VictorJuiz/thesis huggingface dataset:
Molecular Evolutionary Investigations of Natural and Disease-associated Variants in the Helix 3-5 Motif in Rhodopsin

In vitro experimental assays of function combined with computational codon models of molecular evolution, intramolecular coevolutionary analyses and protein modelling were implemented to investigate how natural variation focused around the helix 3-5 motif in rhodopsin might be linked to evolutionary adaptations in novel aspects of rhodopsin structure and function. Natural fish variants, some at rhodopsin sites not typically deemed as functionally important, were found to alter kinetics suggesting a potential underlying molecular mechanism for human visual disease Retinitis Pigmentosa (RP) associated mutations at site 164 near this motif. This study further identifies natural variation at other nearby sites of uncharacterized functional importance found to be under positive selection and/or inferred to be coevolving with a functionally important site/network. This appears to form a novel extended structural and functional domain via newly discovered epistatic interactions. This thesis illustrates the significance of such a multifaceted approach to understanding protein structure and function.

Advisor: Chang, Belinda S.W.
Low-profile Radial Leaky-wave Apertures for Satellite Applications

Reliable and robust communication with fast-moving satellites in the low-earth orbit requires high gain antennas that are able to electronically steer and direct power to moving targets. In this work, a low-profile leaky-wave solution is proposed that combines the full-space beam-scanning capabilities of transmitarrays and the low-complexity feeding properties of radial leaky-wave antennas that can be used for ground base-station applications. A 2564-element low-profile array (of height 0.5 wavelengths at 19.5 GHz) with a true-time delay phase-shifting mechanism has been designed and simulated which generates a sharp pencil beam of gain, 25 dBi, and is steerable to any arbitrary angle. In addition to the reduction in profile and weight, the demonstration shows minimal beam-squint effects with a 1dB gain bandwidth of 2% and a 3 dB gain bandwidth of 3-5% operating at the K-band, a characteristic not easily attained in large reconfigurable apertures.

Keywords: Leaky-Wave Antenna
Low-Complexity
Low-Profile
Radial Antenna
Reconfigurable Antenna
True-Time Delay
Advisor: Hum, Sean V
Integrating Mass Spectrometry and Computational Chemistry for the Identification of Persistent and Bioaccumulative Organic Compounds

The environmental fate and behavior of many persistent, bioaccumulative, and toxic (PB) compounds are unknown, requiring better analytical tools for detection in the environment. Nontargeted screening (NTS) enables measurement of numerous compounds while mass spectral prediction may be useful when reference standards and spectra are unavailable. A combined suspect screening and NTS method using high-resolution mass spectrometry was developed and used to screen electronics waste dust for suspected PB compounds. Two different computational mass spectral prediction methods were tested with 35 PB compounds. The screening identified 67 compounds or formulae, suggesting utility as an exploratory tool for identifying unknown PB compounds. One computational method produced good matches to two recently identified compounds, suggesting benefit for identifying unknown compounds. The results of this thesis suggest that suspect screening, NTS, and mass spectral prediction may be effective tools for detection and identification of PB compounds in the environment.

Keywords: Computational chemistry
Environmental chemistry
Mass spectrometry
Organic pollutants
Advisor: Simpson, Myrna J
Jobst, Karl J
Detection to Prevention: Portable Diagnostics and On-demand Therapeutic Manufacturing

Access to healthcare remains challenging globally. The 2015-2016 Zika and 2014-2016 Ebola outbreaks have highlighted the need for rapid point of care diagnostic tests. Meanwhile, according to the World Health Organization, 1.5 million children die from vaccine preventable diseases each year. A majority of these children live in rural areas, and centralized manufacturing of vaccines makes the distribution in remote areas challenging, leaving communities with unmet needs. To address these issues, cell-free systems offer an alternative that can be freeze-dried and rehydrated at the point-of-care for diagnostic or therapeutic applications. Although the activity of cell-free systems has been successfully demonstrated in laboratory settings, their application in real world scenarios requires companion devices. This work reports the development of: 1) a portable diagnostic device that can be used to quantify laboratory-based assays in the field and 2) a molecular platform to enable automated, cell-free protein manufacturing.

Keywords: Cell-Free
Diagnostics
Linear DNA
Synthetic Biology
Therapeutics Manufacturing
Zika Virus
Advisor: Pardee, Keith I
Purinergic Signaling Promotes Heptose-phosphate Import To Stimulate A TIFA-dependent Inflammatory Response

Recently heptose-phosphates (HPs) were identified as microbe-associated molecular patterns detected by the newly discovered ALPK1-TIFA cytosolic innate immune surveillance system. While their detection was implicated in several invasive gram-negative infections, it remains unclear whether extracellularly liberated neisserial HPs (eHPs) are detected during infection. In my thesis I address a curious synergistic relationship between eHPs and the danger signal extracellular ATP. My data suggest that ATP drives cytosolic HP detection by promoting eHP import. Moreover, this is redundantly mediated by different subsets of purinergic P2 receptors, and can be driven by various P2 agonists. My findings, however, do not strongly support our initial hypothesis that P2-activated Pannexin channel may act as a transporter for HP import. Furthermore, I have shown that ATP-driven HP import strictly requires endocytosis, implying the existence of a different intracellular transporter. Importantly, this synergy may drive gonococcal eHP detection as a result of inflammation-associated local ATP release.

Advisor: Gray-Owen, Scott
Improving the Accessibility of Health Services through Portable Diagnostics and Therapeutics Manufacturing

Access to health care can be limited outside of urban areas where centralized facilities are not found. My two thesis projects aim to improve the accessibility of health services through the development of molecular and hardware tools that provide portable and low-cost diagnostics and on-demand protein-therapeutic manufacturing. My first project involves the design, development and assembly of a camera-based plate reader, which was motivated by the need for hardware in our Zika virus diagnostics project in Latin America. This device, called ‘PLUM’, has developed, over time, into a low-cost, self-contained apparatus that serves as both a microplate reader and gel documentation system. My second project contributes to a bench-top device for the automated, portable production of protein-based therapeutics. My work has established the molecular infrastructure for the project and generated ten antivenoms against snake and scorpion venoms, including the in vitro validation of selected antivenoms.

Keywords: Antivenom
Disease Diagnostics
Synthetic Biology
Therapeutics Manufacturing
Zika Virus
Advisor: Pardee, Keith I
Fabrication and Characterization of Bio-based Polyurethane Foams Reinforced with Natural Fibers

With the world evolving towards the use of polymers, there has been an increasing demand to develop high performance, eco-friendly polyurethane (PU) foams for sustainable manufacturing. Herein, three novel studies were carried out to fabricate bio-based PU with natural fillers. The goal of these studies was to enhance the mechanical properties of foam while maintaining high quality and scalability. Initially, natural fillers including chitin, chitosan, lignin, polysaccharide, and hazelnut were embedded into free-rise PU foam to improve the mechanical properties. Consequently, this study helped identify the ideal formulation techniques to fabricate molded foam plaques embedded with hazelnut, chitin, cellulose, and eggshell. These composites were tested against the pure formulation to measure improvements in properties. They were characterized using mechanical, thermal, and morphological analyses to measure the scale-up potential of natural fiber-based PUs. In the last study, alternative reagents and formulation adjustments were made to see how they impact foam properties.

Keywords: Eco-friendly
Materials Science
Mechanical Properties
Polyurethane foam
Sustainable
Thermosets
Advisor: Naguib, Hani
Analysis of Alternative Ventilation Strategies for Multi-family Buildings Using CONTAM Simulation Software

Many high-rise multi-family buildings use a pressurized corridor ventilation system, which often has poor performance. This study examined three ventilation strategies including: a pressurized corridor ventilation system, a direct-to-suite ducting system, and a suite-based Heat Recovery Ventilator (HRV) system. A building model was constructed in a multizone ventilation analysis software using an archetype building. Airflow simulations were performed under summer and winter conditions. The resulting outdoor airflow delivery rates to the suites and corridor pressure differentials were compared for each strategy. The results show that the suite-based HRV strategy is able to provide adequate ventilation airflow to individual suites in both seasons. In the pressurized corridor system and the direct-to-suite ducting system, the airflow delivered to suites at the top of the building is higher than that delivered to suites at the bottom of the building. This uneven airflow distribution is more pronounced in winter due to stack effect.

Keywords: Centralized Systems
Decentralized Systems
HVAC
Indoor Air Quality
Outdoor Air
Suites
Advisor: Touchie, Marianne
Investigating the Phosphorylation of C-Terminus of HSC70-Interacting Protein (CHIP) in Modulating PINK1/Parkin Mediated Mitochondrial Quality Control

Mitochondrial dysfunction has been implicated in both sporadic and familial forms of Parkinson’s Disease (PD). Mutations in PINK1 and Parkin lead to early-onset autosomal recessive PD; these two proteins are known to be involved in maintaining mitochondrial quality control however it is unknown how their function is regulated. BAG5 is a co-chaperone protein known to impair Parkin’s E3 ubiquitin ligase function and its translocation to mitochondria and enhance neurodegeneration in models of PD. In a BAG5 interactome, the phosphorylation of the co-chaperone CHIP at serine 19 (S19) was upregulated upon mitochondrial dysfunction. We show that phosphorylation of CHIP is enhanced in the mitochondrial fraction only upon mitochondrial depolarization, and phosphorylation of CHIP modulates Parkin recruitment to mitochondria which may impact downstream mitochondrial clearance. p25 a known activator of kinases CDK5 and GSK-3β was identified to enhance CHIP phosphorylation. Understanding how mitochondrial quality control is modulated is essential to understanding PD.

Keywords: Co-chaperone
Mitophagy
Neurodegeneration
Parkin
Parkinson's Disease
PINK1
Advisor: Kalia, Suneil K
Development of Fungal-selective Molecules and Strategies to Target Hsp90

Invasive fungal infections have notoriously high mortality rates. A promising therapeutic strategy is to selectively target regulators of fungal stress responses, such as the essential molecular chaperone Hsp90, which enables virulence traits and antifungal drug resistance. The utility of current Hsp90 inhibitors as antifungals is limited by toxicity due to host chaperone inhibition. To address this challenge, my research aims to achieve fungal selectivity in targeting Hsp90 or its regulatory circuitry. I performed structure activity relationship analysis with >100 analogs of an Hsp90 inhibitor scaffold, which identified the first fully synthetic fungal-selective Hsp90 inhibitors. I also utilized chemogenomics to define the Hsp90 network in an important fungal pathogen, Cryptococcus neoformans, for which the circuitry through which Hsp90 regulates drug resistance and virulence remains enigmatic. I identified deletion mutants hypersensitive to Hsp90 inhibition, implicating genes that alter virulence traits, including fungal-specific components, providing an expanded set of targets for therapeutic intervention.

Advisor: Cowen, Leah E
Liposome Formation from Acoustically Cavitated Microbubbles for Local Molecular Capture

Microbubble cavitation in tumour vasculature has been investigated as a means to release biomarkers into the bloodstream for personalized therapy. However, even using this method, certain tumour subtypes result in biomarker release too low for detection. To overcome this limitation, this thesis proposes to use phospholipids from microbubbles after cavitation as a means to capture biomarkers, here, fluorescent molecules (i.e. Dsred2 protein and fluorescein) present in the local environment, for later isolation. For this evaluation, new microbubbles, composed of 3-14 mg/mL of DPPA/DPPC, were designed and synthesized. The concentration of liposomes formed was found to increase with phospholipid concentration and acoustic pressure (from 1.97x106 to 4.78x107 /mL). Microscopy showed colocalization of particles, DsRed2, and fluorescein, indicating molecular capture. This capture suggests a new means for isolating biomarkers in the bloodstream for future applications in personalized cancer treatment.

Keywords: focused ultrasound
liquid biopsy
microbubbles
Advisor: Matsuura, Naomi
Nickel-catalyzed Cross-coupling Reactions of N-Hydroxyphthalimide Esters

Nickel catalysis has emerged as a powerful alternative to traditional cross-coupling methods, opening new avenues to carbon–carbon bond formation. Derived from readily available carboxylic acids, redox-active N-hydroxyphthalimide (NHPI) esters can be used as cross-coupling partners in Ni-catalyzed reactions to form a broad range of C(sp3)–C(sp2) and C(sp3)–C(sp3) bonds. This thesis focusses on two novel applications of Ni-catalyzed NHPI ester chemistry: β-alkylation of cyclopropanol-derived homoenolates and α-arylation of esters. The key reaction optimization details, preliminary kinetic studies, and substrate scope of the β-alkylation reaction will be presented, and investigations toward the development of an enantioselective variant of the α-arylation reaction will be discussed, focusing on factors that affect selectivity and synthesis of starting materials toward this goal.

Advisor: Rousseaux, Sophie A.L.
Calcineurin as a Potential Target of TRPM7 Signaling in Migration and Invasion of Glioblastoma Cells

Transient receptor potential melastatin 7 (TRPM7) is a divalent cation channel that plays critical roles in various cancers including glioblastoma (GBM), the most malignant brain tumor in adults. As modulation of TRPM7 activity affects GBM cell behaviors, better understanding of this pathway could reveal novel therapeutic targets. Calcineurin, a Ca2+-dependent phosphatase, is also crucial for GBM cell survival and migration. Although it may potentially interact with TRPM7, this possibility has not been explored. To address whether calcineurin contributes to TRPM7 signaling in GBM cells, I showed an interaction between TRPM7 and calcineurin proteins, which may be direct or within a protein complex. TRPM7 is suggested to function upstream instead of downstream from calcineurin, which implicates calcineurin as a potential mediator of TRPM7 signaling. In summary, calcineurin interacts with TRPM7 and is suggested to mediate the TRPM7 signaling pathway as a downstream target in glioblastoma cell migration and invasion.

Keywords: calcineurin
cyclosporine A
glioblastoma
TRPM7
Advisor: Sun, Hong-Shuo
Investigation of Proteasome Architecture, Activity, and Interactors in Arabidopsis thaliana under Abiotic Stresses

The 26S proteasome plays a critical role in protein homeostasis via turnover of cellular proteins. Changes in subunit expression, assembly/disassembly of the holoenzyme, and association of non-canonical activators or inhibitors can fine-tune proteasome activity, although such pathways have not been explored in plants. This thesis examines the influence of abiotic stresses on structure, function, and interactors of the Arabidopsis thaliana proteasome. I found that oxidation and salinity decreased the cellular ratio of 26S to 20S proteasomes, altered proteasome subunit composition, and reduced binding of proteasome-associated proteins (PAPs) such as heat-shock and assembly chaperones. Additionally, oxidative stress specifically activated the 20S proteasome; a process which might be promoted by ATP deficiency. Further characterization of PAPs revealed that PBAC1, a 20S assembly chaperone, dampens oxidative damage to the germinating seed. Overall, findings suggest that regulation of proteasome activity, either through PAPs or ATP availability, is necessary for appropriate stress responses in Arabidopsis.

Keywords: Abiotic stress
Arabidopsis
Proteasome
Proteasome-associated proteins
Advisor: Zhao, Rongmin
Gazzarrini, Sonia
Free Sugars in the Canadian Food Supply: Changes from 2013 to 2017 and Modelling the Impact of Sugars Reformulation on the Nutritional Composition of Prepackaged Foods and Beverages

This thesis assessed changes in free sugars contents of Canadian prepackaged foods and beverages between 2013 and 2017 and compared two sugars-focused reformulation strategies on the nutritional composition of Canadian foods. Overall, there have been no changes in free sugars contents since 2013 (median change 0 g per 100 g/mL, p=0.4922); although decreases were observed in 3 of 17 major food categories, the largest for beverages (-2.7 g; -10.8 calories/100 mL, p

Keywords: Canada
food supply
nutritional composition
prepackaged foods
reformulation
sugars
Advisor: L'Abbe, Mary R
Oncogenic Fusion Transcripts in Pediatric Papillary Thyroid Carcinomas

Papillary thyroid carcinoma (PTC) is the most common malignancy amongst adolescent and young adult women. Clinical and genomic features of PTC in children differ from those in adults. A substantial proportion (~50%) of pediatric PTC (PPTC) lack any of the common driver mutations typical of adult PTC. Thus, molecular diagnostics developed for adults may not be valid in children. We applied recently developed bioinformatic pipelines to RNASeq analysis of a large, prospectively established repository of PPTC. This study set out to identify known and novel fusion oncogenes as candidate drivers of tumorigenesis. Analysis of 38 samples resulted in identification of 16 previously reported oncogenic fusions and three novel candidate fusions. In conducting these analyses, we have reduced the proportion of cancers with unknown drivers from approximately 50% to 6%. Moreover, gene expression analysis identified three distinct categories of tumours. These studies represent the first unbiased genomic approach to childhood PTC.

Advisor: Wasserman, Jonathan
Vascular Disruption Therapy in Lung Cancer using Endobronchial Ultrasound and Ultrasound Active Agents

Tumour vascular disruption therapy (VDT) hampers tumour growth by inhibiting its supply of oxygen and nutrients. One strategy in VDT is to use ultrasound and ultrasound active agents (UAAs) (i.e. microbubbles and nanodroplets) to locally damage tumour vessels. Despite pre-clinical successes, lung cancer VDT by ultrasound and UAAs remains challenging as conventional ultrasound cannot penetrate the lung. Diagnostic endobronchial ultrasound (EBUS) enables ultrasound access into the lung and have the potential to be combined with UAAs to implement lung cancer VDT. Here, UAAs were characterized for stability and acoustic response in vitro and employed in vivo with EBUS to examine their potential in VDT in a mouse tumour model. The in vivo pilot study revealed that while applying EBUS and microbubbles showed little tumour vascular disruption effect, a substantial effect in vascular disruption was demonstrated when nanodroplets were used with EBUS (73% decrease in tumour microbubble perfusion).

Keywords: Cancer treatment
Lung cancer
Microbubbles
Nanodroplets
Tumor vascular disruption
ultrasound
Advisor: Matsuura, Naomi
Neuroqueer Phenomenology: Interrogating the Nature of Autistic Social Exclusion

This thesis conducts virtual archival research by analyzing the blogs of seven autistic advocates/activists. It conducts a queer phenomenology of the narratives of autistic women and non-binary people which reveals that autistic advocates/activists neuroqueer mainstream understandings of autism as deficit-based. Instead the blogs are filled with reparative narratives that question dominant understandings of autistic emotions, behaviours, and communications. In line with the social model of disability, this thesis argues that the blogs examined challenge the mainstream notions of the source of autistic individuals’ socio-spatial exclusion – that it is not in the autistic people’s lack of orientation towards others but rather in an ableist society that is uncomfortable with difference. These results contribute to the field of Critical Autism Studies which has yet to interrogate the intimate relationships of autistic women and nonbinary people.

Keywords: Autism Spectrum Disorder (ASD)
feminist
geography of health
neuroqueer
queer phenomenology
social disability model
Advisor: Wakefield, Sarah
Characterization of VPS33B and VPS16B in α-Granule Biogenesis in Megakaryocytes

Platelets contain storage vesicles known as α-granules, made by their precursor megakaryocytes. Loss of α-granule biogenesis causes arthrogryposis, renal dysfunction and cholestasis syndrome when VPS33B, encoding vacuolar protein sorting-associated protein 33B (VPS33B), or VIPAS39, encoding VPS33B-interacting protein apical-basolateral polarity regulator spe-39 (VPS16B), undergo loss-of-function mutations. VPS33B and VPS16B form a complex, which I hypothesize interacts with other proteins to facilitate α-granule cargo sorting and synthesis. Using a VPS33B antibody, I localized this protein within primary human megakaryocytes via confocal immunofluorescence microscopy. This represents the first time that endogenous VPS33B has been localized in megakaryocytes, removing the potential for experimental artefacts present in previous fusion-tagged imaging attempts. I have also investigated the interactome of VPS33B using a combination of affinity purification mass spectrometry analysis and co-immunoprecipitation experiments. These experiments identified several novel VPS33B interactors, including proteins involved in early and late endosomal trafficking pathways, and in the regulation of cytoskeletal networks.

Keywords: alpha-granule
ARC syndrome
megakaryocyte
neonatal cholestasis
VIPAR
VPS33B
Advisor: Kahr, Walter H.A.