VictorJuiz/thesis huggingface dataset:
Modulating the Reactivity of Electrophilic Warheads for Pharmacokinetic Efficacy

The targeted covalent inhibitor (TCI) approach in drug discovery presents many potential benefits to cancer therapy. The goal of this approach is to trigger apoptosis of rapidly dividing tumour cells by covalently binding a therapeutically relevant protein target. Ultimately the goal is to develop personalized treatments that are more effective and less toxic than general chemotherapy. JP-4-94 is a potent covalent investigational cancer therapeutic with promising in vitro and in vivo results. Herein, we describe studies undertaken to further understand the structural mechanisms through which JP-4-94 elicits a cellular response. Specifically, this dissertation will explore the role of π-stacking in conformationally protecting the warhead in JP-4-94 to further optimize its pharmacological properties. Through our findings, a class of potent, second-generation inhibitors has been identified.

Keywords: cancer
drug discovery
electrophilic warhead
JP-4-94
pentafluorobenzenesulfonamide
targeted covalent inhibitor
Advisor: Gunning, Patrick T
The Role of Selective Breeding and Microbiome Composition in Chicken Health

In the past 50 years, selectively breeding for accelerated growth has resulted in compromised immune response in commercial chickens. As well, emergence of antimicrobial resistance prompted bans on use of antibiotic growth promoters (AGPs) in chicken feed; alternative supplements that can mimic the impact of AGPs in preventing infections are needed to minimize production losses. In this study, I performed whole genome sequencing analysis of domestic chicken breeds, focusing on three lineages that underwent intensive selective breeding, to detect genetic changes that impact immune response and growth. My results identify two genes, TLR3 and PLIN3, whose genetic variants may enhance growth performance at the expense of immune function. I also characterize the impacts of AGPs on the chicken microbiome through 16S rRNA sequence surveys. Lastly, meta-analysis of the chicken cecal microbiome identifies Lactobacilli species as keystone taxa that are likely crucial for constructing microbial consortia to replace AGPs.

Advisor: Parkinson, John
Designing E1 Inhibitors: Divergent Approaches using Small Molecular Scaffolds and Peptidomimetics

Post-translational modification of proteins via the attachment of ubiquitin and/or ubiquitin-like proteins mediate cellular homeostasis, and dysregulation of this labelling machinery has been implicated in numerous diseases. The E1-activating enzymes provide attractive targets for cascade intervention via inhibitors. Precedent was set by MLN4924, a potent NAE (E1) inhibitor that advanced in clinical trials for various cancers. Herein, we describe the use of small molecule and peptidomimetic approaches to inhibit the E1 enzymes, UBA5 and SAE. SAE inhibition was achieved using novel small peptide mimetics of the SUMO C-terminus. For UBA5, we delineated the mechanism of action of a previously reported UBA5 inhibitor, 5C-Z, and further development was terminated. Since no UBA5 inhibitors existed, we started a new therapeutic project to identify peptide mimetics of UFM1. Initial results were promising, with low µM activity against UBA5 enzyme activity. Independently, a separate study identified a novel and potent covalent inhibitor of UBA5.

Keywords: peptidomimetics
post-translational modification
small molecule inhibitors
therapeutics
ubiquitin-like proteins
Advisor: Gunning, Patrick T
Nutritional programming effects of probiotic lactobacilli on bone health in CD-1 Elite mice

Recent investigations have demonstrated that probiotics beneficially improve bone structure in adult rodent models. The aim of this study was to investigate if maternal administration of the probiotic mixture Lacidofil® (Lactobacillus rhamnosus R0011 and L. helveticus R0052) since conception beneficially programs bone health of 2 month old offspring. Female CD-1 mice received either Lacidofil® or sterile water throughout pregnancy and lactation. At weaning, offspring were randomized to stay on their mother’s respective treatment of switched to the opposite diet until age 2 months. Offspring receiving probiotics since conception had higher fecal levels of the R0011 strain. Maternal administration of Lacidofil® improved trabecular bone microarchitecture at the proximal tibia in male but not female offspring and cortical bone microarchitecture at the midpoint tibia in both sexes. Therefore, probiotic interventions targeting mothers during pregnancy and lactation may beneficially program the infant microbiome and bone health into young adulthood.

Keywords: Bone
Microbiome
Nutrition
Probiotics
Programming
Advisor: Comelli, Elena M
Examining the dynamics and clinical relevance of Sox2+ cells in the Ptch1 heterozygous model of medulloblastoma

Medulloblastoma is the most common malignant pediatric brain tumour. Current therapies fail to provide those affected with quality and quantity of life, necessitating a greater understanding of the mechanisms driving growth. Previous studies in the irradiated Ptch1+/- model have postulated a growth hierarchy derived from rare, therapy-resistant, tumour-propagating cells that exhibit cardinal features of stemness. Utilizing the same model, I describe a direct role for Sox2 in conferring a stemness program in the tumour-propagating fraction. In an allograft model, I define a paradigm for combination therapy of both stem and progenitor cell-types using a transgenic ablative strategy in parallel with the Smoothened antagonist GDC-0449. I then provide evidence for proliferative heterogeneity within the Sox2+ compartment, identifying dividing and non-dividing cells as molecularly distinct cell states. These findings identify targeting Sox2+ cells as a requirement for disease cure and propose antagonizing the quiescent state may re-sensitize these cells to conventional therapies.

Keywords: cancer
medulloblastoma
quiescense
sonic hedgehog
Sox2
stem cells
Advisor: Dirks, Peter B
Characterizing the Bcl-2 Associated Athanogene 5 Interactome in the Context of Parkinson’s Disease

Aberrant alpha-synuclein aggregation is associated with the onset and progression of Parkinson’s disease (PD). This has made molecular chaperones, a class of proteins responsible for maintaining proteostasis, an enticing therapeutic target. BAG5 is a co-chaperone protein that inhibits the chaperone, Hsp70, and promotes PD-like alpha-synuclein aggregation and neurodegeneration. The mechanisms of how BAG5 impairs proteostasis and promotes apoptosis are unclear. The purpose of this project was to characterize the BAG5 interactome to guide further studies of its role in physiological and disease states. A novel interaction between BAG5 and the autophagy adaptor protein, p62, was discovered and investigated, as it pointed to a potential mechanism by which BAG5 could modify alpha-synuclein aggregation. p62 reduced and BAG5 enhanced alpha-synuclein self-association in vitro. BAG5 also promoted p62 stability, suggesting a function of the interaction on other p62-dependent proteostasis pathways.

Keywords: BAG5
Chaperones
p62
Parkinson's disease
Proteomics
Advisor: Kalia, Suneil
Optimization and Applications of Slow-Proton-Exchange (SPE) Nuclear Magnetic Resonance pH Sensors

The measurement of pH is ubiquitously important in biochemistry, clinical medicine, and industrial processes. There are still improvements to be made in this field, especially in terms of accuracy, non-invasiveness for biomedical applications and real-time monitoring. Herein, a new series of NMR sensors have been evaluated and applied that employ the Slow-Proton-Exchange (SPE) sensing mechanism. Three sensors, SPE1, SPE2, and TUC, exhibit the SPE phenomenon and thus can be used in unconventional conditions to accurately and reliably quantify pH. The second generation SPE2, optimized from the previous SPE1 with biocompatible pKa and broader operating pH window, has been used to detect real-time pH changes in a series of enzymatic hydrolysis reactions, simulating a metabolic process. All sensors SPE1, SPE2, and TUC have been utilized in DMSO to measure the strengths of organic acids and characterize activity, expanding the application scope from aqueous to organic solvents.

Advisor: Zhang, Xiao-an
CELL-SPECIFIC GENE EXPRESSION PATTERN OF α5-SUBUNIT CONTAINING γ-AMINOBUTYRIC ACID SUBTYPE A RECEPTORS IN HUMAN AND MOUSE PREFRONTAL CORTEX

Converging evidence suggests that a selective deficit in somatostatin (SST)-expressing neurons signaling contribute to major depressive disorder. Preclinical studies show enhancing signaling specifically at α5-subunit containing γ-aminobutyric acid subtype A receptors (α5-GABAARs) provide a potential means to remediate low SST cell function. Understanding the cellular localization α5-GABAARs has implications for therapeutic mechanisms. Hence fluorescence in situ hybridization was used to investigate the α5-GABAARs gene expression in pyramidal cells (PYCs) and three interneuron subgroups (i.e. vasoactive intestinal peptide (VIP)-, SST-, and parvalbumin (PV)-expressing cells) in human and mouse prefrontal cortex. Our findings show more similarities than differences between mouse and human α5-GABAARs gene expression: PYCs (~50%), PV neurons (~20%), VIP neurons (0%) and the only difference were found in SST cells (human: 8%; mouse: 0%). Collectively, the result suggests that the characterization of α5-GABAARs gene expression pattern is important to understand the potential inhibition mechanisms that may mediate through α5-GABAARs.

Advisor: Sibille, Etienne
Redox Behaviour and Stability of Manganese Porphyrins Based MRI Contrast Agents

Magnetic resonance imaging (MRI) routinely uses contrast agents (CAs) to enhance the contrast between native tissue and the target. Currently, gadolinium based CAs (GBCAs) dominate the clinical MRI applications. However, GBCAs are limited by their low contrast enhancement efficiency and growing concerns about Gd associated toxicity. To address these limitations, we develop a new family of manganese(III) porphyrin (MnPs) CAs as non-Gd alternatives with improved sensitivity and biocompatibility. In this thesis, we further evaluate the potential of our MnPs as CAs. We expand the use of our blood pool agent, MnP2, to act as an oxygen sensor for MRI (Chapter 2) and for the first time, a potential ratiometric imaging sensor for MRI (Chapter 3). Lastly, we investigate and demonstrate the remarkable high stability of MnTCP against conditions that cause metal dissociation in GBCAs.

Keywords: Contrast Agent Stability
Manganese Porphyrins
MRI Contrast Agents
Oxygen Sensor
Ratiometric MRI
Advisor: Zhang, Xiao-an
Development of a Capacitive MEMS Force Sensor for Touchscreen Applications

This thesis presents the design and development of a capacitive MEMS force sensor to overcome the limitations associated with current force sensors used in touchscreens. The sensor uses two elastic materials that provide a dual-range of force sensitivity ensuring the sensor is able to sense light touch forces and able to withstand heavy ones. The fabrication process of the sensor was developed at the Toronto Nano Fabrication Centre at the University of Toronto. The fabricated sensor was experimentally tested to measure forces ranging from 50 mN to 5 N, with a force threshold of 625 mN that defines the boundary between the high sensitive region for light touches and the moderate sensitivity region. Sensor sensitivity was found to be 3.728pF/N (19.12 %∆C/N) in the first force region with maximum nonlinearity of 0.118 pF. In the second region, the sensitivity was 0.3194 pF (3.2 %∆C/N) with maximum nonlinearity of 0.3194 pF.

Advisor: Ben Mrad, Ridha
Identification of Plant Growth-promoting Bacterial Endophytes using Culture-dependent In Vitro and Laboratory In Planta Methods

This study examined a collection of 220 bacterial endophytes isolated from herbaceous plants growing in petroleum-contaminated soils for plant growth promotion abilities. 12% of endophytes tested induced statistically significant growth benefits in Arabidopsis. The strongest plant growth promoting endophyte, Plantibacter flavus strain 251, increased A. thaliana fresh biomass and total root length by 4.7 and 5.8 times respectively over control plants and contained genes for auxin and ACC deaminase production. In vitro tests showed that 26% of endophytes from 19 different genera were potentially capable of nitrogen fixation, while 42% of endophytes from 16 different genera were capable of phosphate solubilization. Of the potential nitrogen fixers, 80% demonstrated free-living nitrogen fixation capability when grown in nitrogen-free media. None of the three endophytes tested improved Arabidopsis tolerance to drought stress. Overall, this study showed that a large variety of bacterial endophytes are capable of direct plant growth promotion.

Keywords: Arabidopsis
Bacteria
Endophyte
Nitrogen fixation
Phosphate solubilization
Plant growth promotion
Advisor: Fulthorpe, Roberta
Fast and Long: Characterizing Biofilm Growth Dynamics with Holographic Microscopy

In this thesis, we applied a 4D imaging pipeline based on digital holographic microscopy (DHM) to characterize the development of Pseudomonas aerugi-nosa biofilms. A technique that can recover 3D information from a 2D image, DHM has unique advantages for three-dimensional imaging and is particularly well suited for tracking the dynamics of microscopic biological and physical phenomena. We characterized the growth dynamics of Pseudomonas aeruginosa biofilms to reveal how individual colonies aggregated to form a dense final network. Itwas found that inhibition of a specific hydrolase production encouraged the formation of a denser biofilm structure. This finding assists in guiding directions for developing drugs that can alter specific molecular pathways responsible for biofilm formation and structure. While DHM proved to be a powerful strategy for tracking biofilm formation, it is a computationally intensive approach. Accordingly, we explored the potential of convolutional neural networks (CNN) for reducing the reconstruction and image processing time. The integration of advanced computational approaches with improved hardware strategies, along with the fact that it is a label-less imaging approach, establishes DHM has a powerful new biophysical imaging platform for studying developmental dynamics.

Keywords: 3D imaging
convolution neural network
holographic microscope
in vivo imaging
p.aeruginosa
Advisor: Yip, Christopher
High Fat Diet-mediated p38α Activation in the Liver Contributes to the Onset of Insulin Resistance and Hepatic Steatosis

The mechanisms underlying the paradox of selective hepatic insulin resistance are not well understood. Mitogen-activated protein kinases play a pivotal role in the onset of hepatic metabolic dysregulation, however current data fails to establish a definitive role for p38. We generated a liver-specific p38α knockout (p38αKO) mouse model to investigate the role of p38α in regulating hepatic glucose and lipid metabolism following 1-week of high fat diet (HFD) feeding. Short-term HFD feeding increased hepatic p38 activation in mice. Moreover, p38αKO mice were protected from the development of HFD-induced hepatic and peripheral insulin resistance. HFD-mediated hepatic p38α activation increased plasma cytokines, suggesting a possible mechanism driving liver-periphery crosstalk in the development of peripheral insulin resistance. Lastly, HFD-induced activation of hepatic p38α promoted hepatic fat accumulation, potentially via enhanced hepatic PPAR-γ expression. These findings suggest that selective p38α inhibition may provide a new approach for treatment of insulin resistance and hepatic steatosis.

Keywords: Hepatic Steatosis
High Fat Diet
Insulin Resistance
Liver
p38
Advisor: Giacca, Adria
The Study of Energy Levels and Reactions at Oxide-oxide Heterojunction Interfaces with Photoelectron Spectroscopy

Oxide-oxide heterojunction interfaces (OHIs) play a crucial role in the development of next generation thin-film devices due to their high tunability. The formation of OHIs is complex as it can involve events such as charge transfer, interfacial diffusion, and chemical reactions. These events contribute to the electronic band structure at an OHI and its ability to perform an intended application. In this work, multiple transition-metal-oxide/oxide OHIs were formed and systematically studied with in-situ photoelectron spectroscopy. The chemical compositions and electronic band structures at the OHIs were found deviating from those of the bulk materials and the driving forces behind the observed phenomenon are discussed. Evidence of charge transfer such as band bending and interface dipoles were also observed at the OHIs and the results were found to be deviating from the existing energy level alignment rules. The findings of this thesis should be taken into consideration when designing OHIs.

Keywords: Heterojunction
Interface
Oxide
Photoelectron Spectroscopy
Thin Films
XPS UPS
Advisor: Lu, Zheng-Hong
Soot, Flow Field, and Spray Structure in Turbulent Swirl-Stabilized Spray Flames of Jet A-1/Biofuel Blends in a Model Gas Turbine Combustor

The effects of ethanol, n-butanol, and m-xylene addition to swirl-stabilized Jet A-1 spray flames were investigated in a model combustor with 94 mm x 94 mm cross-section and 188 mm length. Dopants were added in concentrations up to 20% by energy content for a 10 kW total thermal output; two air flow rates were used for each blend. Droplet size distributions, time-averaged flow fields, as well as time-averaged soot volume fractions and primary particle sizes were measured using the Fraunhofer diffraction technique, stereoscopic particle image velocimetry, and auto-compensating laser-induced incandescence, respectively. Measurable differences in spray distributions and flow fields were observed for all additives compared to neat Jet A-1. In all blend flames, an additional time-averaged soot volume fraction peak absent for neat Jet A-1 was observed below 30 mm above the combustor base. While total soot loading generally increased with ethanol and m-xylene addition, it decreased with n-butanol addition.

Keywords: Biofuel
Laser diagnostics
Primary soot particle size
Soot in Jet A-1
Swirl-stabilized flames
Turbulent spray combustion
Advisor: Gülder, Ömer L.
Impact of Putative Chemo-preventative Agents on Prostate Cancer Diagnosis among Men with a Negative First Prostate Biopsy

In-vitro data has shown that certain medications may decrease prostate cancer (PCa)-cell death. We clinically assessed the role of several medications’ in modulating PCa outcomes, using Cox-regression multivariable models with time-varying covariates. Using linked health administrative data in Ontario, 21,512 men >66 years with a single negative biopsy between 1994-2016 were identified. Hydrophilic statins were associated with a 20%, 18%, and 32.4%, decreased likelihood of undergoing prostate biopsy, being diagnosed with and dying from PCa, respectively. 5ARIs and pantoprazole were associated with an increased risk of being treated with androgen deprivation therapy (ADT). Alpha-blockers and proton-pump-inhibitors were associated with a 46% and 50% increased risk of PCa-specific death, respectively. Lastly, metformin conferred a protective effect with 38%, 21% and 28% reduced risk of undergoing another biopsy, being diagnosed with PCa and receiving ADT, respectively. These results require reassessment of these medications’ role in men at risk to develop PCa and PCa patients.

Keywords: Chemoprevention
Metformin
Prostate biopsy
Prostate cancer
Proton pump inhibitors
Statins
Advisor: Fleshner, Neil
Microsatellite Wiring Harness and Attitude Hardware Development for the Defiant Platform

Resilient and effective hardware is essential for sustained satellite operation. Any hardware that exists on a satellite must be well designed and undergo rigorous testing to be suitable for space flight. The DEFIANT platform is a microsatellite design that facilitates assembly and integration to shorten the development time of new satellite missions. In this thesis, the design of a wiring harness for the DEFIANT microsatellite platform is presented in detail followed by unit level testing and analysis of two attitude sensors and one attitude actuator. The wiring harness design methodology will be discussed emphasizing the simplistic design for effortless satellite integration and achieving repeatable and consistent assembly results through a straightforward manufacturing process. In addition, various attitude determination and control sensors and actuators present on the DEFIANT platform are tested and analyzed to quantify performance and survivability for operation in space. Throughout this thesis, the author will be assessing the impact on the system level design and assembly of a satellite that stem from unit level hardware designs, or test and analysis results.

Advisor: Zee, Robert E
Bringing the Patient Voice to Professionalism in Medical Education

Purpose: Our purpose was to explore patients' perceptions of professional behaviour in medical learners as a first step to considering patients' potential roles in assessing professionalism. Methods: A constructivist grounded theory interview study with 12 patients (6F, 6M) from one urban teaching hospital. Each participant watched 5 video scenarios that depict common professionally challenging situations faced by medical students and were then asked to discuss how they thought the students should handle these situations. Results: Participants' responses largely echoed those of medical students/faculty. They also conveyed an understanding of the multiple competing factors students must balance and expressed empathy regarding some of the pressure students face. Finally, participants identified principles not previously raised by students or faculty. Conclusion: Knowing what patients perceive as important will allow educational/assessment efforts to be refined to reflect their values. Our work can inform emerging initiatives to include patients in the assessment of medical learners.

Keywords: Assessment
Constructivist Grounded Theory
Medical Education
Patients
Professionalism
Qualitative
Advisor: Ginsburg, Shiphra
Investigating the Role of Mucin-related Genes in the Dauer State of C. elegans

The nematode Caenorhabditis elegans, like many organisms, can mount adaptive responses to diverse stimuli that often involve altered gene expression in different cell types. High temperature, low food availability and the presence of a stress pheromone trigger the alternative developmental state in C.elegans known as dauer. Although the genetic mechanisms that govern this developmental state are well understood many questions still remain. My work has identified a potential link connecting the pharyngeal gland toxin-related (phat) genes and the dauer state. Specifically, I have observed that one of these genes, phat-2, encodes a protein that is localized to the pharyngeal lumen during normal development, but redistributes to the intestinal lumen in dauer animals. The phat genes encode proteins with SHK domains, which are found in mucin related proteins. My work has contributed to better understanding the significance of this redistribution on dauer development and physiology.

Keywords: dauer
mucin
pharynx
phat
stress
Advisor: Calarco, John A