Environmental and Life Sciences

The study examines the phytochemical and phytohormone profiles of two ecotypes of Doliocarpus dentatus (Capadulla) from Guyana with an emphasis on their potential therapeutic applications, particularly in the context of erectile dysfunction. The research concentrates on the red and white ecotypes, which are visibly differentiated by the colouration of their inner and outer bark; moreover, the red ecotype is widely regarded by traditional knowledge to be more efficacious in treating erectile dysfunction. The study seeks to provide much-needed scientific evidence to support the traditional medicinal uses of D. dentatus and aims to accomplish this by providing semi-targeted and targeted analysis of its bioactive compounds.The thesis employs a multi-faceted approach, commencing with Chapter 2, an examination of the international and national frameworks that govern natural product research in Guyana, thereby ensuring ethical and sustainable practices. Chapter 3, Liquid chromatography-mass spectrometry-based metabolomics was utilized to analyze the phytochemical profiles of the red and white ecotypes of D. dentatus. Approximately 847 compounds were identified, with 138 tentatively classified as potentially therapeutic, particularly polyphenols exhibiting antioxidant properties. Chapter 4 focus on the phytohormone profiling revealed that the red ecotype generally exhibited higher levels of active cytokinins, particularly trans-zeatin (tZ) and cis-zeatin (cZ), compared to the white ecotype. A strong correlation was identified between specific cytokinins and secondary metabolites such as flavonoids and alkaloids, suggesting complex interactions that may enhance the therapeutic potential of D. dentatus. Chapter 5 further analysis of total phenolic content, flavonoid content, and their antioxidant capacities demonstrated differences between the red and white ecotypes, with the red ecotype generally showing higher levels of these compounds. Both ecotypes demonstrated significant antioxidant activity, with the red ecotype showing enhanced radical scavenging capacity. The study also revealed a diverse range of bioactive compounds, including flavonoids, terpenoids, and alkaloids, which may contribute to the plant's reported medicinal properties. This semi-targeted and targeted analysis provides novel insights into the phytochemical and phytohormone profiles of D. dentatus ecotypes, offering a scientific basis for their traditional medicinal uses and potential therapeutic applications. The findings suggest that D. dentatus, particularly the red ecotype, may have significant potential for developing new drugs, especially in the context of erectile dysfunction therapy.

Author Keywords: antioxidant, Bioactive compounds, liquid chromatography-electrospray ionization tandem mass spectrometry, metabolomics, secondary metabolites, therapeutic properties

DNAJC5, an HSP40 member, supports synaptic vesicle release and protein folding byactivating HSP70 ATPase activity. In humans, it localizes to presynaptic terminals and endomembrane compartments that are involved in protein trafficking. Mutations in DNAJC5 cause CLN4 disease, a rare adult-onset Batten disease. Dictyostelium discoideum, a model for neurodegenerative research, encodes a putative homolog of DNAJC5, Dnajc5 (DDB0306688), which remains uncharacterized. This study examined Dnajc5 localization and function in D. discodieum. Dnajc5 localized to the endoplasmic reticulum, cytoplasm and nucleolus under both growth and starvation conditions, suggesting a role in proteostasis. Unlike human DNAJC5, Dnajc5 was absent from endomembrane compartments and extracellularly during starvation. Protein quantification revealed increased levels during early development, peaking at the mound stage, and declining thereafter—paralleling gene expression. Immunoprecipitation of Dnajc5 showed no serine phosphorylation or ubiquitination, unlike human DNAJC5. These findings suggest functional differences despite a possible common role in proteostasis.

Author Keywords: actinomycin- D, CLN4, Dictyostelium discoiduem, DNAJC5, Immunoprecipitation, multicellular development

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

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

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

Lake whitefish (Coregonus clupeaformis) are ecologically, economically, and culturally significant across their range, yet little is documented about the species' spawning behaviour. Recruitment of lake whitefish has dramatically declined over the past two decades across many regions of the Laurentian Great Lakes, most notably in lakes Huron and Michigan, prompting research efforts to fill critical knowledge gaps in the life history of this species. Understanding the reproductive ecology of lake whitefish, including documenting aspects of spawning behaviour, may reveal clues about factors contributing to the declines. This study used fine-scale acoustic telemetry to characterize sex-specific movement patterns and habitat associations of lake whitefish during the spawning season. A VEMCO Positioning System (VPS) was deployed at an active spawning shoal in Georgian Bay (Lake Huron), with guidance provided by Saugeen Ojibway Nation members with local ecological knowledge about the shoal and the lake whitefish population. In the fall of 2020, 50 lake whitefish were captured and tagged at the spawning shoal; 28 of those fish were observed the following spawning season in 2021. A clear increase and decrease was observed in the presence of individuals in the study area over the spawning period. Both sexes moved into shallower waters at night and deeper waters during the day at rates of 0.162 m/h and 0.08 m/h, respectively. Decreased rates of movement and horizontal distance travelled were detected during the day leading up to a peak activity phase where 22 fish were present. At night during this peak activity phase, males moved 30.0% faster on average than females (0.204 ± 0.13 and 0.143 ± 0.10 m/s, respectively). This study provided a unique opportunity to work with local First Nations to understand lake whitefish spawning behaviour, providing insights into the reproductive ecology of a population undergoing concerning declines in recruitment and abundance.

Author Keywords: Coregonine restoration, Coregonus clupeaformis, Fine-scale acoustic telemetry, GLATOS, Spawning habitat, Two-Eyed Seeing

Naphthenic acids are a major contaminant of concern and a focus of much research around remediation of oil sand process affected waters, OSPW. Using activated carbon adsorbents are an attractive option given their low cost of fabrication and implementation. A deeper evaluation of the effect naphthenic acid structural differences have on uptake affinity is warranted. In this thesis an in-depth exploration of naphthenic acid adsorption onto activated carbon is provided including many more model naphthenic acid species than what have been assessed previously in adsorption studies. Both adsorption kinetics and isotherms at the relevant alkaline pH of OSPW using several different carbon adsorbents with pH buffering to simulate the behaviour of real OSPW were evaluated. Given the time sensitive application of most adsorbents towards treating contaminated waters such as OSPW, achieving fast adsorption rates for model naphthenic acids is an important goal worth considering. Textural properties of activated carbon most conducive for fast adsorption kinetics were assessed using several candidate model species. Clear evidence is presented, demonstrating the influence of both the pore size distribution and particle size of porous adsorbents on uptake rates of naphthenic acids, demonstrating that careful optimization of these adsorbent properties can result in adequate uptake rates. Adsorption isotherms were used to assess model naphthenic acid affinity towards activated carbon. Uptake for the model naphthenic acids varied considerably regardless of the activated carbon used, ranging from 350 mg g-1 to near zero highlighting recalcitrant species. The equilibrium data was explored to identify important structural features of these species and key physiochemical properties that influence adsorption. It was demonstrated that certain naphthenic acids are resistant to adsorption when hydrophobic adsorbents are used. Adsorption isotherm modelling helped explore interactions occurring at the interface between naphthenic acids and adsorbent surfaces. Naphthenic acid hydrophobicity was identified as an importance physiochemical property for achieving high adsorption capacities onto activated carbon. Evidence is also presented that indicates favorable hydrogen bonding between naphthenic acids and surface site hydroxyl groups, demonstrating the importance of adsorbent surface functionality for naphthenic acid uptake. The adsorption mechanism was further explored through use of a thermodynamic analysis of the model naphthenic acid system using activated carbon. Standard state enthalpy and isosteric enthalpy of adsorption values were used to further support the proposed mechanisms occurring between model species and activated carbons. This research highlights the challenges associated with removing naphthenic acids from OSPW through adsorption and identifies how adsorbent surface chemistry modification will need to be used to increase the removal efficiency of recalcitrant naphthenic acid species when using activated carbon.

Author Keywords: Activated Carbon, Isotherms, Kinetics, Modelling, Naphthenic Acids, Thermodynamics

The Great Lakes represent nearly a fifth of the global freshwater surface supply, and support culturally, economically, and ecologically important fish species such as Walleye (Sander vitreus). With water temperatures projected to rise by several degrees in the coming century, understanding the energetic impacts on fishes is crucial for effective habitat and fisheries management. I measured the swimming performance, accelerometer-based activity, and metabolism of walleye in relation to body size, sex, and water temperature to assess potential responses to climate variability. Both acceleration and swim speed predicted metabolic rate with reasonable accuracy. Temperature had a positive effect on oxygen consumption whereas body mass had a negative effect. Critical swimming speed increased with temperature, and tailbeat frequency had positive relationships with swim speed and acceleration. My laboratory-based calibrations should enable remote field monitoring of energy use of walleye (via accelerometers) and help conserve an important species through bioenergetic modelling.

Author Keywords: accelerometry, bioenergetics, climate change, metabolism, respirometry, walleye