the central question of: Which community-based monitoring factors and parameters would provide the information needed by local resources users and decision-makers to make informed choices for managing Arctic Char populations in light of CVC? This question is investigated through an exploratory research approach and a mixed method research design, using both scientific and social science methods, and quantitative (scientific ecological knowledge and observation) and qualitative (Inuvialuit knowledge and observation) information. It is formatted as three journal manuscripts, an introduction, and an integrative discussion. The first manuscript examines potential habitat parameters for monitoring landlocked Arctic Char condition in three lakes on Banks Island in the Inuvialuit Settlement Region. The second manuscript examines potential local environmental parameters for monitoring landlocked Arctic Char growth in the same three lakes. The third manuscript investigates aspects of Arctic Char community-based monitoring programs (CBMP) in the Canadian North that have led to the sustained collection of useful data for management of the resource. This dissertation makes contributions to the field of research by demonstrating the utility of a mixed methods approach. The results demonstrate similarities and differences in char growth and condition within and among Capron, Kuptan and Middle lakes on Banks Island. This supports both lake-specific and regional climate-driven changes, meaning both lake habitat and local environmental monitoring parameters should be used in char CBMP. The investigation of char CBMP across northern Canada demonstrates that an adaptive monitoring approach is important for subsistence fisheries, as changing lifestyles and environmental changes impacting a fishery can have direct effects on the successful operation of char CBMP. Author Keywords: Arctic Char, community-based monitoring, environment, Inuit Knowledge, mixed methods, Traditional Knowledge
Elders And Indigenous Healing in The Correctional Service Of Canada
In our communities, we are continually challenged to reflect on effective responses to the people and events that put us at risk. This study is an examination of two distinctly different world-view responses: the colonial, dominant culture and the Indigenous world-view. The retributive understanding of the dominant culture applies assumptions about the nature of the world that are vested in colonial, paternal, and punitive processes aimed to extract compliance as a means of deterrence. Conversely, the consensual precepts of Indigenous world-view are rooted in community-based practices that require a process of collaboration and cooperation to create integrated relationships that glean responsibility. This study brings light to bear on the ongoing relational dissonance that exists between the following: the disproportionate representation of men and women of Aboriginal descent held under federal warrant in Canada; the legislated mandate contained within the Canadian Corrections and Conditional Release Act that places successful community reintegration as a primary objective for the Correctional Service of Canada (CSC); and the role, place, and function of Elders who work in CSC reception centres, healing programs, and Pathways Initiatives. This study explores the variables, assumptions, and differing world-views that contribute to the disproportionate representation of incarcerated adults of Aboriginal descent and the challenges that impede successful community reintegration. In order to effectively examine and make sense of the relational dissonance that exists between correctional theory and institutional practice, the research is driven by a central question: What is the role, place, and function of Elders in the delivery of Indigenous healing programs within Canadian federal prisons? The outcome of this work reveals practices of decolonizing justice and healing that can move assumptions and challenge paternal understanding. It is an approach that has the capacity to peel away relational dissonance, thus allowing space for public policy that sustains consensual understandings of community. Key Words: Indigenous, settler colonial, dominant culture, retributive justice, restorative justice, indigenous justice, Elder, healing, healing program, disproportionate representation, successful community reintegration, relational dissonance. Author Keywords: Elder, healing program, indigenous justice, relational dissonance, retributive justice, successful community reintegration
Fate and Effects of Silver Nanoparticle Addition in a Lake Ecosystem
The potential release of nanoparticles into aquatic environments is raising global concerns. As antimicrobials, silver nanoparticles (AgNPs) are among the most prominent form in use. Despite this, their fate, long-term toxicity, and ecological relevance have yet to be investigated largely under natural settings with seasonality and environmental complexity. To better understand the environmental significance, we released AgNPs into Lake 222 at the Experimental Lakes Area over two years. AgNPs remained suspended in the water column and were detected throughout the lake and in the lower food web. Total Ag concentrations ranged from below 0.07 to 18.9 μg L-1 in lake water, and were highly dynamic seasonally both in the epilimnion and hypolimnion depending on the physical, chemical and biological conditions of the lake. Approximately 60% of the measured Ag mass in October was present in the sediment in 2014 and 50% in 2015 demonstrating relatively high sedimentation and removal from the water column. During winter months, Ag was largely absent in the water column under the ice. After ice melt and before summer stratification, Ag concentrations increased in the lake suggesting AgNPs may not be tightly bound to the sediment and are able re-enter the water column during spring mixing events. Despite temporal variation, total Ag was highly synchronous across spatial locations for both years, indicating rapid dispersal upon lake entry. When investigating AgNP sizes using spICPMS, size distributions were similar across spatial locations, with the 40-60 nm size class constituting approximately 60% of all particles identified. Large aggregates (>100 nm) and dissolved Ag were infrequently detected within the lake. Ag accumulated in the lower food web ranging from 0.27-16.82 μg Ag mg C-1 in the bacterioplankton and 0.17-6.45 μg Ag mg C-1 in algae (particulate fraction). Partial least squares models revealed the highest predictors of Ag accumulation were dissolved nutrients including DOC, TDN, TDP in bacterioplankton. Major predictors for particulate Ag included temperature, dissolved oxygen, and sampling date. The diversity of predictors among biological compartments emphasizes the importance of understanding the role of environmental complexity within the lower food web. Despite Ag accumulation we did not detect strong negative effects on the lake food web. An increase in particulate and bacterioplankton chlorophyll-a occurred after addition in contrast to reference lakes, which may indicate a hormetic response to low dose AgNP concentrations. Our findings provide the first whole-lake perspective regarding Ag fate and toxicity, suggesting small scale experiments may overestimate environmental responses. Author Keywords: Ecotoxicity, Fate, Lower food web, Silver Nanoparticles, Whole-lake addition
Code of Bimadiziwin
Indigenous peoples and organizations have a long history of incorporating cultural knowledge and teachings into program and organizational design and structure. The approach to incorporating cultures into Indigenous organizations is not uniform, nor is the ways that they are understood. This dissertation focuses on Nogojiwanong Friendship Centre, in Peterborough Ontario and their approach to incorporating Indigenous cultures into their organization from 2010-2014. The intention of this dissertation is to build knowledge of Indigenous perspectives of organizational structure, grounded in Anishinabe teachings. The teaching circle, vision- time – feeling –movement, guides my learning process and the structure of the dissertation. In using an Anishinabe framework the importance of relationships and the Anishinabe clan system are foundational to my understanding, and will be discussed at length. The purpose and goal of this research is twofold. First, to show the complexity, intentionality and depth to an Indigenous research process; a process that is often nuanced in the literature. Second, to show how Anishinabe thought can (and does) provide a framework for a service delivery organization, in its governance and program and service delivery. The thesis of this dissertation is that Anishinabe knowledge is not always visible to outsiders, but it was present at Nogojiwanong Friendship Centre in the ways they approached research, governed themselves and delivered programs and services. Key Words: Indigenous Knowledge, Indigenous Governance, Indigenous Research Ethics, Indigenous Research Framework Author Keywords: Indigenous Governance, Indigenous Knowledge, Indigenous Research Ethics, Indigenous Research Framework
Time to adapt
To better understand species’ resilience to climate change and implement solutions, we must conserve environments that maintain standing adaptive genetic variation and the potential generation of new beneficial alleles. Coding trinucleotide repeats (cTNRs) providing high-pace adaptive capabilities via high rates of mutation are ideal targets for mitigating the decline of species at risk by characterizing adaptively significant populations. Ultimately, adaptive genetic information will inform the protection of biological diversity below the species level (i.e., “Evolutionarily Significant Units” or “ESUs”). This dissertation investigates cTNRs within candidate genes to determine their prevalence and influence under selection in North American mammals. First, I evaluated the potential for somatic mosaicism in Canada lynx (Lynx canadensis), and found that tissue-specific mosaicism does not confound cTNR genotyping success in lynx. Second, I assessed a selection of clock gene cTNRs across characterized mammals and found that these repeats are abundant and highly variable in length and purity. I also identified preliminary signatures of selection in 3 clock gene cTNRs in 3 pairs of congeneric North American mammal species, highlighting the importance of cTNRs for understanding the evolution and adaptation of wild populations. I further evaluated the influence of selection on the NR1D1 cTNR within Canada lynx sampled across Canada using environmental correlation, where I estimated the variation in NR1D1 cTNR alleles explained by environmental and spatial variables after removing the effects of neutral population structure. Although most variation was explained by neutral structure, environment and spatial patterns in eastern lynx populations significantly explained some of the variation in NR1D1 alleles. To examine the role of island populations in the generation and distribution of adaptive genetic variation, I used 14 neutral microsatellites and a dinucleotide repeat within a gene linked to mammalian body size, IGF-1, and found that both genetic drift and natural selection influence the observed genetic diversity of insular lynx. Finally, I estimated the divergence dates of peripheral lynx populations and made recommendations towards the conservation of Canada lynx; high levels of genetic differentiation coupled with post-glacial colonization histories and patterns of divergence at cTNR loci suggest at least 4 ESUs for Canada lynx across their range. Author Keywords: adaptation, Canada lynx, candidate genes, coding trinucleotide repeats, evolution, natural selection
Bringing Knowledges Together
The natural world and environmental issues present critical points of convergence between Indigenous and non-Indigenous people and their knowledge systems. This qualitative study engaged with 18 Indigenous and non-Indigenous environmental practitioners in interview conversations to explore their experiences in cross-cultural environmental collaborations. The research undertakes a complexity theory approach to answer the following research questions: 1.a) What skills, values, knowledges and approaches do environmental practitioners need to enable Western and Indigenous knowledge systems to come together in addressing environmental challenges? 1. b) What does effectiveness and/or success look like in cross-cultural environmental collaboration? 2. How can post-secondary and professional development educational programs impart the skills, values, knowledges and approaches that their students need to effectively engage in work that brings together Indigenous and non-Indigenous people and their knowledge systems in addressing environmental challenges? This study applied multiple lenses to analyze and interpret the data. The author’s own reflections as both a practitioner and researcher working and teaching in crosscultural environmental contexts were a central component of the study. Through this analysis a set of skills, values, knowledges, approaches, attributes, and roles emerged. The findings reaffirm the importance of respect, relationship, responsibility, and reciprocity as central values in Indigenous praxis and identify additional values. The application of a critical theory lens illuminated that subtle racism and microaggressions influence environmental collaboration between Indigenous and non-Indigenous people. The study proposes a curriculum and program design for post-secondary and professional development contexts, that draws upon multiple pedagogies to prepare learners to work cross-culturally in respectful ways. These findings are relevant to environmental practitioners currently working in the field and contribute to a further articulation of an emerging Indigenous Environmental Studies and Sciences (IESS) pedagogy. Author Keywords: Cross-cultural collaboration, Curriculum Development, Environmental Education, Indigenous Studies, Professional Development


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