Trent University

The neuronal ceroid lipofuscinoses (NCLs), collectively referred to as Batten disease, are a group of neurodegenerative diseases that affect all ages, primarily children. Batten disease is caused by mutations in 1 of the 13 ceroid lipofuscinosis neuronal (CLN) genes (CLN1-CLN8, CLN10-CLN14), each of which causes an NCL subtype when mutated. One of the NCL subtypes, CLN5 disease, is caused by mutations in the CLN5 gene. CLN5 is a soluble lysosomal protein that localizes to the endoplasmic reticulum (ER), the Golgi complex, the cytoplasm, and extracellularly. CLN5 has four putative molecular functions, including as a ceramide synthase, glycoside hydrolase, depalmitoylase, and bis(monoacylglycerol)phosphate synthase. CLN5 plays various roles within the cell, such as lipid metabolism, autophagy, and proteasome degradation. However, the function and the exact pathway in which CLN5 is involved are unclear. In addition, CLN5 is a secreted protein that, as shown via bioinformatics analysis, contains a signal peptide sequence. Furthermore, there are currently 70 CLN5 disease-causing mutations reported in the NCL mutation database. 12 CLN5 disease-causing mutations have been studied thus far in terms of their cellular impact, as well as the release of CLN5 to a certain extent. However, there is a lack of research into the functionality of the signal peptide in CLN5 and an in-depth analysis of the molecular impact of mutations in CLN5 disease. Consequently, this Ph.D. thesis focused on using comparative transcriptomics to reveal biological pathways affected by cln5-deficiency, revealing mechanisms that regulate the secretion of Cln5 and CtsD, and using Dictyostelium to gain insights into the molecular effects of mutations in CLN5 disease. Comparative transcriptomics reveal many differentially expressed genes that are linked to phenotypes observed in cln5-deficient cells and identified pathways affected in other CLN5 disease models, such as autophagy. Furthermore, novel findings, like affected expression of lysosomal enzymes and pathways, including secretion, are identified within the comparative transcriptomics analysis. Subsequently, this research also shows the secretory role of the signal peptide in Cln5 and CtsD. Finally, this Ph.D. thesis revealed that mutations in CLN5 disease affect the lysosomal biology and secretion of Cln5 and other lysosomal enzymes.

Author Keywords: Batten disease, CLN5, Dictyostelium discoideum, Enzymes, Lysosome, Secretion

Since the mid-Pleistocene, evolutionary histories of North American species were shaped by extreme climatic oscillations involving major range and habitat shifts at a rapid pace. The peopling of the continent and the subsequent human colonisation waves created further pressures affecting North American faunal and plant populations. Cervidae (deer family) are a diverse group which arrived in North America approximately 5 million years ago, and is represented on the continent by several extant species. The overarching aim of my thesis is to understand how North America's dynamic history shaped the evolutionary trajectory of the region's Cervidae species. In Chapter 2, I investigated the speciation and hybridisation history of the sister species white-tailed (Odocoileus virginianus) and mule deer (Odocoileus hemionus) using whole genome data of individuals from across their ranges, including zones of sympatry and allopatry. I found negligible patterns of ancient gene-flow suggesting white-tailed and mule deer divergence occurred via drift and their hybridisation is the result of secondary contact. In Chapter 3, I furthered our understanding of the Odocoileus species pair evolutionary history through explicit demographic inference and selection analyses. I used deer samples from across North America and found strong signals of climate- and human-induced population declines. Particularly, this work highlights the impact of European settlers and patterns of conservation concerns for mule deer. For Chapter 4, I clarified the phylogenetic relationship of a contentious taxon, Torontoceros hypogaeus, that went extinct during the late Pleistocene extinction event. I analysed 11k years old DNA of the single specimen representing the species, performed phylogenetic and divergence analyses, and found it belongs to the Odocoileus genus as Odocoileus (Torontoceros) hypogaeus which should be included in North America's late Pleistocene extinction list. Finally, in Chapter 5, I investigated genetic diversity over time in five North American Cervidae using contemporary and ancient DNA. I found patterns of change in genetic diversity that are consistent with known dispersal and demographic histories of our target species. Altogether, my thesis provides valuable insight into the evolutionary history of Northern American Cervidae, and on how they have been impacted by the continent's dynamic past.

Author Keywords: Cervidae, Demographic history, Extinction, Human impact, Hybridisation, Speciation genomics

Rare earth elements (REEs) are in high demand globally for the green transition and high technologies. The growing demand leads to their release into aquatic ecosystems from various point and non-point sources, which creates urgency to investigate their fate and enrichment. This thesis further investigates the biogeochemical fate and REE uptake mechanisms throughout aquatic ecosystems. Rare earth element concentrations and fractionations were quantified to determine the natural uptake mechanism of three REE exposure pathways (dissolved, diet, and particulate) into aquatic organisms. Pelagic organisms accumulated heavy REEs, indicating they primarily uptake dissolved REEs. Benthic organisms were characterized by REE patterns specific for diet and particulate REEs. Furthermore, lanthanum (La) enrichment was investigated in a lake treated with La-based coagulants using La anomalies. Lanthanum enrichment in the water and organisms were directly related to La dispersion from sediments. This research provides information on preferential exposure pathways and REE enrichment in aquatic ecosystems.

Author Keywords: bioaccumulation potential, fractionations, lanthanum enrichment, metal organotropism, rare earth elements, uptake mechanisms

While hospitals were seen as high-risk zones during the COVID-19 pandemic, little is known about how older hospital volunteers and volunteer-based programs navigated that period. Using the Peterborough Regional Health Centre (PRHC) in Ontario, Canada as a case study, this thesis research explores the pandemic and post-pandemic challenges of older voluntarism in a regional health care setting. In-depth interviews and focus groups were held with 21 volunteers and two program managers. Data analysis was done thematically using NVivo 15 qualitative analysis software. The findings covered major themes encompassing older volunteers' experiences during and post pandemic, the dynamics of digital technologies adoption in hospital volunteerism, challenges faced by older hospital volunteers and the volunteer program, and long-term measures to sustain hospital volunteer programs post-pandemic. The findings demonstrate that sustaining a robust volunteer program post-pandemic requires recognizing volunteers' contributions while also addressing their evolving (technological) needs, ensuring workplace health and safety, and actively involving volunteers in decision-making.

Author Keywords: COVID-19 pandemic, digital technology, hospitals, Older volunteers, volunteer experiences, volunteer-based program sustainability

Acid mine drainage (AMD) and metal-contaminated tailings represent some of the most inhospitable aquatic environments on Earth, characterized by low pH, elevated metal concentrations, and chronic carbon limitation. Yet these systems support microbial consortia with remarkable resilience. Among the most conspicuous inhabitants is Euglena mutabilis, an acidophilic protist traditionally regarded as an indicator species of AMD but seldom thoroughly investigated. This thesis reframes E. mutabilis at the center of a fungal-algal-bacterial (FAB) consortium, demonstrating that its cadmium tolerance and persistence are emergent properties of the consortium.

Culture-based experiments revealed that E. mutabilis survival under cadmium stress declined when fungal and bacterial partners were disrupted, underscoring their indispensability. Glucose supplementation revealed the consortium's capacity for structural and metabolic reorganization: fungal hyphae bound algal cells into flocs, bacterial associates proliferated, and hormone production shifted. Hormone profiling suggested a distributed signaling system in which fungi contributed cytokinins (CKs) and gibberellins while algae produced methyl-thiolated CKs, jasmonic acid, and salicylic acid. Transmission electron microscopy revealed bacterial-like inclusions within algal vacuoles, suggesting facultative endosymbiosis or phagotrophic retention. Transcriptomic analyses revealed that cadmium stress suppresses light-harvesting complexes and growth-promoting hormone biosynthesis while activating metal transporters and chloroplast sequestration mechanisms.

Beyond stress physiology, the FAB consortium unlocked chemical diversity inaccessible to axenic cultures. Molecular networking revealed that environmental consortia consistently produced unique metabolite families, often linked to silent biosynthetic pathways. Metagenomic sequencing linked these products to bacterial gene clusters further supporting the view that metabolic innovation is an emergent property of the collective.

Together, these findings suggest that the FAB consortium should be understood not as a loose association but as a microbial superorganism. This framing extends beyond the holobiont concept by dissolving the hierarchy between host and symbiont: E. mutabilis, fungi, and bacteria are all indispensable, and the identity of the host itself becomes blurred.

By reframing E. mutabilis as the nucleus of a microbial superorganism, this work highlights both theoretical and applied significance. It advances ecological understanding of how life persists under geochemical extremes, while pointing to new opportunities for sustainable bioremediation and natural product discovery through the deliberate cultivation of naturally evolved microbial consortia.

Author Keywords: Algal symbiosis, Bioremediation, Co-culture, Hormones, Microscopy, Transcrioptomics

This study examined how to incorporate Inuit Qaujimajatuqangit [Inuit knowledge] into elementary life science teaching in Nunavut. Interviews were conducted with Kivalliq teachers and elders to understand what teachers have done to incorporate Inuit Qaujimajatuqangit into their practice and interviewed elders to understand what Inuit Qaujimajatuqangit is, how it was shared, and used prior to the introduction of schools. The researcher used critical narrative inquiry to interrogate their practice in relation to the narratives of the elders and teachers. This research argues that Inuit Qaujimajatuqangit can be incorporated by Indigenizing science learning through content, processes, values, and Inuktut language of instruction; and decolonized by challenging the influences of standard Canadian curriculum. Sharing stories to construct elementary life science curriculum is a viable method for enabling culturally responsive and culture-based science education.

Author Keywords: decolonize, elementary science, Indigenous knowledge, Inuit Qaujimajatuqangit, Inuit science learning, life science education

Social anxiety involves negative thoughts and self-focused attention during social interactions. This self-evaluation can involve reflections regarding the body or body image, which may have an impact on social experiences. Body image is experienced in a negative (body dissatisfaction) and positive (body appreciation) way. The present study investigated the relation between symptoms of social anxiety and various aspects of body image in older adolescents and young adults. Quantitative results demonstrated considerable overlap between social anxiety and body image, with the qualitative results further supporting the rationale that symptoms consistent with social anxiety occur within those with body image concerns. Seven themes emerged and they were physical attributes, societal influence, appearance-driven coping strategies, impact on social life and relationships, discomfort with appearance, social avoidance, and appearance monitoring.

The ancient Maya utilized aspects of their landscape within their religious rituals and ceremonies, including caves. The study of ritual cave use is known as Maya cave archaeology and archaeologists in this subfield suggest that all holes in the earth, be it natural or man-made were viewed as ritually significant spaces to the ancient Maya (Brady and Layco 2018). This thesis analyzes the mortuary pattern of a chultun in relation to natural cave rituals and/or burials to determine if both types of subterranean spaces functioned in ritually similar ways. Through excavation of a dual-chambered chultun at the site of Ka'kabish, this research established a parallel pattern between burials found in natural caves and the burials within a chultun/artificial cave. In so doing, this thesis provides much needed data in support of applying Maya cave archaeology theories and practices in the excavation and study of ancient Maya chultuns.

Author Keywords: Belize, cave burials, chultuns, Maya archaeology, Maya cave archaeology, mortuary archaeology

Wetlands are highly susceptible to the invasion of invasive species. The invasive hybrid cattail (Typha × glauca) is prevalent in the southeastern Prairie Pothole Region (PPR) wetlands. However, concerns arise about its recent proliferation in the northwestern PPR without maternal T. angustifolia. To determine taxonomic distribution, I used species-specific PCR-RFLP and microsatellite markers for genotyping 245 samples from 50 northwest PPR sites. I found 75% T. latifolia, 7% T. angustifolia, 16% T. × glauca, and 2% backcrossed or advanced-generation hybrids. F1 T. × glauca has expanded in western PPR without its mother species, and the low occurrence of later-generation hybrids indicates their recent range expansion. Additionally, T. angustifolia offspring make fewer hybrids, which suggests that reproductive barriers may limit hybridization between parental species. This study highlights the vulnerability of prairies to cryptic invasions by Typha hybrids, and early detection of invasive species is a critical factor in wetland management success.

Metaphors are a ubiquitous component of communication, which are either conventional (familiar) or novel phrases. Metaphors are useful for discussing abstract concepts such as emotions that can be difficult to discuss literally, and as such benefit social relationships (Nippold et al., 2017). Research on contributors to novel metaphor production is limited and previous methodologies have been flawed, however some research suggests a role for executive function (EF; e.g., Menashe et al., 2020). Additionally, figurative language comprehension and metaphor production have been demonstrated to rely on overlapping abilities (Benedek et al., 2014). The current study examined figurative language comprehension and EF in novel metaphor production in 112 young adults aged 17-29 years. Neither individual nor groupwise analyses revealed any relations between EF or figurative language comprehension and novel metaphor production. However, an association with nonverbal IQ was found, suggesting that abstract reasoning abilities may play an important role in metaphoric ability.

Author Keywords: Executive function, Figurative language comprehension, Metaphor generation, Novel metaphor