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This thesis aimed to address potential sources of bias in electronic fish tagging studies in order to advance the methods used by future studies. I first provided a review and meta-analysis of intracoelomic tagging effects in fishes, summarizing the existing literature and assessing the extent to which previously identified research gaps have been filled. I also included the first large-scale meta-analysis on tagging effects, examining the 2% rule using empirical evidence from a broad representation of all published studies. I then assessed the performance of a newly miniaturized predation-sensing acoustic transmitter (Innovasea V3D), demonstrating that V3D transmitters can mitigate predation biases by correctly identifying most predation events without false positives. I finally examined if immobilization via MS-222 or TENS alters the behaviours of fishes in the wild following tagging, and identified the time required for fish to re-establish normal behaviour following transmitter implantation.

Author Keywords: Acoustic telemetry, Electronic tagging, Fish ecology, Predation, Systematic review, Tagging effects

AbstractOral Language and the Approximate Number System – A Preliminary Study Janice Shewen The approximate number system (ANS) involves the processing of rudimentary quantity and is thought to be an innate developmental building block for mathematics and its sister construct, the symbolic system. The conventional belief is that the ANS is language independent; however, this notion is questioned and explored in the current study, which represents a preliminary investigation into the concurrent and longitudinal relations between different aspects of oral language and the ANS in 4-year-old children and one year later when they were 5. A sample of 26 children (13 boys;13 girls) with average intelligence completed standardized measures of oral language and verbal memory, and a computerized quantity discrimination task that required children to accurately discern between two visually presented quantities. Correlational analysis showed concurrent and longitudinal relations between different aspects of language and quantity discrimination. This suggests that different aspects of language predict quantity discrimination over a one-year period and challenge the current and accepted theory that the ANS is a language independent system. The findings also have implications for early childhood education – avenues to strengthen a child's ANS via targeted oral language instruction, curricula, and subsequent provision of experiences. The findings also support early oral language screening to monitor or provide opportunities for improving quantity approximation skills. This early intervention could impact later symbolic processing and mathematic success. Keywords: Non-symbolic system, approximate number system, quantity discrimination, symbolic system, oral language, morphology, syntax, semantics, relational concepts.

Author Keywords: Approximate Number System, Non-symbolic system, oral language, quantity discrimination, symbolic system

This dissertation, titled "Echoes of Injustice: Regulating Indigenous Masculinity through Canadian Legal and Colonial Systems, "examines how the Canadian criminal justice system—through its denial of colonial violence and its regulation of Indigenous masculinity—has contributed to the ongoing criminalization and marginalization of Indigenous men. By critically engaging with both historical and contemporary legal frameworks, including the Indian Act, restorative justice practices, and landmark cases such as R. v. Gladue and Blackwater v. Plint, this research traces how colonial narratives remain embedded in Canadian jurisprudence. These narratives often portray Indigenous men as inherently violent, deviant, and in need of regulation. The central research question guiding this work is: How has the Canadian criminal justice system, through its denial of colonial violence and its regulation of Indigenous masculinity, contributed to the continued criminalization and marginalization of Indigenous men? Grounded in the theoretical frameworks of Frantz Fanon and Michel Foucault, this dissertation argues that the legal system not only fails to address the structural impacts of settler colonialism but also actively reproduces colonial violence by projecting it back onto Indigenous male bodies. In doing so, it reinforces pathologizing narratives and obstructs opportunities for meaningful healing and justice. Each chapter applies this theoretical lens to specific legal cases and state policies, demonstrating how Indigenous men are constructed as threats to colonial order and denied recognition as victims of systemic trauma. Using a counter-narrative methodology, this dissertation challenges dominant legal and academic discourses, revealing how they obscure the lived realities of Indigenous men and sustain one-dimensional portrayals that rationalize state control. The counter-narrative approach is not merely a tool for alternative interpretation; it is a necessary act of decolonial resistance—one that disrupts colonial knowledge production and reclaims interpretive authority. By centring Indigenous voices and rejecting pathologizing settler narratives, this methodology contributes to the broader project of Indigenous resurgence: the revitalization of Indigenous masculinities, sovereignties, and justice systems on Indigenous terms. Ultimately, this work calls for a fundamental reimagining of justice—one that dismantles colonial legal foundations and embraces decolonial frameworks rooted in healing, accountability, and the resurgence of Indigenous masculinities.

Author Keywords: Colonial Violence, Colonialism Criminalization, Gladue Principles, Indian Act, Indigenous Masculinity, Restorative Justice

Coherent anti-Stokes Raman scattering (CARS) microscopy is a label-free chemical imaging modality that uses CARS as a contrast mechanism to spatially resolve materials based on their molecular vibrational spectra. Due to the presence of a non resonant background that obfuscates the chemical information contained in CARS spectra, CARS images suffer from poor contrast and cannot be readily used for quantitative chemical analysis. Over the past two decades, spectral retrieval methods have been developed to obtain Raman-like spectra from CARS spectra. These methods promise to improve image contrast and enable reliable quantitative analysis. In this work I systematically evaluate a selection of the forefront spectral retrieval methods, including both analytical and machine learning approaches, to determine how well they perform at the task of non resonant background removal. The more recent machine learning methods demonstrate remarkable performance on spectra resembling the training dataset but are not as suitable as the analytical methods in general. The analytical methods based on the discrete Hilbert transform thus remain preferable due to their ease-of-use and general applicability.

Author Keywords: chemical imaging, coherent anti-stokes raman scattering, kramers-kronig analysis, machine learning, non-resonant background, spectral phase retrieval

Crop losses due to pathogens, pests, and weeds account for 20–40% of global production, with fungal pathogens responsible for the most significant yield reductions and economic impact. The diseases caused by fungi spread through dormant spores, which protect its genetic material under adverse conditions. Dormancy is maintained until favorable germination conditions are met. Despite their importance in the fungal lifecycle, the molecular transitions from dormancy to germination remain poorly understood. The research presented uses the basidiomycete Ustilago maydis, the causal agent of Common Smut of Corn, to investigate fungal spore dormancy and germination. It aims to 1) identify the molecular transitions and stages of teliospore germination and 2) the roles of RNA helicases during teliospore germination. RNA-seq and respiration analyses were used to propose teliospore germination stages and a microdissection technique was developed for studying these stages. Transcriptomic analysis identified patterns of gene transcript level changes during germination, with GO term enrichment identifying genes involved in cell morphogenesis, metabolism, and RNA metabolism. Several RNA helicases were identified with potential roles during dormancy and germination. Previous work in the Saville Laboratory proposed that mRNAs are stored as dsRNA in dormant teliospores. I hypothesized that RNA helicases function to make these mRNAs available for translation upon germination. Forty-six RNA helicases were identified in U. maydis, and 28 RNA helicases were proposed to have roles in growth, pathogenesis, stress response, and teliospore dormancy and germination. The RNA helicases udbp3 and uded1 were selected for functional analysis by creating mutant strains. The results suggest that udbp3 negatively regulates osmotic stress response, potentially modulating stress-responsive genes during dormancy. The altered uded1 expression in mutant strains leads to slow and polarized growth and dsRNA formation. This suggests uded1 represses translation by stabilizing sense/antisense transcripts in dormant spores and then reactivates translation during germination. These findings increase our understanding of the molecular events during teliospore germination and offer insights into factors contributing to disease progression in fungal plant pathogens.

Author Keywords: gene expression, genome annotation, RNA helicases, RNA-seq, teliospore germination, Ustilago maydis

Amyloid fibrils are fibrous protein aggregates that arise from misfolding and self-assembly processes, collectively referred to as amyloidosis. These aggregates are strongly associated with incurable neurodegenerative disorders, including Alzheimer's disease (AD), Parkinson's disease, and Amyotrophic Lateral Sclerosis (ALS). Elevated levels of Reactive Oxygen Species (ROS) and dysregulated metal-ion homeostasis often impaired by environmental and lifestyle factors can induce oxidative stress that undermines cellular antioxidant defenses, which cause the amyloid formation and toxicity. This thesis investigates multiple amyloidosis models, emphasizing the contribution of metal ions and ROS to aggregation pathways, and evaluates the potential inhibitory or protective roles of cytokinin (CK) plant hormone.Chapter 2 focuses on Gelsolin amyloidosis, a hereditary condition driven by point mutations that promote aberrant amyloid formation. Using microscopic and spectroscopic approaches, this work characterizes the aggregation behavior of peptides derived from domain 2 of plasma gelsolin and secreted by muscle cells. Three peptides were studied: the wild-type(WT) sequence and two clinically relevant mutants, K184N and N187Y. Each variant exhibited distinct aggregation rates, reflecting mutation-dependent effects on self-assembly. Furthermore, two CKs Kinetin (Kin) and trans-Zeatin (tZ) were shown to modulate gelsolin aggregation, suggesting their potential as anti-aggregation molecules. Chapter 3 revolves on the aggregation properties of TDP-43 peptides associated with ALS pathology. Within the RRM I domain, two cysteine residues serve as key redox-active sites susceptible to oxidation. ESI-MS and spectroscopic methods were used to analyze three peptide variants: WT, a mutant (MT) in which cysteine were substituted with alanine, and WT-S, a disulfide-linked dimer. All variants displayed higher aggregation under mildly acidic conditions. CKs, Kin and isopentenyl-adenine (iP) showed antioxidant capacity and their influence on peptide stability. Chapter 4 investigates the effects of copper(II)-induced oxidative stress in C2C12 muscle cells and evaluates cellular responses to various CK forms. ESI-MS profiling identified 20 CKs in copper-treated samples and revealed 24 untargeted metabolites with significant level changes, indicating their possible involvement in metal-induced oxidative pathways. In conclusion, this thesis highlights the multifaceted roles of CKs in biological systems, particularly their potential to mitigate ROS overproduction, counteract metal-driven amyloidgenesis, promote fibril destabilization, and lessen oxidative stress.

Author Keywords: Amyloid, Anti aggregation, cytokinins, inhibition, Peptide aggregation, Protein aggregation

The objective of this thesis is to collect and analyse wild clay from the vicinity of previously identified and excavated archaeological sites near Pigeon and Rice Lakes, and comparing the characterized clay samples to archaeological pottery samples from the sites. The purpose of this research is to explore the resource exploitation in the landscapes around sites, and investigate the behaviours associated with resource exploitation and pottery manufacture. Through the application of X-Ray fluorescence spectrometry (XRF), each sample from four clay sources was analysed for its chemical composition, and compared to the chemical composition of Middle and Late Woodland Period pottery to investigate the similarities or differences between sources and finished items. The results demonstrated overlap between a source east of Rice Lake and pottery excavated from Chiminis-1 and Jacob Island-2.

Author Keywords: Clay Sourcing, Ontario Archaeology, Pottery, Resource Exploitation, Woodland Period, X-Ray Fluorescence Spectrometry

This thesis employs zooarchaeological, taphonomic, and spatial analysis to reconstruct subsistence behaviors of Middle Paleolithic Neanderthals using layer V of Abric del Pastor as a case study. Located in Alcoy, Alicante, Spain, Abric del Pastor is a cave shelter with occupation layers dated from MIS 5 through 3. The faunal assemblage is examined on two time scales: i) a longer time frame focused on large scale human occupation and use and ii) another, shorter time frame in an attempt to distinguish possible shorter anthropogenic events. The layer V assemblage is comprised of at least two occupation events, Occupation A and Occupation B. These are two relatively well-preserved anthropogenic accumulations dominated by medium sized taxa. In these occupations, the carcasses were likely transported from a separate kill site to the cave shelter to be processed and consumed. The taxonomic and taphonomic patterns uncovered in these occupation events are similar suggesting consistent behavioral patterns throughout Layer V. Ultimately, the faunal assemblage is typical of other MIS 5-3 rock shelters in the Iberian Peninsula. By examining the subsistence practices of layer V, dated to MIS 4, this work aims to fill a gap in the MIS 4 Iberian Peninsula literature and add to the conversation on how early hominins adapted to the changing climate.

Author Keywords: Abric del Pastor, Iberian Peninsula, Middle Paleolithic, Palimpsest, Time Perspectivism, Zooarchaeology

A key knowledge gap in aeolian transport research concerns the adjustment of saltation processes to the extreme conditions found within high-latitude regions. A series of wind tunnel experiments were carried out under full climate control and over a wide range in humidity. Particle entrainment and transport within shearing flows of varied wind speed were monitored over beds of varied temperature, and ice content to determine their affect on 1) particle trajectory, 2) saltation cloud height, 3) particle velocity, 4) surface erosivity, 5) mass transport rate and 6) vertical dust flux. Particles were found to have higher velocities over cold beds than dry beds. With a 3% increase in bed moisture content, a significant increase in particle velocity was measured. Fewer particles are ejected from a bed with moisture than a dry bed. The mass transport rate was measured to be 23% higher at -10 degrees Celsius compared to 30 degrees Celsius.

Author Keywords: Aeolian processes

Dissolved inorganic carbon in drainage waters is a direct measurement of carbon dioxide (CO2) removal from enhanced rock weathering (ERW) in soils. In this study, square metre scale field experiments (2021–2023) were conducted in Peterborough Ontario, Canada, each amended with kimberlite residues from Gahcho Kué Diamond Mine (Northwest Territories, Canada) or olivine powder at high application rates (100–400 t/ha). Porewater chemistry data, coupled with a water budget analysis derived from precipitation and soil moisture data, were used to quantify solubility trapping by amendment weathering revealing maximum rates of 0.04 t CO2/ha over 2 yr for olivine and 0.9 t CO2/ha over 3 yr for kimberlite. This research presents kimberlite mine wastes as an ERW feedstock alternative to basalt as projects scale-up and require more rock. Additionally, high dosage monitoring plots ensure detection of a CO2 removal signal in open systems and should be considered for large scale projects.

Author Keywords: CO2 removal, Enhanced rock weathering, Field experiment, Kimberlite, Mine wastes, Olivine