A pipeline for discovery-based research on human T cell development : integrating spatial omics and PSC-T cell platforms

T cells play a critical role in adaptive immunity by recognizing self, versus non-self antigens, effectively protecting against pathogens and damaged or cancerous body cells. The application of T cells in cellular medicine to treat cancer and immunological disorders, as well as in personalized medicine to model disease pathologies, is rapidly expanding due to the potent role of T cells as mediators of the adaptive immune response. Pluripotent stem cell-derived T (PSC-T) cells have the potential to expand access to immunotherapies and disease modeling. However, current in vitro technologies have failed to recapitulate the signaling environments necessary to guide PSC-T cells towards mature helper and cytotoxic T cells in defined, feeder-free culture systems. T cells develop in the thymus, an organ specialized to support stage-specific T cell training via organization into spatially-defined niches. Previously, understanding of human T cell development and thymus niche biology was limited to interpretations from experimental animal models and observational learnings from patient populations with genetic mutations. These interpretations have proven challenging to adapt for in vitro PSC-T cell culture technology development. Here, we employ closed-loop learning to probe human T cell development. We first apply spatial multiomic technologies to create a spatially-defined map of tissue niches guiding T cell development in human postnatal thymus. We then test key insights into thymus niche biology in vitro using our PSC-T cell differentiation platform, demonstrating how our in vivo reference can be applied in vitro to guide T-lineage branching towards mature helper and cytotoxic PSC-T cells. Finally, we use our PSC-T platform to discover novel insights into the contribution of T cell receptor specificity to T-lineage branching. An additional insight from this work is how sex-based differences in thymus regulation and T cell development arise, and the potential for PSC-T platforms to model sex-based differences in T cell development and function. Overall, these data represent a unique resource to investigate how human thymus niche biology guides T cell development, validate niche signaling insights via PSC-T technology development, and demonstrate a novel technology to study and perturb human immune system development.Applied Science, Faculty ofBiomedical Engineering, School ofGraduat

Development of novel stable GRPR-targeting radiopharmaceuticals with low pancreas uptake for cancer diagnosis and therapy

Gastrin-releasing peptide receptor (GRPR) is overexpressed in multiple cancers, making it a promising target for diagnosis and therapy. However, most clinically evaluated GRPR-targeted radiopharmaceuticals show high accumulation in the pancreas and limited metabolic stability, which may restrict their diagnostic and therapeutic applications. This dissertation focuses on developing radiolabeled GRPR-targeting ligands with reduced pancreas uptake and improved metabolic stability to enhance diagnostic and therapeutic efficacy for GRPR-expressing tumors. Inspired by a series of GRPR antagonists published by Schally’s group, we first developed four radiolabeled GRPR antagonists based on the [Leu¹³ψThz¹⁴]Bombesin(7-14) sequence and three radiolabeled GRPR agonists by restoring the reduced peptide bond between residues 13-14 (Leu¹³ψThz¹⁴) in the [Leu¹³ψThz¹⁴]Bombesin(7-14) sequence with a normal amide bond. The antagonist [⁶⁸Ga]Ga-TacsBOMB2 and agonist [⁶⁸Ga]Ga-TacBOMB2 showed good tumor uptake and minimal pancreas uptake. Then we modified our lead agonist and antagonist candidates (TacBOMB2 and TacsBOMB2) with unnatural amino acid substitution to strengthen the bonds at the potential cleavage sites of neutral endopeptidase (NEP) to improve the stability. Our findings indicate that the Tle¹⁰ and NMe-His¹² substitutions markedly improve the stability of the GRPR agonist TacBOMB2 without affecting its binding affinity. Though, with no significant improvement in stability, NMe-Gly¹¹ substitution was shown to improve the tumor uptake and provide a better tumor-to-background contrast ratios for [⁶⁸Ga]Ga-TacsBOMB5 derived from TacsBOMB2. Then we labeled our lead candidates with ¹⁷⁷Lu for further evaluations. However, shorter tumor retention and lower absorbed radiation doses in PC-3 tumor xenograft were observed for all our ¹⁷⁷Lu-labeled GRPR-targeted ligands compared with the clinically validated [¹⁷⁷Lu]Lu-RM2, indicating further optimizations are still needed to prolong the tumor retention for therapeutic applications. To avoid the oxidation of Thz, we replaced the Thz¹⁴ with Pro¹⁴ to potentially prolong the shelf-life of our top GRPR-targeted radiopharmaceuticals. GRPR antagonist, [⁶⁸Ga]Ga-ProBOMB5 (DOTA-Pip-[DPhe⁶,NMe-Gly¹¹,Leu¹³ψPro¹⁴]Bombesin(6-14)), showed great tumor uptake, minimal accumulation in pancreas, and excellent tumor-to-background contrast ratios among all the novel GRPR-targeted tracers in this dissertation. Our results are encouraging to support clinical translation of [⁶⁸Ga]Ga-ProBOMB5 as a diagnostic radiotracer for detecting GRPR-expressing lesions, particularly the lesions in or adjacent to the pancreas.Medicine, Faculty ofGraduat

Characterization and improved lifetime management of serverless cloud systems

The full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.Applied Science, Faculty ofElectrical and Computer Engineering, Department ofGraduat

Indigenizing oral health providers’ curriculum worldwide and in Canada

Objectives: Curriculum Indigenization refers to any approach or philosophy of education for delivering Indigenous content and cultural perspectives to the learners. It remains unknown as to whether or not Indigenous content is addressed in the training of oral health providers worldwide, and in Canada. This study undertook a scoping review and a survey of all Canadian dental and dental hygiene programs to investigate the extent to which Indigenous content in addressed within oral health education curricula. Methods: The Joanna Briggs Institute’s methodology was followed for the scoping review. The search encompassed literature available until November 1, 2023. Two reviewers performed literature screening independently. “Indigenous”, “education”, and “oral health” were used as initial keywords. An anonymous survey was distributed electronically among all 10 dental and 35 dental hygiene schools across Canada between September and October 2023. The survey focused on Indigenous education objectives, content, method of delivery, assessment, barriers, and facilitators to address such content in the curriculum. Descriptive (means and frequencies) data analyses were performed using SPSS software version 29.0 (SPSS Inc., IL, USA). Results: A total of 948 records were identified for the scoping review, and 23 studies met the criteria for data extraction. The most covered content included Indigenous culture, with rural and clinical placements being the most employed delivery methods, and surveys the most employed assessment technique. For the survey, 90% of dental (n=9) and 71% (n=25) of dental hygiene programs responded, from which 32 had Indigenous content (9 dental: 23 dental hygiene). Lecture format was the most employed teaching approach, and Indigenous people’s health was the most covered topic. A packed curriculum was the most mentioned barrier in offering Indigenous content, followed by Indigenous faculty shortage. Conclusions: Indigenous culture worldwide and Indigenous health in Canada are the most frequently covered contents according to the scoping review. The survey revealed progress in including Indigenous content within Canadian dental and dental hygiene programs, but challenges such as overcrowded curricula and faculty shortages persist. Future efforts should focus on overcoming these barriers and evaluating the long-term impact of these educational programs on health outcomes for Indigenous populations.Dentistry, Faculty ofGraduat

Serum and Plasma miRNA Expression Levels in Sudden Sensorineural Hearing Loss

Sudden sensorineural hearing loss (SSNHL) is a rapidly developing acquired idiopathic disorder. Differential expressions of microRNAs (miRNAs) have been identified in the acute serum of SSNHL patients. miRNAs are transmitted in both serum and plasma, but it is unknown which better reflects changes associated with inner ear disease. Therefore, we sought to compare the serum and plasma miRNA expression levels in adult SSNHL patients. We extracted and reverse transcribed total RNA from serum and plasma, and analyzed the product with quantitative real-time PCR. hsa-miR-191-5p was used for normalization, and miRNA expression levels were calculated using the delta Ct method. Serum and plasma samples from 17 SSNHL patients (mean age 51.9 years, standard deviation 13.9 years) showed no significant differences in miR-128-3p, miR-132-3p, miR-375-3p, miR-590-5p, miR-30a-3p, miR-140-3p, miR-186-5p, and miR-195-5p expression levels on Wilcoxon signed-rank test analyses. We conclude that plasma and serum are equally suitable for investigating potential miRNA SSNHL disease markers.Medicine, Faculty ofOther UBCOphthalmology and Visual Sciences, Department ofSurgery, Department ofReviewedFacultyResearche

Late Quaternary controls on sediment dynamics and yield in paraglacial landscapes : a spatially and temporally nested approach

It is becoming increasingly important to understand how mountain regions will respond to accelerated glacier retreat and land use changes. Long-term records that capture the inherent variability of these systems and document past landscape responses and recovery from glaciation are essential for contextualizing contemporary changes and enabling future predictions. Sediment storage landforms are useful archives of past landscape response and are important for linking onsite erosion to sediment yield at the outlet. This thesis employs a spatially and temporally nested approach to provide a long-term record of sediment dynamics and yield while linking insights across different scales. In particular, we investigate Holocene sediment dynamics, focusing on the controls, variability, and interactions of sediment supply, storage, and yield in glacierized mountain catchments. First, we construct a contemporary bed material sediment budget for the 94 km² Fitzsimmons Creek watershed using field surveys, net-change lidar analysis, and geomorphic mapping. Active channel, floodplain, and landslide sources each contributed roughly one-third of the total sediment yield at the outlet. Historical sediment yield, quantified through field surveys and air photo analysis, varied by a factor of 17 over 76 years, driven primarily by a large landslide-flood event and gravel extraction activities. Second, we explore the inter- and intra-catchment variability in sediment dynamics for tributaries of the 875 km² Green River watershed throughout the Holocene. We approach this through geomorphic mapping, geochronology, postglacial erosion and storage estimates, and longitudinal analyses of channel and valley characteristics. We propose a conceptual model linking geology, glacial history, and postglacial history as controls on sediment dynamics, explaining the observed longitudinal patterns in postglacial mountain watersheds. Finally, we synthesize the Holocene history of the 3,765 km² Lillooet River watershed focusing on controls on sediment dynamics, sediment supply, and yield. In line with our conceptual model, we demonstrate how topographic steps result in a unique hypsometry of sediment storage and fragment the sediment cascade. Our findings reveal that specific sediment yield varies by more than five orders of magnitude across space and time within the same watershed, underscoring the importance of considering landscape organization and its’ control on sediment dynamics.Arts, Faculty ofGeography, Department ofGraduat

Electrophilic stress induction in macrophages and its application to disease models of immune hyperactivation

Inflammation, while necessary for repairing damage and preventing infection, can be pathological when it occurs at an inappropriate location or for a prolonged period; making the attenuation of inflammation an outstanding clinical need. Electrophiles are chemical species that readily accept an electron pair from nucleophiles to form a covalent bond and in the cellular context can initiate a stress state by interfering with basal function. Activating Transcription Factor 3 (ATF3) is upregulated in states of cellular stress but also has an orchestrating role in negatively regulating canonical pro-inflammatory pathways. In Chapter 1 I hypothesize that by upregulating ATF3 via exogenous electrophile treatment excessive inflammation can be attenuated. I use two electrophilic compounds to test this: 1) DMF, a cell permeable electrophile and 2) GDS, a novel compound (the adduct of reduced glutathione and DMF) – I theorize that GDS functions as a buffered electrophile that maintains a precise and stable amount of electrophile available to the cell. In Chapter 2 using cultured macrophages I demonstrate GDS’s buffered electrophile reaction dynamics, how it establishes a state of electrophilic stress resulting in ATF3 upregulation through putative succination of NRF2, its inflammation attenuatory effect, and how it differs from DMF. In Chapter 3 I use transcriptomics, epigenomics, and metabolomics to characterize the phenotype of GDS treated macrophages, interrogate the contribution of ATF3 to these altered phenotype, and comprehensively contrast its effect to that of DMF. In Chapter 4 I use GDS in vivo for the first time, establish its tolerability, and demonstrate its therapeutic efficacy in a mouse model of multiple sclerosis. Finally, in Chapter 5 I describe buffered electrophiles’ properties mathematically, propose the utility and future development of novel buffered electrophiles, and end by revisiting the hypothesis.Medicine, Faculty ofGraduat

On the integral points of elliptic curves

In this thesis, we focus on developing and implementing algorithms to find integral points on elliptic curves and generating useful data, based on Mordell's correspondence between integral points on elliptic curves and binary quartic forms, and existing algorithms to solve Thue equations arising from this algorithm. We then generate data of integral points for all elliptic curves up to some height, and summarize the average number of integral points and curves with many integral points or large integral points.Science, Faculty ofMathematics, Department ofGraduat

NC4Touch : an open-source platform for rodent behavioural training

Touchscreen-based cognitive testing has become a popular tool for assessing a wide spectrum of neuropsychological functions in both human and animal models. Specifically, rodent touchscreen paradigms were pioneered in the 1990s and have undergone significant refinement, with modern commercial systems—such as the Bussey-Saksida system—offering advanced features and greater standardization. Commercially available rodent touchscreen chambers have become very popular tools, benefiting from consistent hardware, software, and training protocols. These systems offer many advantages, including automated data collection, high throughput, strong translatability, and improved standardization across studies—contributing to more replicable and reliable outcomes. However, their high cost presents a significant financial barrier to widespread adoption. Recent open-source initiatives address these limitations by leveraging affordable components (e.g., Raspberry Pi, Arduino) and publicly shared designs and software. Projects such as the ArduiPod Box, the Raspberry Pi touchscreen operant chamber, and Visiomode illustrate different approaches to creating cost-efficient, customizable systems. Despite offering substantial financial and design flexibility, these setups often face their own challenges, including limited user interfaces, data handling constraints, and incomplete hardware documentation. Consequently, there remains a need for an open-source solution that combines user-friendliness, robustness, scalability, and aesthetic appeal while maintaining affordability. Therefore, we developed a customizable, cost-efficient (approximately $500) cognitive touchscreen chamber called NC4Touch for mouse and rat behavioral experiments. It features capacitive touchscreens alongside a feeding port, allowing straightforward training for tasks such as visual pairwise discrimination. Moreover, the user-friendly graphical interface provides real-time control and customization of tasks, supports video recording, and includes robust data management features. We validated the chamber’s operational efficiency and refined training protocols for pairwise visual discrimination tasks in multiple cohorts of rodents. Constructed using readily available microcontrollers, hobbyist-grade hardware, and a custom-built housing, this open-source apparatus offers an accessible solution comparable in performance to commercial systems. Its semi-modular design allows users to modify both hardware and software for various tasks, ranging from basic stimulus-response assays to complex visual discrimination paradigms.Applied Science, Faculty ofBiomedical Engineering, School ofGraduat

Multi-scale multi-physics compositional study of energy materials

This thesis presents the development of advanced computational frameworks tailored for rational materials design, with a particular focus on high-entropy alloys (HEAs) and nano-crystalline materials for energy applications. The research is divided into three main components, each addressing critical aspects of material behavior for energy-related applications. The first component introduces a temporal multi-scale multi-physics framework for simulating the long-term diffusion of radiation-induced defects in nano-crystalline materials. By integrating molecular dynamics (MD) simulations with electronic effects and atomistic diffusion models, this framework elucidates the self-healing mechanisms of nano-crystalline materials under radiation, revealing how grain boundaries effectively absorb interstitial atoms and migrate vacancies, thereby reducing defect populations over time. The second component focuses on the inclusion of electronic effects in atomistic simulations of HEAs exposed to radiation. A spatial multi-scale framework, featuring modifications to the ℓ2T-MD method, is developed to accurately model the impact of electronic properties on defect formation. The third component tackles the exploration of HEA configurational space for catalytic applications. A machine learning framework, aiming to correct the estimations of the alchemical perturbation density functional theory (APDFT), is developed to predict binding energies on HEA surfaces with high accuracy and minimal computational cost. This approach enables efficient high-throughput screening of HEAs for catalytic processes, such as carbon dioxide reduction, thereby facilitating the discovery of optimal catalytic materials. Collectively, this thesis contributes to advancement of the field of computational materials science by introducing novel methodologies that enhance predictive capabilities for HEAs and nano-crystalline materials. These contributions are pivotal in optimizing material properties for radiation resistance and catalytic performance, offering significant potential for advancing sustainable energy technologies and addressing pressing environmental challenges.Applied Science, Faculty ofMechanical Engineering, Department ofGraduat