VictorJuiz/thesis huggingface dataset:
Tonian Macroalgae from the Mackenzie Mountain Supergroup in the Wernecke Mountains, Yukon Territory
Keywords: Mackenzie Mountain Supegroup
Macroalgae
taphonomy
Tonian

Early eukaryotic fossils are crucial to understanding the evolution of the Earth's biosphere and geosphere. Molecular clock estimates suggest that crown-group members of key algal lineages evolved and diversified by the Tonian Period (1000 to 720 Ma), but this diversification is poorly reflected in the fossil record. Previously undocumented, centimeter-scale macrofossils were recovered from the outer shelf marine facies of the ca. 950 Ma Dolores Creek Formation, Wernecke Mountains (northwestern Canada, Chapter 2). Three distinct size classes were identified. The larger fossils are interpreted as eukaryotic macroalgae with a likely green algal affinity, making them among the oldest macroalgae yet recognized and filling a critical gap in algal evolution. Analytical microscopy, including scanning electron microscopy and tomographic x-ray microscopy, were used to investigate fossil preservation and develop a taphonomic model (Chapter 3). The fossil preservation consists of pyritization and aluminosilicification, similar to accessory mineralization observed in the Paleozoic Burgess Shale-type preservation. The macroalgae are defined as a new genus and species based on their morphology including an unbranching, uniseriate thallus with uniform width and elliptical to globose holdfasts (Chapter 4). Larger specimens are classified as probable vendotaenids while smaller mm-scale specimens display branching but remain undefined as a form taxon as theylack distinguishing morphological characteristics. The unstable redox conditions that defined the macroalgae's paleoenvironment in the Wernecke Mountains were constrained using geochemical analyses (Fe speciation, major/trace elements, and TOC, Chapter 5). Considering the macroalgae within a paleoenvironmental context allows us to place realistic constraints on these organism's paleoecology and paleobiology. The Dolores Creek macroalgae along with the recently reported ca. 1000 Ma multicellular chlorophyte from North China and ca. 1000 Ma photosynthetic, eukaryotic algae from the Congo Basin, provide evidence that benthic green algae colonized shallow marine habitats by the early Tonian Period. These discoveries indicate that there are glaring omissions in the fossil record that need to be addressed in future studies by recovering new fossils and characterizing their habitats to aid in reconstructing the late Proterozoic biosphere.
The Economic Evaluation of Adult Immunization Programs: The Importance of Local Context and the Example of Pneumococcal Vaccination
Keywords: Economic Evaluation
Health Technology Assessment
Pneumococcal Disease
Public Health
Vaccination

Infectious diseases represent a unique challenge in healthcare policy decision-making, as the risk of disease is subject to change based on factors specific to the local context, which can evolve over time. Given this dynamic nature, it is critical to tailor economic evaluations of interventions targeting these diseases to the jurisdiction and timeframe in which they will be applied. The research comprising this thesis sought to address these challenges through a systematic review, population-based studies of health administrative data, and an economic evaluation. This was implemented through the example of evaluating a potential pneumococcal vaccination program, with a specific focus on publicly funding the 13-valent pneumococcal conjugate vaccine (PCV13) for older adults (65+). Streptococcus pneumoniae is a gram-positive bacterium that represents one of the most common causes of community-acquired pneumonia (CAP), imposing a significant health and financial burden across the world. Due to the decline in vaccine-type pneumococcal disease among older adults since PCV13's inclusion in the Ontario infant immunization program, the cost-effectiveness of publicly funding PCV13 for immunocompetent older adults remains unclear. The first study was a systematic review examining the impact of pneumococcal disease on health state utility values, focusing specifically on the syndromes of acute otitis media, CAP, bacteremia and meningitis. The second study was a population-based retrospective matched cohort study assessing the incidence of disease and healthcare costs attributable to CAP from the Ontario healthcare payer perspective using health administrative data. Exposed subjects were found to have substantially higher healthcare costs than comparable unexposed subjects for up to one year post index date. The third study applied the data developed in the first two studies to conduct an economic evaluation of adding PCV13 to the current immunization program in Ontario. The cost-utility analysis employed a microsimulation health state transition model, with the results indicating that adding PCV13 is unlikely to be cost-effective due to the substantial decline in disease caused by vaccine serotypes. Overall, this thesis demonstrates an approach to assessing the cost-effectiveness of vaccination programs, highlighting the influence of local factors such as serotype distribution on cost-effectiveness.
The Ion Channel TRPV5 Regulates B Cell Signalling and Activation
Keywords: B cells
Calcium
Ion channels
TRP channels

B cell activation leads to the production of antibodies that protect us from infection. Recognition of antigen by B cells begins with the B cell receptor (BCR) recognizing and binding antigen, which initiates BCR signalling and antigen internalization. Calcium is an important secondary messenger during B cell activation and calcium signalling in B cells is best characterized by the store operated calcium entry (SOCE) pathway that triggers ion channels on the plasma membrane, predominantly known to be calcium release-activated calcium (CRAC) channels. Patients that have mutations in the proteins of this pathway present with severe immunodeficiency; however, murine B cells deficient in CRAC channel components mount normal antibody responses, suggesting that alternative channels may be important. We identified a member of the calcium permeable transient receptor potential (TRP) ion channel family, TRPV5, as a candidate channel expressed in B cells by a qPCR screen. We found TRPV5 polarized to BCR clusters upon stimulation in a RhoA dependent manner and siRNA knockdown of TRPV5 in a murine B cell line impaired calcium flux upon BCR stimulation. To further investigate the role of TRPV5 in B cell responses, we generated a murine TRPV5 knockout (KO) by CRISPR-Cas9. TRPV5 KO mice had normal B cell development and mature B cell numbers. TRPV5 KO B cells had impaired spreading and contraction in response to membrane-bound antigen. Surprisingly, calcium influx upon BCR stimulation in primary TRPV5 KO B cells was not impacted; however, differential expression of other calcium-regulating proteins, such as ORAI1, which we found was expressed 5-fold higher in TRPV5 KO B cells than WT B cells, may contribute to a compensatory mechanism. Despite no difference in calcium signalling, BCR signalling measured by phospho-tyrosine residues was reduced in TRPV5 KO B cells. Consistent with this, immunization induced T-dependent (TD) antigen-specific antibody titers were reduced in TRPV5 KO mice compared to WT mice. Thus, our findings identify a role for TRPV5 in BCR signalling and B cell activation.
Engineering the Fractal Properties of Podocytes
Keywords: Biomaterials
Fractals
Kidney Podocytes
Organ-on-a-chip Engineering
Shape Cues
Tissue Engineering

Nature efficiently self-organizes cells and tissues into complex fractal forms, where fractal structures have cascading features that are statistically similar to the whole. While fractality of a tissue’s structure has been associated with healthy or pathological state, an understanding of whether fractal patterning of the native milieu contributes functionally to tissue maturation, and how cells interpret such shape cues, is not well understood. This thesis uses kidney podocytes as a model system to study the role of fractal patterning of shape cues in tissue development and function in vitro. Podocytes are a major component of the glomerular filtration barrier and exhibit a complex, sieve-like, branching cell architecture. Disruption of podocyte architecture is involved in many kidney diseases, yet is poorly understood. New lab-based approaches are thus needed to accelerate kidney research. However, podocytes are difficult to cultivate in vitro. Here, out-of-plane microscale curved shape cues, biomimetic of glomerular capillaries, were developed as a 2½-D topographic organ-on-a-chip surface and augmented with low and high extents of fractality, to study the role of microenvironment shape in podocyte development in vitro. It was discovered that the micron-scale curvature of polydimethyl siloxane scaffolds exhibited differential surface charge density compared to flat regions, which was correlated with extracellular matrix organization that led to assembly of cell structures and hierarchical cell branching in vitro, delineated using a novel fluorescent “Mosaic” assaying technique. Fractally stimulated cells reflected biological complexity more completely than flat cultures in applications of drug testing, coronavirus infection, and a cells-as-sensors approach to patient serum diagnostics, supporting overall podocyte maturation. RNA-sequencing confirmed maturation and further identified a signature of genes and pathways enhanced uniquely by shape stimulation. This thesis contributed to the understanding of the unique role of fractally-patterned shape cues in supporting podocyte maturation in vitro, and harnessed this knowledge to develop advanced laboratory tissue modeling tools. This work thereby addressed some challenges of cultivating podocytes in vitro, and sets a precedent for how fractal frameworks may support higher-fidelity bioengineering that may extend to other tissue engineering and regenerative medicine applications broadly.
Exploring Novel Drug Targets and Combination Therapies to Extend the Life of Current Antifungal Agents
Keywords: Antifungal
Candida
Drug Discovery
Drug Resistance
Fungi
Molecular Genetics

Fungal infections are a relatively unacknowledged contributor to human disease, despite global mortality rates being on par with well-known diseases such as malaria or tuberculosis. This growing threat has been met with the prophylactic overuse of a limited arsenal of antifungals, leading to the rapid emergence of multidrug-resistant pathogenic fungi. The rate at which resistance continues to emerge is greatly outpacing the rate of antifungal discovery, highlighting the urgent need for novel therapeutic strategies. My research aims to define the genetic circuitry underpinning antifungal drug resistance and to devise therapeutic strategies to abrogate resistance in human fungal pathogens. To identify new genes involved in tolerance and resistance to the azole antifungals, we screened a homozygous deletion library, covering ~11% of the Candida albicans genome, in the presence of fluconazole. We identified 13 genes for which deletion enhanced susceptibility to the azoles, two of which were also important for azole resistance acquired by diverse mechanisms. Mechanistic studies of the retromer component, Pep8, and RHO-GTPase activating protein, Rgd1, highlighted the central role of stress response signaling and genome plasticity in antifungal resistance. Taking a multi-pronged, chemical biology approach, we aimed to identify novel chemical scaffolds with antifungal activity against diverse fungal pathogens. By profiling a targeted set of synthesized macrocyclic peptides, we identified several molecules that enhanced fluconazole activity against diverse Candida species, including the drug-resistant pathogens Candida glabrata and Candida auris. We also leveraged the RIKEN NPDepo collection to perform multiple high-throughput screens against four prominent human fungal pathogens, both in the absence and presence of fluconazole. From this, we identified a broad-spectrum inhibitor, NPD6433, that targets fatty acid synthase, and an azole-potentiating compound, NPD827, that disrupts membrane homeostasis through interactions with sterols. Further, we demonstrated that both molecules circumvent biofilm formation in a rat catheter model of candidiasis that mimics central venous catheters in patients. Collectively, this research unlocks new opportunities for antifungal drug development and provides insight into adaptive mechanisms governing antifungal drug resistance.
Healthy Ageing in a Foreign Land? Examining Health Care Inequities Faced by Older Racialized Immigrants in the Canadian Community Health Survey (2015-2018)
Keywords: Health Care Access
Immigrant
Minority Ageing
Racial Minority
Social Determinants of Health Inequality
Social Epidemiology

Background: Canada's demographic landscape has transformed to be more multicultural and multi-ethnic, resulting from an increasing inflow of racialized immigrant populations from the Global South, made possible by the abolition of racially discriminatory immigration policy in the 1970s. Although there is a significant body of Canadian research examining immigrants’ access to care, contemporary immigration scholarship has typically examined immigrants as a monolithic population while the intersecting lens of “race” and “immigration” has been largely overlooked. The invisibility of racialization in immigrant research has been criticized for its European-centric worldview. Therefore, this three-paper dissertation aims to make racialized immigrants’ ageing experiences visible through a racial-nativity lens in health equity and health care equity. Methods: A combined dataset was generated to pool over four annual circles (2015-2018) from the Canadian Community Health Survey (CCHS). Statistical methods including Chi-square tests, binary logistic regression, multinomial logistic regression and classification and regression tree analysis (CART) were used. Results: Racialized immigrant older adults systematically bear an excess burden of compromised conditions in physical and mental health consequences, including undiagnosed depressive symptoms (Chapter 2, C#2), unrecognized depressive symptoms (Chapter 2, C#2), poor-fair self-rated mental health (C#3), perceived stressful life (C#3), co-morbidity of mood and anxiety disorders (C#3), poor-fair self-rated health (C#4), and multiple chronic conditions (C#4), compared to the dominant Canadian-born White populations. Moreover, racialized immigrant older adults experienced inequities in access to various types of care across different settings, including depression diagnosis (C#2), mental health consultations from family doctors, psychologists, and social workers (C#3), unmet healthcare needs due to affordability and acceptability barriers (C#4), and unmet needs for treatment of chronic physical conditions (C#4), compared to the dominant Canadian-born White populations. Conclusion: These systematic differences in health conditions and differential patterns of accessing necessary health care services, by race-nativity status, are judged to be unfair in a way that undermine Canada's mandate of universal health coverage. These health and health care inequities are also remediable which warrant interventions to address problems with provisions of health care resources to racialized immigrants at interpersonal, organizational, and policy levels.
An Evaluation of Primary Biliary Cholangitis as a Lifelong Disease: Insights from Canadian Cohort Studies
Keywords: Liver Disease
National Study
Observational Study
Primary Biliary Cholangitis
Registry

Primary Biliary Cholangitis (PBC) is a rare chronic autoimmune liver disease that results in morbidity, mortality, and quality of life impairment. This thesis includes four projects designed to inform our understanding of the progression of a patient’s journey with PBC and contribute new knowledge that may inform clinical decision making and advance clinical research. The first study investigated patterns of biochemical response to long-term ursodeoxycholic acid treatment. This study found that achievement of adequate biochemical response was associated with improved liver transplant-free survival regardless of prior history of inadequate response, highlighting response as an important longitudinal treatment goal. The second study aimed to evaluate the real-world effectiveness of obeticholic acid (OCA), a new second-line therapy. This study found that OCA was associated with improvements in biochemical surrogates of outcome and was well tolerated. The third study investigated associations between ethnicity and disease severity, quality of life, and survival. This study found that Indigenous Canadians presented with more advanced disease, had impaired quality of life, and worse liver transplant-free survival compared to White patients. The fourth study investigated the in-hospital burden of liver disease and compared the burden of PBC to other common liver diseases. This study found that liver disease inpatients had premature morbidity, mortality, and high resource use and that PBC inpatients represented a similar resource burden to other common liver diseases. These findings provide evidence to support clinical decision making for patients with PBC and contribute to a growing body of literature.
Diagnostic Applications of Circulating Endothelial-centric Biomarkers in Cardiovascular Diseases
Keywords: Biomarkers
Cardiotoxicity
Endothelial Cells
Endothelium
MicroRNAs
SARS-CoV-2

The endothelial lining of blood vessels is a critical determinant of cardiovascular homeostasis. Endothelial dysfunction, characterized by an imbalanced release of vasomodulatory factors, pro-inflammatory molecules, and induction of reactive oxygen species, has been recognized as a major contributor to a plethora of cardiovascular (CV) ailments. Recently, novel circulating factors, including endothelial-enriched proteins, microRNAs (miRNA), and extracellular vesicles (EVs) have been suggested as a more informative and specific means of not only diagnosing CV diseases but also predicting outcomes. However, it remains unknown whether these novel circulating markers (i) accurately reflect endothelial dysfunction, (ii) provide incremental biological insights over existing markers, and (iii) have clinical utility. To address these lingering questions, this thesis reports a combination of in vitro and clinical studies to assess (i) endothelial-centric biomarkers, (ii) circulating miRNAs, and (iii) EV characteristics. To this end, chapter one highlighted the association of endothelial-centric markers (e.g., angiopoietin-2 [Ang-2], endothelin-1, and myeloperoxidase [MPO]) with mortality during SARS-CoV-2 infection while whole plasma transcriptomics revealed pathways for endothelial-focused intervention. Subsequent in vitro testing of endothelial barrier stabilizing treatments (e.g., angiopoietin-1 mimetics and Slit2-N) abrogated COVID-19 induced endothelial permeability. Extending these concepts to the context of cancer therapy, chapter two revealed how tyrosine kinase inhibitor therapy during chronic myelogenous leukemia differentially modulated the expression profiles of endothelial-centric biomarkers (e.g., increased vascular cell adhesion molecule and Ang-2) while not affecting high-sensitivity C-reactive protein; a commonly used inflammatory marker. Finally, chapter three looked at endothelial dysfunction in the context of cancer-therapy related cardiac dysfunction (CTRCD) during breast cancer therapy. These studies revealed that underlying inflammation (i.e., heightened expression of MPO), as well as endothelial-activation (i.e., increased Ang-2) prior to cancer treatment, may be associated with CTRCD. Whole plasma and EV transcriptomics further highlighted the potential of miRNAs to act as not only biomarkers but elucidate complex disease pathways, the latter of which included cellular senescence and apoptosis. In the broader context, these studies highlight the central role of endothelial activation/dysfunction in CV diseases and emphasize the utility of multi-omics datasets in diagnosis and prognostication.
Integrating Qualitative and Geospatial Data to Understand Environmental Change in a Diverse Cambodian Landscape
Keywords: Climate Change
Environmental Change
Interviews
Land Use
Remote Sensing
Water Resources

A surge of anthropogenic activities has led to irreversible, destabilizing environmental conditions in recent years. Increased calls for stronger management and policy regulations on land use, climate change, and water resources have reached paramount levels globally, as citizens and governments reframe their role in this call to action. Research on these topics: land use, climate change, and water resources span across the world, highlighting the severity and urgency in every country and region. This research focuses on a case study in the Global South, which has undergone significant social, ecological, and economic shifts that have resulted in both positive and negative impacts on the environment and human well-being. In examining these impacts, this research examines how systematic changes in lifestyle and policy have impacted people and their environments and what reform needs to be put in place to ensure environmental sustainability for the future. In doing so, in this research project, I engage in an exploratory study that combines geospatial data (remote sensing/GIS) to analyze system level spatiotemporal changes and semi-structured interviews with residents to analyze local level individual experiences. Together the integration of these two methods helps to address the scalar challenges of environmental research and offers adequate consideration to the interconnection of people and their environment and where future work and policy needs to be focused. Results reveal the processes occurring across the landscape and highlight land transitions, temperature changes, and water resource shortages that are important for understanding broader evolving patterns, while interviews reveal uneven experiences, not just across different land types (rural mountain, rural agricultural lowlands, urban) but also within communities, drawing out issues pertaining to access, distribution, adaptive capacity, and education that all need to be improved. Within geography, planning, and environmental studies, this research offers critical insight regarding the underlying processes and experiences that drive environmental change, the impacts of those changes on humans, and where more research and attention needs to be directed when planning for the future.