Restricted Theses and Dissertations
Permanent URI for this collection
This collection is the result of a joint project between the Faculty of Graduate Studies and Libraries and Cultural Resources which provides Graduate students with the opportunity to archive their thesis with University Archives in our digital repository.
If you are a Graduate student submitting your final thesis to PRISM, please ensure you have read and submitted all required documents: http://grad.ucalgary.ca/current/thesis
If you require technical assistance please contact thesis@ucalgary.ca
The electronic theses and dissertations on this site are for the personal use of students, scholars and the public. Any commercial use, publication or lending of them in libraries is strictly prohibited.
Browse
Recent Submissions
Item Embargo From Palestine to Turtle Island: Essays on TransIndigenous Literatures(2025-01-17) Ababneh, Mahmoud; Prud'homme-Cranford, Rain; Srivastava, Aruna; Vanek, MorganThis manuscript dissertation/thesis explores the relationships between Turtle Island and Palestine, contributing to larger discussions in TransIndigenous studies, global Indigenous studies, and within comparative literary studies fields broadly. From Palestine to Turtle Island: Essays on TransIndigenous Literatures creates a dialogue between Indigenous arts and aesthetics centring Indigenous ways of knowing across nations, specifically on Turtle Island and in Palestine, wherein engaging with narrating history and centring Indigenous voices beyond national and exceptionalist narratives about the U.S., Israel, and Canada as colonial states. While I trace possibilities emancipating from juxtaposing Indigenous histories, I pave the way to question our current moment as an extension of settler colonial structures. This manuscript investigates how writers and artists such as Steven Salaita, Armand Garnet Ruffo, James Welch, Aicha Yassin, Charolette DeClue, and Susan Abulhawa reclaim Indigenous voices and histories, reminding readers that settler colonialism is not a past event. They also present Indigenous stories that are past, present, and futurity, surviving despite settler structures of erasure and silence. Additionally, this dissertation aims to situate Palestinian literary and cultural productions in dialogue with Anishinaabe, Cheyenne, and other productions of Algonquin Indigenous artists of Turtle Island. I examine the productive possibilities of this cross-cultural communication to uncover how Indigenous works challenge dominant narratives and offer pathways for resistance, resilience, and healing.Item Embargo Development and Characterization of Catalysts for Fuel Cell and CO2 Electrolyzer Applications(2025-01-14) Moghaddasisaen, Pezhvak; Birss, Viola; Shimizu, George; Karan, Kunal; Dolgos, Michelle; Marriott, RobertThis thesis explores advanced catalysts for energy conversion, focusing on two key projects. The first project explores doped PtRu catalysts to improve CO tolerance in proton exchange membrane (PEM) fuel cells. Using density functional theory (DFT), Pd- and Rh-doped PtRu catalysts were identified as promising due to their resistance to CO poisoning. These findings suggest the potential to enhance PEM fuel cell anode durability and reduce fuel purification requirements, though experimental validation is needed. The second project focuses on nitrogen-doped carbon catalysts for electrochemical CO2 reduction (CO2RR). Jialang Li’s thesis ([86]) demonstrated that nitrogen doping lowers the energy barrier for CO2 reduction, enhancing catalytic activity. In my study, both Vulcan XC 72-R and CIC-85 were investigated. Untreated carbon black (Vulcan XC 72-R) and CIC-85 were found to be inactive for CO2RR. Acid treatment increased the surface oxygen content but did not significantly enhance catalytic activity. However, when acid-treated Vulcan car- bon or CIC-85 was subjected to high-temperature ammonia treatment, substantial nitrogen doping was achieved, as confirmed by advanced surface characterization techniques. My results show that increased oxygen content from acid treatment facilitated greater nitrogen incorporation during ammonia doping, significantly improving CO2RR activity and selectivity. These findings highlight the role of oxygen content in enabling higher nitrogen doping and improving performance for CO2 reduction. These results contribute to both theoretical and experimental advancements in the development of catalysts for sustainable energy applications.Item Embargo Identifying Graft Versus Host and Graft Versus Leukemia Allo-Immune Reaction After Stem Cell Transplantation(2025-01-15) Kalra, Amit; Khan, Faisal Masood; Storek, Jan; Lewis, Victor Anthony; Mansoor, AdnanAllogeneic hematopoietic stem cell transplantation (HCT) is a curative therapy for hematological malignancies. Two major allo-immune reactions take place in the recipient after HCT: the beneficial graft versus leukemia (GvL) wherein the donor immune cells identify and eradicate the leukemic cells of the recipient and the graft versus host (GvH) where the donor immune cells react against the normal cells of the host causing a debilitating illness called graft versus host disease (GvHD). The primary objective of this doctoral research was to distinguish between GvH and GvL allo-immune reactions by meticulously profiling the immune recovery at multiple time points post-HCT. Immune reconstitution in both adult and pediatric HCT recipients was evaluated at the transcriptomic level via gene expression profiling of 579 immunity-related genes using NanoString technology and at the cellular level through flow cytometric analysis of cell subset counts. Peripheral blood mononuclear cells from HCT recipients were analyzed at Day14, Day28, Day56, and Day84 posttransplant. An immune signature characterized by higher counts of T cells and overexpressed T cell-related genes, was identified in patients who developed acute GvHD grades 2-4 as early as Day14 posttransplant. The gene expression signature showing overexpressed T cell related genes especially CD161 expressing cytotoxic T cells was validated in an independent validation cohort. T cell counts and related transcriptomes were notably higher in cytomegalovirus (CMV) seropositive donor and recipient (D+R+) patients compared to other serostatus groups. The recovery pattern was similar in both adult and pediatric patients. The influence of CMV D+R+ on T cell reconstitution was not significant at early time points (Day 28) but became evident at 2 and 3 months post-transplant. Signatures indicating a lack of GvL response were observed at 3 months (Day 84) post-transplant characterized by downregulated expression of CD8 Tcell genes, including TIGIT and EOMES in patients at high risk of relapse. While this study succeeded in partially differentiating GvH and GvL allo-immune reactions through temporal and differential T cell gene expression profiling, further comprehensive transcriptomic analysis in larger cohorts is essential for a complete understanding of the separation between GvH and GvL.Item Embargo Devices and computational methods for preclinical mechanistic deep brain stimulation studies in freely moving rodents(2025-01-13) Bisht, Anupam; Murari, Kartikeya; Kiss, Zelma; Whelan, Patrick; Fear, Elise; Voigts, JakobDeep brain stimulation (DBS) is a therapeutic technique used for the treatment of neurological and psychiatric diseases. Optimization and patient-specific application of DBS remain a challenge as mechanisms of the therapeutic action of DBS on the brain remains unknown. Currently, the instrumentation available for preclinical DBS research focused on performing freely moving animal experiments is limited. The proposed work addresses this gap through major improvements of existing devices and the development of supporting computational methods for data analysis. This work has been divided into four aims. Motivated from a previously developed gradient refractive index lens based point detector system, aim 1 involved development of a wireless miniaturized intrinsic optical imaging system (called TinyIOMS- Tiny intrinsic optical monitoring system) to measure changes in hemoglobin concentration from surface regions of the brain (e.g., motor cortex which is the main output center of DBS brain targets). A comparison of signals with a standard wide-field intrinsic optical imaging system was done to validate the signal reliability of TinyIOMS. Further, we showed the hemodynamic signals recorded could be used to distinguish between brain states (sleep vs awake) by performing continuous recordings for about 7 hours to about 2 days (via intermittent recordings). Aim 2 involved investigating motion artifacts for a single f iber system (SFS) that has shown variability in the measured hemodynamic signals (blood flow and oxygen saturation) from deep brain regions (commonly stimulated during DBS) during previous DBS studies. In this work, we showed that while the blood flow signal is sensitive to motion artifacts, oxygen saturation is not. Further, a motion artifact correction algorithm was developed to correct motion artifacts that occur during experiments using a regression-based approach utilizing light at 680 nm, a wavelength that is relatively less sensitive to hemodynamics. Since the biological interpretability of hemodynamic changes during DBS recorded in the SFS signals was limited, one approach is to compare it with well-established signals, e.g., electrophysiology or GCaMP-based fiber photometry. In aim ii 3, we have further extended the SFS design to enable stimulus-locked (e.g., footshocks, DBS) simultaneous recording of both hemodynamics and GCaMP-based fluorescence signals. In aim 4, a previously developed miniaturized DBS device was improved in mechanical and electrical design, and the software was upgraded to enable wireless programming and timed stimulation. This device was used to stimulate a novel target for DBS, the A13 region of the medial zona incerta in rats. We observed that DBS evoked a robust locomotor response with an overall non-noxious behavioral effect which is important data for clinical translation. Overall, this thesis advances the technology for performing electrical stimulation and the monitoring of hemodynamics in freely moving animals.Item Embargo Indigenous Health in Postgraduate Medical Education: Pathways for Enhancing Anti-racism Literacy and Praxis for Advanced Trainees(2025-01-13) Ramé, Ana Karen; Henderson, Rita Isabel; Paolucci, Elizabeth Oddone; Crowshoe, Lynden John; Roach, Pamela; Altabbaa, GhazwanRacism is detrimental to health; it widens gaps in health inequities by marginalizing specific populations and sustaining structures that perpetuate harm. This results in social fragmentation that hampers the capacity of affected communities to achieve well-being. Racial hierarchies tend to characterize aspirations for equity as unachievable, using the complexity of the need to shift institutions, attitudes, and whole cultures to undermine expectations that equity be a core component and not simply an added benefit of a just society. This doctoral thesis aims to mitigate the impact of racism on health disparities experienced by Indigenous peoples in Canada by addressing unequal treatment in health systems through the advanced training of healthcare professionals, specifically medical residents across specialties. It is aligned with the Truth and Reconciliation Commission of Canada’s (TRC) Call to Action #24, which emphasizes the expansion of “skills-based training in intercultural competency, conflict resolution, human rights, and anti-racism” for all health professionals in Canada. Decolonial and anti-racist education are promising pathways explored here for advancing healthcare equity, as they place historical, political, and social experiences at the centre of the learning process and objectives. These pedagogies promote the active involvement of learners, an approach that would seem to suit advanced medical trainees whose programs usually involve practice-based experiential learning mentored by established physicians. Such training also offers the possibility for adult learning approaches known to favour behaviour change, such as critical self-reflection over time. However, medical residency and fellowship training often involve limited exposure to the lived realities of Indigenous patients and, in turn, limited direct feedback or guidance from these. This complicates possibilities for integrating historical, political, and social components of Indigenous-focused anti-racism. This thesis presents a largely qualitative body of work that approaches these dilemmas in three parts. It begins by eliciting guidance from semi-structured interviews conducted in one Canadian province with Indigenous individuals who have accumulated experiences in health systems and health professional training (n=12). It then draws on a document analysis of formal Indigenous training in post-graduate medical education (PGME) across Canada. Finally, it returns to perspectives on health professional learning among advanced medical trainees through semi-structured interviews with non-Indigenous residency preceptors (n=19) and residents (n=14) across specialties. These sources offer insight into Indigenous guidance for PGME training in Indigenous health and anti-racism in Canada, current approaches across medical schools, and needs and possibilities for growing Indigenous-focused anti-racism learning from mentors and mentees within PGME programs. This work emphasizes that addressing anti-Indigenous racism in healthcare is essential for achieving Indigenous health equity. Integrating insights from 45 interviews and the scanning of 1179 curricular documents related to PGME with a close review of 46 containing any form of Indigenous content, this work offers a preliminary index of specialty-specific Indigenous health and anti-racism content as a potential starting point for more refined curricular development. An important implication of this work is greater clarity around how training may incorporate unique dilemmas faced in distinct medical fields and the cultural, social, and geopolitical diversity of Indigenous peoples in Canada.Item Embargo Evaluating the Phenotypic Consequences of DNA-PKcs Deficiency(2025-01-14) Kenny, Jacey; Lees-Miller, Susan; Billon, Pierre; Moorhead, GregoryDNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a serine/threonine protein kinase with a well-established role in the repair of DNA double strand breaks. Similarly, Ataxia-Telangiectasia Mutated (ATM) is a protein kinase that plays a central role in downstream signalling response to DNA damage. DNA-PKcs and ATM are members of the phosphatidylinositol 3-kinase-like protein kinase (PIKK) family, which serve critical roles in the cellular response to DNA damage. To better understand the non-canonical roles of DNA-PKcs and ATM, our lab generated human cell lines with CRISPR/Cas9-mediated disruption of these proteins, marking the starting point of my project. My work demonstrates that loss of DNA-PKcs and/or ATM expression results in slower proliferation compared to parental cells, while inhibition of DNA-PKcs or ATM kinase activity had a comparatively minor effect on cell proliferation. My data suggests that this phenotype is not due to increased apoptosis, endogenous DNA damage or cell cycle defects. Comparison of the metabolite profiles of the matched control and CRISPR cell lines suggested enrichment of amino acids in the HeLa CRISPR DNA-PKcs cells which led me to hypothesize that the CRISPR cell lines have a reduced rate of protein translation. I present evidence that cells deficient in DNA-PKcs and ATM exhibit impaired global, new protein translation, revealing a potentially novel mechanism for the slow growth phenotype. This work adds to a growing body of evidence encouraging further exploration of DNA-PKcs and ATM as therapeutic targets in cancer and other diseases.Item Embargo Correlating Obstructive Symptoms with Stricture Severity in Ileal Crohn’s Disease(2024-11-28) Saunders, Bethany; Lu, Cathy; Bonni, Shirin; Novak, Kerri; Ma, Christopher; Ganesh, AravindCrohn’s Disease (CD) can manifest as inflammatory (non-stricturing), fibrostenotic (stricturing) and fistulizing or penetrating phenotypes. Stricturing CD, the main focus of this thesis, involves luminal narrowing and, which is often progressive leading to obstruction of the affected bowel segment. Obstructive symptoms (OS) in CD strictures can be assessed using the Stricture Definition and Treatment (STRIDENT) trial-used OS scoring system and CREOLE OS score. Clinically, OS are typically linked to advanced strictures, strictures can often result in dietary restrictions and surgery. No studies have been published to date, evaluating the severity of CD strictures and OS. Understanding the correlation between symptoms and strictures is crucial as regulatory bodies assess drug efficacy based on symptom response in CD trials. Intestinal ultrasound (IUS) accurately evaluates strictures morphology, with stricture severity and length, using established criteria: bowel wall thickness > 3mm, luminal narrowing (<1cm), with any pre-stenotic dilation (PSD) size (cm). The aim of this thesis based stsudy aims to determine if the OS of pain, bloating, nausea and/ or vomiting when comparing among CD phenotypes, and if specific OS correlate with any of the definitive stricture parameters.Item Embargo Acute and Chronic Physiological Responses to Endurance Exercise of Varying Durations: Neuromuscular, Hematological, and Integrative Outcomes(2025-01-10) Tripp, Thomas; MacInnis, Martin; Edgett, Brittany; Gibala, Martin; Manske, Sarah; McNeil, ChrisThe integrative action of several physiological systems supports increased skeletal muscle energy demand during exercise. Physiological systems structurally and functionally adapt when exercise stresses are regularly imposed during a period of training. These adaptations, in turn, reduce the homeostatic stress for a given exercise bout. In particular, the impacts of exercise duration and exercise frequency on acute and chronic exercise responses are poorly understood. During prolonged exercise, physiological systems are activated to support muscle contraction, but metabolite accumulation and substrate depletion inevitably occur. During a training program, the balance between the number of times an exercise stress is experienced and the amount of stress per instance implicates exercise frequency along with duration as factors influencing physiological adaptations. This dissertation sought to address gaps in our understanding of the acute responses to differing exercise durations, and to compare chronic training adaptations when total exercise volume is the same. Study 1(Chapter III) showed that near-infrared spectroscopy measures of muscle oxidative capacity are sensitive to contraction intensity, necessitating intensity controls when the technique is used in future studies. Study 2 (Chapter IV) characterized neuromuscular fatigue kinetics during high-intensity interval training and showed that the largest deficits occur early during exercise, implying that additional exercise stress diminished during later bouts. Study 3 (Chapter V) investigated erythropoietic signalling when exercise duration is doubled. I found that increases in erythropoietin mass were not different after both exercise durations, despite hypervolemia only occurring after longer exercise. Study 4 (Chapter VI) aimed to probe whether the acute differences I found between exercise durations impacted training adaptations. This study showed that both long, low-frequency (a Weekend Warrior pattern) and shorter, high-frequency training similarly improved maximal oxygen uptake, hemoglobin mass, muscle oxidative capacity, and exercise capacity. The findings of this dissertation suggest that for some exercise responses, duration does not substantially augment the magnitude of acute stress/signalling events; however, when comparing different frequencies of exposure to that exercise stress, training adaptations were not different. Future studies should address how this acute stress/signal-to-chronic adaptation discrepancy occurs in the context of exercise duration and training frequency.Item Embargo Optimizing personalized treatment strategies for coronary artery disease using deep learning and reinforcement learning(2025-01-10) Ghasemi, Peyman; Lee, Joon; White, James Alexander; Lee, Joon; White, James Alexander; Har, Bryan Jonathan; Greenberg, MatthewCoronary artery disease (CAD) is a leading global cause of mortality and morbidity, affecting approximately 295 million people and resulting in 9.5 million deaths in 2021. Despite advancements in medical interventions that have reduced CAD mortality in high-income countries, significant challenges remain in delivering optimized, personalized care, particularly in settings characterized by high patient variability. Traditional decision-making in the treatment of obstructive CAD—encompassing percutaneous coronary intervention (PCI), coronary artery bypass grafting (CABG), and medical therapy—relies predominantly on population-level data from randomized controlled trials. However, this approach often neglects individual patient characteristics and the sequential nature of CAD treatments. This thesis employs machine learning (ML), with a focus on reinforcement learning (RL) and deep learning techniques, to improve CAD treatment decision-making. Specifically, it develops an offline RL framework designed to provide personalized treatment recommendations for patients with CAD, utilizing a large cohort from Alberta, Canada. Chapter 3 addresses the challenge of processing high-dimensional clinical data for ML applications. Through extensive experimentation with several unsupervised feature selection techniques, this study identifies the weight-adjusted concrete autoencoder as the most effective method for extracting efficient and interpretable features from diagnostic (ICD-10) and therapeutic (ATC) code databases. The selected features serve as the foundation for the analyses in subsequent chapters. Chapter 4 forms the core of this thesis, presenting an offline RL framework named RL4CAD to optimize CAD treatment recommendations tailored to individual patient profiles. Off-policy evaluation of RL4CAD models demonstrates their superiority over traditional physician-driven decision-making, achieving significant reductions in major adverse cardiovascular events. By using conservative RL models, we balanced the optimal recommendations with the current clinical practice. Moreover, this framework introduces interpretability to RL-based decisions by employing models with limited state spaces and identifying key features that influence outcomes. In Chapter 5, the thesis addresses the challenge of distribution shifts across diverse patient populations, such as variations in sex and treatment site, which complicate the optimization of CAD treatment using RL. By stratifying patient cohorts by these features and independently evaluating physician behavior and RL-derived policies, significant disparities in clinical practices were identified. To mitigate these challenges, transfer learning was integrated into the RL framework, enabling the model to adapt to diverse patient subgroups with minimal data and retraining. This approach effectively addressed distribution shifts, improving the RL models’ capacity to deliver personalized and equitable CAD treatment recommendations in patient populations that they had not been trained on. Collectively, the innovations in feature selection, RL-guided decision-making, and addressing distribution shifts contribute a scalable, data-driven solution for CAD management. By delivering personalized treatment recommendations that account for patient and practice variability, this work advances the potential of RL-driven precision medicine in cardiovascular care. Furthermore, the findings from this thesis establish a foundation for applying RL to other complex and dynamic treatment domains.Item Embargo Applying Dynamic Capabilities in Business Model Innovation: An Exploratory Case Study in a Self-Managing Organization(2025-01-07) Mayer, Matthew; Osiyevskyy, Oleksiy; Woiceshyn, Jaana; Suddaby, Roy; Saunders, Chad; Mihalache, OliDespite a significant amount of literature on business model innovation (BMI) suggesting the importance of organizational design as a firm-level moderator for successful BMI outcomes, few studies have addressed it directly. Self-managing organizations (SMO) are a type of less-hierarchical organization that aims to redefine hierarchical structures, especially the role of traditional managers. Like any firm, SMOs that innovate well may enjoy Schumpeterian entrepreneurial rents and, if effective at continually reconfiguring their resources, may sustain a competitive advantage in line with the dynamic capabilities (DCs) theoretical perspective. Despite practitioners suggesting that SMOs are better at adapting and responding to environmental conditions, few public-facing examples of BMI in these organizations exist in either popular management literature or scholarship. This intensive, exploratory case study researched an SMO that transformed its resources several times to pursue an array of BMIs over time. Interviews, observation and archival data were collected over 18 months. The study results showed that balancing hierarchical tensions, enacting collaborative routines for knowledge creation and configuring a community of leaders are foundational DCs when BMI is practiced in an SMO. In addition to outlining the routines and practices for DCs for BMI in an SMO, the study also proposed a model for how these DCs are applied. For scholars and practitioners, the study discusses the role of a manager, innovation champion and network for SMOs engaging in BMI. In practice, identifiable organizational routines and processes are present, and practices can be strategically selected to enact multiple DCs simultaneously. The exploratory nature of this case study elucidated future research to advance the field of BMI and SMOs.Item Embargo Preconditioning and weaning beef cattle: impacts on health and behaviour of beef calves and cows and the stakeholders’ perspectives(2025-01-09) Mijar, Sanjaya; Orsel, Karin; Pajor, Ed; van der Meer, Frank; Pearson, JenniferWhile preconditioning benefits calf health and performance, its adoption remains challenging due to uncertainties surrounding commingling preconditioned (PC) and auction-derived (AD) calves, as well as various social, financial, and market barriers in the beef industry. Furthermore, limited understanding of weaning stress on beef cows complicates preconditioning efforts aimed at minimizing stress and promoting animal welfare. Chapter 2 determined the impacts of commingling PC and AD calves in the feedlot in varying proportions, revealing that PC calves, regardless of commingling, showed reduced bovine respiratory disease (BRD)-related morbidity and lower treatment rates than AD calves. Chapter 3 investigated calves’ behavioural and physiological responses to stress related to feedlot transitioning, finding that PC calves showed better adaptation to the feedlot environment with increased eating and rumination, though hair cortisol levels did not differentiate stress responses. Chapter 4 explored beef industry stakeholders’ perspectives on preconditioning, identifying key motivators and barriers to its implementation. Five overarching themes were identified: Ranchers’ satisfaction and accountability and Thriving calves as motivations; and Lack of incentives, The quest for preconditioning proof, and Supply shortfall as barriers. Chapter 5 assessed weaning stress in three different weaning methods by measuring physiological and behavioural responses in beef cows, finding that nose-flap (NF) weaned cows exhibited fewer vocalizations, and less walking and pacing compared to abruptly or fenceline (FL) weaned cows. Fenceline weaned cows also had increased fecal glucocorticoid metabolites concentrations post-weaning compared to NF and abruptly weaned cows. Overall, this thesis highlights the health and feeding performance advantages of preconditioning calves outperforming AD calves, irrespective of commingling. This thesis also identifies underlying motivations and barriers to preconditioning adoption, and offers recommendations for strengthening preconditioning verification, fostering trust, and providing financial incentives to encourage broader adoption of preconditioning practices. Additionally, this thesis suggests the need for cow-calf operators to recognize that cows experience weaning stress differently than calves and to select less stressful weaning method aligning with specific ranch goals and production targets. Future research should emphasize extensive commingling protocols, weaning stress impacts on calves in utero and after birth, and a broader survey on preconditioning adoption in Canada.Item Embargo Biochemical Characterization of the Arabidopsis Chloroplast Localized Phosphatase Shewanella-Like Protein Phosphatase 1(2025-01-09) Johnson, Jayde Jarin; Moorhead, Greg; Turner, Raymond; Fraser, MarieShewanella-like protein phosphatase 1 (SLP1) is a newly discovered member of the phosphoprotein phosphatase class of protein phosphatases. In Arabidopsis, SLP1 was previously confirmed to be chloroplast localized. Mass spectrometry based phosphoproteomics analysis of different Arabidopsis lines identified 126 high confidence SLP1 substrates, all of which were predicted/known chloroplast proteins. Identification of 126 substrates suggests SLP1 is a major regulator of chloroplast metabolism. Analysis of the substrates indicated SLP1 preferentially dephosphorylates serine or threonine near acidic residues. Similarly, a chloroplast localized protein kinase, casein kinase 2α4 (CK2), prefers acidic substrate motifs. Interestingly, many of CK2’s substrates are also SLP1 substrates, suggesting SLP1 and CK2 act antagonistically to balance chloroplast phosphostatus. CK2 has been studied for decades, with SLP1 studies beginning only recently. Herein I build on previous biochemical characterizations of SLP1 using phosphorylated peptides in enzyme assays. I use reagents to simulate diurnal fluctuations of redox, pH, and metabolite/protein concentrations in the stroma in vitro and found that SLP1 is activated by chloroplast thioredoxin m. I use structural prediction tools to connect changes in SLP1 activity to structural features such as a predicted disulfide bond. Predictions also suggest which residues may be responsible for preferential dephosphorylation at acidic motifs. The structural predictions guided SLP1 bioinformatics as novel regions of SLP1 were predicted and confirmed through sequence analysis of SLP1 homologues. Then, I explore the SLP1 substrate Calvin Cycle Protein of 12 kDa (CP12), as an example for how SLP1 phosphorylation may play a role in the regulating the Calvin Cycle. I reconstituted the inhibition complex of glyceraldehyde-3-phosphate dehydrogenase, phosphoribulokinase, with wild-type and mutant CP12s in vitro. Using size exclusion chromatography, I observed that the complex formed using phosphomimetic CP12T116D elutes differently from wild-type. Lastly, I generate a proximity labelling construct to explore SLP1 protein-protein interactions. I demonstrate that SLP1 substrates can be labelled with biotin when transiently expressed in tobacco plants. The work here builds on previous studies, identifying areas of chloroplast biology where redox regulation and reversible protein phosphorylation intersect.Item Embargo Fragmented Paths: A Novella and a Journey Through Lands to Find the Self in Home(2024-12-19) Kamangarpour, Golaleh; Mayr, Suzette; Dobson, Kit; Seidel, Jackie LynnThis thesis explores the thematic and narrative intricacies of HomeLand, a novella that delves into the intersections of dreams, memory, and time in the pursuit of identity and belonging. Drawing inspiration from Indigenous and Kurdish philosophies, HomeLand challenges linear conceptions of time and self through a narrative structure that blends magical realism with psychological and cultural exploration. The work questions societal expectations surrounding happiness and fulfillment, drawing on Sara Ahmed’s The Promise of Happiness, and critiques the colonial legacies shaping perceptions of home and identity. Building on these thematic inquiries, the novella engages with Antonio Zadra and Robert Stickgold’s cognitive psychological theories on dreams (When Brains Dream), portraying dreams as pivotal tools for emotional processing, memory integration, and self-discovery. The Aymara philosophy of time, which positions the past as visible and the future as hidden, informs the novella’s fragmented and non-linear structure, reflecting its protagonists’ evolving identities. The thesis situates HomeLand within the broader context of Kurdish literature, addressing how the novella echoes the cultural and historical displacement experienced by Kurdish people while engaging with universal themes of alienation and belonging. Through its narrative, HomeLand interrogates the concept of home, presenting it as both an external and internal construct shaped by personal, cultural, and historical forces. Ultimately, HomeLand argues that the search for home is a fluid and continuous process, highlighting the universal yet deeply personal struggle to reconcile one’s identity in a fragmented world. By integrating insights from literary, cultural, and psychological frameworks, the exegesis positions HomeLand as a contribution to Kurdish literature and as a reflection of the universal human experience.Item Embargo The Effect of the Herbicide Glyphosate on Neurodevelopment and its Influences on Two Genetic Zebrafish Models of Autism(2024-12-27) Lacroix, Rachel; Kurrasch, Deborah; McFarlane, Sarah; Yang, GuangGlyphosate is the world’s most sprayed herbicide, leading to near ubiquity in the environment and increasing exposure for humans and wildlife. Initially glyphosate was thought to be safe for animals since it targets a molecular pathway found only in plants and bacteria, which facilitated the rapid adoption of glyphosate into mainstream agricultural practices. However, growing evidence suggests that glyphosate might be toxic across a wide range of organisms, including humans, leading to growing concerns of glyphosate’s effects on human health. Epidemiolocal findings show a strong correlation between increasing human glyphosate exposure and the rising rates of Autism Spectrum Disorder (ASD) diagnoses, raising the intriguing notion that glyphosate is somehow contributing to the etiology of ASD. The gene x environment hypothesis of ASD suggests that environmental factors, such as herbicides, may interact with autism alleles to perturb neurodevelopment to cause autism. Within this thesis, first I use zebrafish as a model system to characterize the behavioural (Chapter 3) and molecular/cellular (Chapter 4) effects of embryonic exposure to the active ingredient glyphosate alone as well as its commercial formulation RoundUp that also contains a mixture of surfactants that might be toxic. I show that embryonic exposure (10 hours-post fertilization (hpf)-48 hpf) to glyphosate singly or commercial RoundUp causes a range of behavioural deficits, with RoundUp exposed zebrafish showing a stronger phenotype. I also demonstrate that embryonic exposure to RoundUp disrupts neurogenesis and axonogenesis, and causes a concomitant increase in neuronal activity by 5 days-post fertilization (dpf). Next, I use two genetic zebrafish models whereby ASD genes have been mutated. I characterize these ASD lines and test a potential gene x environment interaction by assaying the effects of glyphosate in these zebrafish ASD models (Chapter 5). I show that ASD zebrafish have defects in morphology, behaviour, and brain activity. Behavioural and brain activity phenotypes are modulated with Roundup exposure in a genotype-dependant manner. Combined, these studies demonstrate that glyphosate and its commercial formulation RoundUp is toxic to developing brains in vivo and provide some evidence that exposure to glyphosate-based herbicides might contribute to the increasing rise of ASD diagnoses in children.Item Embargo Troubling the Pixel(2025-01-09) Yeomans, Tanya Michelle; McDermid, Greg John; Mac Namara, Aoife; Stadnyk, Tricia; Xu, Lincoln LinlinMonitoring vegetation recovery in forested environments can be done effectively with satellite time series data. However, most research in this space has relied on Landsat imagery, which has a 30-meter pixel size. Emerging CubeSat technology has much finer spatial resolution and offers new possibilities for monitoring vegetation on small industrial disturbances such as well pads and seismic lines. These features are associated with hydrocarbon exploration and are some of the most extensive disturbances in Alberta’s forests. We used PlanetScope satellite imagery to classify vegetation on small industrial disturbance features across a 309-km2 study area in northern Alberta as either growing or declining, and validated our results with LiDAR data. We found that recovery classification on medium-sized well pad features was significantly better than for medium and narrow linear features. We also found that disturbances in some ecosite types (low-density treed wetland, upland mesic, and upland dry sites) were easier to classify than others (transitional and wetland treed) and that linear features oriented in a north-south direction were easier to classify than those oriented east-west. Our research demonstrated that 58% of pixels on disturbed linear features in our study area displayed some degree of spectral regeneration, alongside 76% of the evaluated pixels on wellpads. We believe that the privilege of working with this emergent imagery comes with a responsibility to think deeply on how we use, transform, and interpret the data. To investigate the intersection between landscape, technology, and people, we employed arts-based research methods to trouble the pixel – the fundamental data unit in our remote-sensing research. By creating a textile pixel and documenting it in our study area, we were able to reflect on the parallel methodologies at play in our work, and to identify practical interventions into our scientific practice that allows us to more deeply engage with our data. This includes providing care instructions for our scientific products, slowing down our processes with manual tasks, and dedicating time to witness our data in-situ. Our hope is that through sharing our experiments in investigating our positionality to remote sensing, others are encouraged to reflect on their own practices.Item Embargo Brain-first versus Body-first: Exploring aspects of gut microbiota in Parkinson’s disease(2025-01-08) Kiani, Pardis; McCoy, Kathy; Sycuro, Laura; Martino, DavideParkinson’s disease (PD) is pathologically characterized by the irreversible aggregation of misfolded α-synuclein protein, forming what is known as Lewy Pathology, which is observed in multiple regions of the brain and gut. The “brain-first” and “body-first” hypothesis proposes distinct patterns of Lewy pathology distribution in the early stages of the disease, which categorizes clinical sub-phenotypes of PD. The “brain-first” sub-phenotype is thought to have predominant involvement of the amygdala, while the “body-first” sub-phenotype involves the enteric nervous system. In mouse models, the microbiota has been shown to be involved in promoting α-synuclein pathology and characteristic motor features in PD. This study aims to investigate whether microbiota from PD patients characterized as “brain-first” or “body-first” sub-phenotypes will induce divergent gastrointestinal functions and motor deficits in human microbiome-associated mice. Human PD microbiome-associated mice were generated by performing fecal microbial transfers from “brain-first” and “body-first” PD donors into germ-free C57BL/6 and dbl-PAC-Tg(SNCAA53T)Snca-/- recipient mice. FMT recipient mice were bred and gastrointestinal and motor functions in these offspring were analyzed. In dbl-PAC-Tg(SNCAA53T)Snca-/- mice, slow intestinal transit, indicative of decreased intestine motility, and increased gastrointestinal permeability were observed in “body-first” group compared to “brain-first” sub-phenotype. No significant motor function differences were detected between the two PD sub-phenotypes in these mouse models. Additionally, male dbl-PAC-Tg(SNCAA53T)Snca-/- “body-first” mice demonstrated a better ability to differentiate preferred odors in the olfactory preference test, whereas those colonized with microbiota from "brain-first" PD patients showed more olfactory dysfunction. Together, these results suggest that gut microbiota from PD patients may influence non-motor impairments associated with PD sub-phenotypes.Item Embargo Bovine Foot Rot and its Microbiological Relationship with Bovine Digital Dermatitis(2025-01-07) Pyakurel, Susan; Orsel, Karin; De Buck, Jeroen; Morck, Douglas Walter; Jelinski, MurrayBovine foot rot (BFR) and bovine digital dermatitis (BDD) are important infectious diseases that cause pain and lameness in feedlot cattle. BFR causes subcutaneous tissue necrosis and is treated using systemic antibiotics whereas BDD affects outer skin layers and is treated using topical treatments, but cases often relapse. Visual diagnosis of BFR and BDD is complicated by inconclusive cases with lesion characteristics indifferentiable as either BFR or BDD. F. necrophorum and Treponema spp. are the bacteria primarily associated with the pathogenesis of BFR and BDD, respectively. Also, several Treponema spp. are found associated with disease stages of BDD, also called M-stages, of which we investigated the active M2 and chronic M4 stages. As reported in Chapter 2, we visually diagnosed cattle as either BFR, BDD-M2, BDD-M4, inconclusive, and healthy groups. We found that the absolute quantity of seven bacterial species associated with BFR and BDD pathogenesis, namely, Fusobacterium necrophorum, Fusobacterium mortiferum, Bacteroides pyogenes, Porphyromonas levii, Treponema medium, Treponema phagedenis, and Treponema pedis, were different among biopsies, swabs, and subcutaneous samples within and between the cattle groups. We also found that routine histology was not effective in differentiating BFR and BDD. Also, a producer survey indicated that the risk factors included in our survey did not increase the odds of cattle being diagnosed with either disease. In Chapter 3, using 16S rRNA gene sequencing on DNA extracted from biopsies, we found that the groups generally had similar bacterial species present, although in different proportions, with the healthy group having the most diverse microbial taxa. . In Chapter 4, using whole genome sequencing and agar dilution assay, we found that most bacterial isolates derived from biopsies from different cattle groups contained tetracycline resistance genes as compared to penicillin and ceftiofur, and phenotypic resistance was also higher for tetracycline as compared to ceftiofur and penicillin. This thesis provides quantitative insights into the potential pathogens and risk factors responsible for BFR and BDD pathogenesis, and the in vitro activities of antibiotics used for treating these diseases, while also demonstrating the comparative effectiveness of diagnostic tools for sample collection and differential diagnosis.Item Embargo Multi-modal Evaluation of Perioperative Hypercoagulability in Orthopaedic Surgery Patients with Metastatic Bone Disease(2025-01-02) Yamaura, Lisa Mariko; Schneider, Prism Steorra; Jenne, Craig N; Monument, Michael James; Skeith, LesliePatients with metastatic bone disease (MBD) are at increased risk for venous thromboembolism (VTE) following orthopaedic surgery. Platelets are critical for thrombus formation, and increasing evidence suggests that the interplay between platelets and inflammation may promote this process. However, in patients with MBD, the extent and duration of post-operative hypercoagulability is poorly understood, and the pathophysiology of VTE in this population remains unknown. We aimed to address these knowledge gaps, and hypothesized that VTE would be associated with hypercoagulability, platelet activation and procoagulation, and elevated concentrations of circulating pro-inflammatory mediators. These hypotheses were tested in 35 patients with pathologic fractures due to MBD who required orthopaedic surgery. Study participants underwent serial phlebotomy over a 6-month post-operative period. Samples were analyzed using thrombelastography (TEG), TEG-based PlateletMapping®, and multiplex immunoassay analyses to quantify the extent and duration of hypercoagulability, platelet receptor pathway activity, and systemic inflammation. For population-specific insight, three subgroup analyses were performed. The 35-participant MBD cohort was dichotomized according to VTE incidence (yes/no) for the first analysis, and then by pathologic fracture type (acute/impending). The third subgroup analysis compared participants with acute hip fractures according to the presence of malignancy (MBD/non-cancer) using a subgroup of 10 participants from the overall MBD cohort, and a subgroup of 10 sex-matched participants without cancer. An additional sub-study was performed in 19 participants from the overall MBD cohort that used high-resolution fluorescence microscopy to visualize the platelet membrane and quantify platelet activation and procoagulation. Findings from this multi-modal study demonstrated that hypercoagulability, platelet receptor pathway hyperactivity, and systemic inflammation were elevated pre-operatively in participants who later developed VTE. This suggests that individuals at high VTE risk can be identified pre-operatively. Additionally, the results of subgroup analyses revealed that participants in the MBD and acute pathologic fracture subgroups were more hypercoagulable than participants in the non-cancer and impending fracture subgroups. Associations between hypercoagulability, platelet activation, and inflammation were observed in patients with MBD, with temporal change in each parameter mirroring the others throughout the study. Therefore, further investigation into platelet- and inflammation-mediated hypercoagulability may uncover novel and/or optimal targets for thromboprophylaxis for patients with MBD.Item Embargo Metabolomics comparison between Delta and Omicron-infected individuals(2025-01-06) Pimentel Guerrero, Eric Iván; Winston, Brent; Lee, Chel; Habibi, Hamid; McDonald, BraedonAt the end of 2019, SARS-CoV-2, the novel coronavirus emerged causing a widespread increase in airway and lung infections that was driven by different viral variants. Only the variants with significant differences in transmissibility, disease severity, reduction in neutralization by antibodies, and reduction in treatment effectiveness were designated as variants of concern (VOC). Among these variants, the Delta and Omicron forms have demonstrated marked differences in transmissibility and disease severity. This study aims to identify the plasma metabolomics differences that characterize Delta-infected compared to Omicron-infected patients, analyze the severity within these SARS-CoV-2 variant infections, and investigate how vaccination status and corticosteroid treatment impacted the plasma metabolomic profiles of these patients infected with these variants. Our hypothesis is that the metabolomic profiles will reveal significant metabolomic differences between the two variants, reflecting their varied clinical outcomes. Furthermore, we hypothesize that the treatments used during each variant’s wave of infection may be reflected in the plasma metabolome of infected individuals. This study demonstrates that not only are there differences in plasma metabolites that distinguish Delta and Omicron-infected individuals, but also that metabolites do differentiate between various degrees of severity.Item Embargo Additive Manufacturing of Continuous Fiber-Reinforced Thermoplastic Composites Using Discrete In-Situ Consolidation(2025-01-02) Elderfield, Nicholas; Wong, Joanna C.H.; Korobenko, Artem; Trifkovic, Milana; Sudak, Leszek Jozef; Shrive, Nigel Graham; Laberge Lebel, LouisAdditive manufacturing using the fused filament fabrication (FFF) process presents a simple, low-cost alternative to traditional methods for producing continuous fiber-reinforced polymer composite parts. However, the current state of this technology is hindered by challenges which prevent industry adoption, including limited material selections, high porosities (>10%), weak interlaminar bonding, and low fiber volume fractions (typically ≤35%). Furthermore, there has been limited exploration of its use for manufacturing non-planar geometries, and methods for accurately modeling the structural behavior of parts are still underdeveloped. This doctoral thesis investigates solutions for addressing each of these challenges. To expand material selection, the production of custom 3D printer filaments is investigated using multi-die pultrusion of commingled yarns. A custom pultrusion system is designed and constructed, featuring a split-die design which enables simple and repeatable adjustment of outlet area to accommodate a wide range of precursor materials. It is observed that reinforcement fibers tend to form tightly-packed clusters during the pultrusion process which resist impregnation by viscous thermoplastic melts. A fiber dispersion metric is devised to quantify the proportion of tightly clustered fibers and estimate the degree of impregnation, which is shown to correlate with flexural modulus and stress at failure. The effects of processing speed and temperature on fiber dispersion are investigated in the production of a carbon fiber-reinforced polyetherimide (PEI) 3D printer filament. It is revealed that impregnation rate is limited by the dispersal speed of fibers away from cluster boundaries, which is impeded by the high viscosity of thermoplastic melts. Achieving acceptable levels of impregnation thereby requires either slow processing speeds or a high degree of commingling between reinforcement and matrix materials in the precursor to reduce initial cluster sizes. To address issues related to porosity, weak interlaminar bonding, and low fiber volume fractions in FFF-processed materials, a discrete in-situ consolidation (DISC) method is introduced. DISC applies localized heat and pressure to individual beads of material after deposition via FFF by pressing and running a heated flat-bottomed tool along each bead’s length. The effectiveness of this process is demonstrated by processing a carbon fiber-reinforced polyamide 12 with a 50% fiber volume fraction, resulting in an 89% reduction in void content and a 640% improvement in interlaminar shear strength in comparison to FFF alone. It is discovered that the porosity of material processed with DISC is highly sensitive to the waviness of fibers in deposited beads, requiring precise synchronization between the filament feed rate and deposition speed to maintain organized fiber networks. When the filament is extruded at a higher rate than the nozzle velocity (i.e., over-extruded) the reinforcement fibers buckle and become wavy, resulting in a disorganized fiber network that accumulates significant strain energy during compaction and deconsolidates rapidly upon the release of pressure. To demonstrate the effectiveness of DISC in the production of non-planar structural components, a rotary axis is incorporated into a custom-built 3D printer and rigid cylindrical shells are manufactured by depositing material onto a rotating mandrel. The first continuous fiber-reinforced multi-turn wave springs are manufactured using this method and are subsequently characterized using cyclical compression testing. To demonstrate a strong end-use application of the FFF and DISC processes, the first additively manufactured bistable slit tube composite shells are produced. These shells, known as deployable booms, have extensive applications in deployable satellite structures due to their ability to be reconfigured between a rigid extended state and a space-efficient stable coiled state. The precise material placement capabilities of the FFF process are used to construct these shells with lattice architectures of various densities. A computational process is introduced which enables automatic generation of finite element models directly from material deposition paths. Homogenization and full-scale modeling techniques are employed to characterize structural behaviors of the deployable booms. The effects of fiber angles, lattice density, and initial shell curvature on the stability and shape of coiled configurations, as well as their impact on flexural rigidity properties, are investigated. Strong agreement is shown between the numerically predicted behaviors and experimental results. Lattice shell architectures are revealed to exhibit higher flexural rigidity properties than continuum architectures on an equal-mass basis. Lastly, bistable shell structures that can coil into unique stable configurations via the tailoring of bead deposition paths are demonstrated. This doctoral thesis presents comprehensive investigations and substantial contributions to the state-of-the-art in the field of additive manufacturing of structural composite parts. It examines many critical aspects of the FFF process, from filament production and additive manufacturing to structural design and end-use applications. Solutions for addressing material quality challenges and geometric limitations are presented, and modelling techniques for accurately predicting structural behaviors of manufactured parts are revealed. By addressing key challenges that have impeded industry adoption, this work has reduced barriers to the broader implementation of FFF technology for structural composite production.