VictorJuiz/thesis huggingface dataset:
Single Cell Profiling of Signaling Pathways and Phenotypic Marker Expression in Philadelphia-like B-cell Acute Lymphoblastic Leukemia

B-cell Acute Lymphoblastic Leukemia (B-ALL) is the most common childhood cancer, but also occurs in adults. It is caused by a broad spectrum of genetic alterations which are used for risk stratification. Across all ages, the Philadelphia-like (Ph-like) subtype is associated with lower survival rates. Kinase activating mutations that converge on either ABL or JAK2 signaling are found in >80% of Ph-like cases. Although clinically approved targeted therapies are available for both subgroups, there is currently no test to rapidly identify them. Therefore, I built a mass cytometry panel to profile signaling and phenotypic markers in 7 BCR-ABL and 4 Ph-like samples. I identified blasts with activating ABL or JAK2 mutations based on expression of pSTAT5 and its reduction by targeted inhibitors. Furthermore, I distinguished Ph-like and BCR-ABL specific clusters that differed in CD14 and CD127 expression. My thesis demonstrates how mass cytometry can be used to identify Ph-like samples.

Keywords: Acute Lymphoblastic Leukemia
B cells
Cancer
Mass Cytometry
Philadelphia-like
Advisor: Guidos, Cynthia
Uncovering Differences in the Learning Cultures of the Engineering and Education Departments

This thesis examines the influence of a discipline on the learning culture exhibited and perpetuated within the engineering and education department through open-ended interviews with 10 graduate-level faculty, in a major Canadian public university. The research uncovers how students perceive of what is valued as knowledge and the processes that their discipline encourages them to use in the pursuit of new knowledge through a grounded theory approach using ten professors’ perceptions on how learning occurs within their disciplines. The research question motivating this study is: What differences can be understood between learning cultures in engineering and education departments? Findings highlight that ways of thinking, critical learning, dealing with uncertainty and training of graduate students are informed by disciplinary expectations. The differences in the ways individuals learn and reason based on their academic identities will lead to a better understanding of one another and provide insight into ways to collaborate effectively.

Keywords: engineering education
interdisciplinary collaboration
learning culture
Advisor: Brett, Clare
No Effect of Leucine-enriched Essential Amino Acids on Myofibrillar Protein Synthesis and Strength or Soreness Recovery after a Novel Bout of Resistance Exercise in Young Recreationally Active Males

We examined the effect of a single dose of leucine enriched essential amino acids (LEAA) on myofibrillar protein synthesis (MyoPS) up to 4h and thrice daily LEAA on muscle strength and soreness up to 96h after a novel bout of lower body resistance exercise in recreationally active young men. Exercise increased MyoPS (by oral D2O) with no difference between LEAA and placebo (by or L-[ring-2H5]phenylalanine) over 1.5-4h of recovery. Isokinetic peak torque at 270°/s and 60°/s decreased ~27% and ~26%, respectively, at 48h and returned to baseline by 96h with no difference between conditions. Total muscle soreness increased ~83% at 48h and returned to baseline by 96h with no difference between conditions. Small to large effect sizes (0.21-0.95) were in favor of LEAA for total muscle soreness and total peak torque over 96h of recovery. LEAA does not enhance acute MyoPS and has equivocal effects on performance recovery after exercise.

Keywords: essential amino acids
performance
post-exercise recovery
protein synthesis
stable isotopes
Advisor: Moore, Daniel R
Close, but not Quite: Memory Accuracy Across Spatial Frames of Reference in Cognitive Aging

Aging is associated with deficits in spatial memory for object locations across egocentric and allocentric spatial frames of reference. However, little is known about how this age-related decline interacts with cognitive status. In this study, we used desktop virtual reality to compare object location memory across spatial frames of reference in older adults, both healthy and at-risk for mild cognitive impairment, relative to younger adults. A coarse-grained accuracy measure was not sensitive to differences in task performance across frames of reference driven by cognitive status. With a fine-grained measure of accuracy, healthy older adults showed no impairments relative to younger adults except when the task required a switch from an egocentric to an allocentric frame of reference. This condition also failed to differentiate healthy from at-risk older adults. Taken together, these findings provide novel insights into the interaction of cognitive status and aging for spatial memory across frames of reference.

Keywords: Aging
Frames of Reference
Spatial memory
Advisor: Barense, Morgan D
The Proteomic Architecture of Human Fetal Neurogenesis

Fetal neurogenesis is a highly complex process that produces the full complement of neurons required for an adult brain yet many of its regulatory mechanisms are unknown. Here, we aim to elucidate some of these pathways by conducting a spatial proteomic profile of human fetal brain regions (n = 8) implicated in fetal neurogenesis. We quantified ~2000 proteins and identified region-specific proteins which may play a functional role in neuronal maturation. Well-established regional markers such as SATB2 in the cortex were found to be significantly upregulated (FDR

Keywords: cerebral organoids
development
fetal
neurogenesis
proteomics
Advisor: Diamandis, Phedias
Role of GABAergic Ventrolateral Periaqueductal Grey Neurons in REM Sleep Control

Rapid eye movement (REM) sleep is controlled by a network of neurons within the brainstem. Cell lesion and activation studies suggest that midbrain GABAergic ventrolateral periaqueductal grey (vlPAG) neurons suppress REM sleep by inhibiting REM sleep-promoting neurons in the sublaterodorsal tegmental nucleus (SLD). Weber et al. (2018) recently showed that optical activation of GABAergic vlPAG neurons suppresses REM sleep, however, they did not determine if optogenetic inhibition of these same neurons promotes REM sleep. Therefore, I determined whether GABAergic vlPAG neurons have the capacity to promote REM sleep when optically silenced in mice. Using inhibitory opsins that were expressed in GABAergic vlPAG neurons, I found no evidence that short-term or long-term silencing of these neurons effects REM sleep expression. Specifically, I found no changes in REM sleep amounts or the propensity to enter REM sleep. Accordingly, I conclude that GABAergic vlPAG neurons play a negligible role in controlling REM sleep.

Advisor: Peever, John H
The Role of Mitochondrial DNA in the Pathogenesis of Kawasaki Disease

Kawasaki Disease (KD) is a multisystem vasculitis in which systemic inflammation progresses to localized damage of the coronary arteries. As inflammation persists, tissue damage and cell death results in the liberation of intracellular contents, including mitochondrial DNA (mtDNA), into circulation where they may detected by the inflammasome, an innate immune complex that produces the proinflammatory cytokine IL-1β. It has been reported that IL-1β expression is elevated in the acute phase of KD. Here, we demonstrate that DNA, from mitochondrial or non-mitochondrial origin, has the ability to activate the NLRP3 inflammasome in macrophages and trigger IL-1β production in a TLR9-dependent manner. Furthermore, elevated levels of circulating DNA (cirDNA) were found to be associated with inflammation in the LCWE murine model of KD. These findings enhance our understanding of mechanisms involved in the recognition of cirDNA and suggest that cirDNA may serve as a potential biomarker of disease activity in KD.

Advisor: Yeung, Rae
Path Integration Using Eye and Hand Movements

Although there is neurological evidence suggesting that the entorhinal cortex performs similar computations on whole-body and eye movements in space, behavioural evidence of the same is lacking in the current literature. Humans can track current position relative to the starting point of a journey using only self-motion cues through the process of path integration. We tested if path integration, a process dependent on the entorhinal cortex, uses movements other than whole-body movements to update self-position. We used novel eye-tracking and tablet tasks in which participants followed a sequence of locations guided by visual or auditory cues. Consistent with results from other real-space studies, we found that participants used different strategies to update position in space depending on task demands. Retracing behavior seen with hand and eye movements suggests that retracing precedes computation of the homing vector during real-space path integration, but future studies are necessary to investigate this further.

Keywords: entorhinal cortex
eye-tracking
path integration
spatial navigation
tablet
Advisor: Moscovitch, Morris
Ryan, Jennifer D
Characterization of AcrIE8: A Novel Family of Type I-E Anti-CRISPR Proteins

Bacteria and their viruses (phages) have been undergoing an evolutionary arms race for billions of years. One of the antiphage defense systems bacteria employ is CRISPR-Cas; however, some phages have evolved to inhibit this system by expressing small proteins called anti-CRISPRs. The work of this thesis focuses on characterizing the diversity, function, and mechanism of action of a novel family of anti-CRISPRs called AcrIE8. Putative homologs of AcrIE8 were tested for their anti-CRISPR activity against the type I-E CRISPR-Cas systems of Pseudomonas aeruginosa, Escherichia coli, and Salmonella enterica. AcrIE8 robustly inhibited both the P. aeruginosa and E. coli systems but not the S. enterica system. Furthermore, initial work on elucidating the AcrIE8 mechanism of action suggests an interaction with the CRISPR-Cas complex to prevent it from binding to its target DNA. Understanding the diversity of anti-CRISPRs and how novel families function will provide greater insights into the evolutionary arms race between bacteria and phages.

Keywords: anti-CRISPR
bacteria
bacteriophage
CRISPR
Advisor: Davidson, Alan R
Navarre, William W
Development, Characterization and Evaluation of Advanced Thermoplastic and Metal Hybrid Composite Structure

There is a need for the development of advanced thermoplastic and metal hybrid composites structures in automotive, aerospace and biomedical applications to reduce weight and improve the properties of the constituent materials. Herein, a novel thermoplastic, polyketone (PK), was studied in aggressive hygrothermal condition, in order to understand and characterize the alterations in mechanical, chemical and thermal properties of the polymer in application. A novel polymer-metal hybrid composite fabrication process by mechanical interlocking was then developed, with PK and a chemically etched aluminum, to improve the barrier and structural stability of the PK material. The adhesion performance of the PK-aluminum composite structure was optimized and studied. Finally, various thermoplastics, polyethylene (PE), polypropylene (PP) and polyphenylene sulfide (PPS) were constructed with the mechanical interlocking adhesion mechanism to form novel thermoplastic-metal hybrid composites, and each hybrid composite system was optimized and studied.

Keywords: Adhesion of dissimilar material
Hygrothermal degradation
Mechanical interlocking
Polyketone
Polymer degradation and stability
Polymer-metal hybrid composites
Advisor: Naguib, Hani E
Characterization of FAMILIAL MATRIN 3 S85C and F115C Mutations in ALS

Matrin 3 (MATR3) is one of the most recently discovered gene that was found to be associated with amyotrophic lateral sclerosis (ALS). Several mutations in MATR3 have been identified in both familial and sporadic ALS cases, but how mutant MATR3 causes ALS is still not understood. Here, we characterized two familial MATR3 mutations by generating mice harboring an ALS-linked mutation S85C or F115C in mouse Matr3 endogenous locus through CRISPR/Cas9. Using cellular models, I also explored how MATR3 mutations change the solubility and localization of the protein, including in the presence of the interactor TDP-43, a key ALS-linked protein. With the implication of environmental stress in ALS, the effect of oxidative stress on protein solubility and localization was also explored. By characterizing novel ALS-linked mutations in MATR3, we hope to gain a better understanding of the molecular mechanisms underlying neurodegeneration, thus providing insights into developing novel therapeutic approaches.

Advisor: Park, Jeehye
System-level Design of Coded-exposure Cameras for Computational Imaging Applications

This thesis presents several contributions to system-level design, implementation and testing of computational cameras for computer vision applications, such as coded-exposure imaging and time-of-flight imaging. The contributions are in the areas of PCB design, firmware design and interfacing software design, and are elements of a larger-scale team-based research project on next-generation computational cameras. Three printed circuit boards (PCBs) and a re-usable firmware bridge have been designed to implement, test and deploy three custom cameras. The functionality of two camera designs in coded-exposure imaging has been validated by our team through two single-frame imaging applications: photometric stereo imaging, and multispectral imaging, respectively. The distance measurement performance of the third camera design in time-of-flight imaging has been improved by a pulse-based time-of-flight distance sensing method and verified experimentally.

Keywords: coded-exposure
computational imaging
systems
time-of-flight
Advisor: Genov, Roman
Kutulakos, Kiriakos N
The Role of NOD1 in the Control of the Non-canonical Inflammasome

During infection, one of the cell’s defense mechanisms is to activate the inflammasome. Activation results in a form of cell death called pyroptosis and in the release of pro-inflammatory cytokines. Although normally a protective mechanism that aids in the clearance of intracellular pathogens, widespread and constitutive activation has been implicated in several inflammatory disorders. There exists an inflammasome independent of caspase-1 known as the non-canonical inflammasome. Although this inflammasome has been well studied in murine macrophages, how it functions in cell types other than immune cells is poorly understood. We found that NOD1 is required for proper activation of the non-canonical inflammasome in the human intestinal epithelial cell line HCT116. Interestingly, NOD1’s role did not translate to murine macrophages suggesting that it’s role may be unique to epithelial cells. Our research reveals a novel form of inflammasome activation unique to epithelial cells that could provide insight into gut innate immunity.

Keywords: immunity
Inflammasome
LPS
Nod1
PRM
sepsis
Advisor: Girardin, Stephen
Study of Cargo Uptake in M-cells Differentiated from Intestinal Organoid Derived Cell Monolayers

Microfold cells or M-cells are specialized epithelial cells that overlay lymphoid gut tissues known as Peyer’s patches. M-cells are known for the uptake and transcytosis of lumenal particles across the epithelial barrier to underlying immune cells. Transcytosis is necessary for inducing tolerance or activating mucosal immune responses. However, the means by which M-cells take up lumenal particles is not well understood. Limitations in our understanding of M-cell transcytosis has been due to lack of a reliable in-vitro M-cell model. We show that organoid-derived monolayers differentiate into functional M-cells upon treatment with RANKL. Live cell imaging revealed that M-cells extrude and retract large membrane blebs to take up bacterial particles. Bleb retraction coincided with the formation of macropinosomes within M-cells. Bleb formation, and uptake of bacterial particles was increased upon potential stimulation with bacterial sonicates. This suggested that M-cells take up particles via bleb-associated macropinocytosis under potential simulation by microbe-associated molecular patterns.

Advisor: Terebiznik, Mauricio
Robinson, Lisa
A CRISPR/Cas9-Mediated FACS Screen Reveals Novel Regulators of Wnt/β-catenin Signalling in Human Embryonic Stem Cells

An important signalling mechanism in stem cell fate determination is the Wnt/β-catenin signalling pathway, which is critical in self-renewal and determination of multiple cell lineages. However, the underlying mechanisms involved in regulating Wnt signalling during self-renewal and differentiation of human embryonic stem cells (ESCs) are not fully understood. This thesis aims to identify and characterize regulators of Wnt/β-catenin signalling in hESCs using a CRISPR-Cas9 genome-wide screening approach. A fluorescent GFP reporter was knocked into the AXIN2 locus of a human ESC line containing an inducible Cas9, to enable screening using flow cytometry for regulators of AXIN2 expression. Validating our approach, several known regulators of Wnt/β-catenin signalling were identified. Novel regulators were also identified as negative regulators of AXIN2 expression, including METTL3 and other genes involved in the N6-methyladenosine RNA modification. While the mechanism remains to be elucidated, this study uncovers a novel link between m6A and Wnt/β-catenin signalling in hESCs.

Keywords: CRISPR
ESC
METTL3
screen
signaling
Wnt
Advisor: Angers, Stephane
Using C. elegans as a Drug-discovery Model for the Childhood Liver Disease Progressive Familial Intrahepatic Cholestasis 3

Progressive familial intrahepatic cholestasis 3 (PFIC3) is a rare liver disease with limited treatment options. PFIC3 is caused by mutations in the phosphatidylcholine transporter, ABCB4. ABCB4 transports phosphatidylcholine to the cell surface to alleviate the hepatotoxicity of bile acids. The C. elegans homologue of ABCB4, PGP-14, is a probable phosphatidylcholine transporter whose mutations lead to sphingomyelin deficit in the pharynx. We postulate that sphingomyelin abundance sensitizes wild type worms to hydrophobic nematocidal molecules including wact-190. In my project, I exploited C. elegans pgp-14 mutants to identify drugs that circumvent the loss of phosphatidylcholine transporters. I screened 2,560 compounds and identified three robust suppressors of pgp-14’s wact-190 resistance: terconazole, nicardipine and amiodarone. I found that terconazole alone can suppress the sphingomyelin deficit of pgp-14 mutants. Therefore, terconazole may induce phosphatidylcholine transport in C. elegans. This work has the potential to make an impact on the health of children afflicted with PFIC3.

Keywords: C. elegans
chemical genetics
chemical screen
molecular genetics
PFIC3
pharmacology
Advisor: Roy, Peter
Circulating Osteocalcin and Memory Performance in People with Type Two Diabetes Mellitus and in the Mouse High Fat Diet Model

Osteocalcin circulates in carboxylated (cOCN) and uncarboxylated (unOCN) forms, and unOCN is thought to have widespread neuroendocrine effects. In type 2 diabetes mellitus (T2DM), circulating cOCN and unOCN concentrations are lower, and cognitive decline is accelerated. In the high fat diet mouse model of T2DM, injections with unOCN improved cognition in a puzzle box test, and when combined with exercise, enhanced cortical expression of brain derived neurotrophic factor. In people with T2DM, fasting serum concentrations of unOCN were significantly associated with long-delayed free recall (β=0.110, p=0.010), as assessed by the California Verbal Learning Test (2nd Ed.) controlling for age, sex and HbA1c. The results show cognitive benefits of unOCN treatment in animals, highlight neurobiological benefits of unOCN when combined with exercise, and identify the relevance of a bone-derived neuroendocrine mediator in human memory.

Keywords: Bone
Diabetes
Metabolism
Neuroendocrinology
Osteocalcin
Advisor: Mitchell, Jane
Swardfager, Walter
Alternative Splicing of Exon 5 in GluN1 Controls Glycine-stimulated Recruitment of AP-2 to NMDA Receptors

The number of surface expressed NMDA receptors (NMDARs) at synapses is dynamic and undergoes clathrin-dependent endocytosis. Aside from gating, glycine triggers the recruitment of the endocytic AP-2 adaptor protein complex to NMDARs and primes them for endocytosis. Here, I provide evidence for the involvement of tyrosine kinases and phosphatases in glycine-mediated AP-2 recruitment. Furthermore, I demonstrate glycine-priming depends on the splicing state of GluN1 exon 5 by measuring glycine-mediated AP-2 binding to endogenous NMDARs from transgenic mice that either completely lack or contain exon 5. Glycine induced AP-2 recruitment and dephosphorylation events at the C-terminus of exon 5-lacking NMDARs, which were absent in exon 5-containing NMDARs. Moreover, the inclusion/exclusion of exon 5 alters basal phosphorylation levels at sites implicated in NMDAR trafficking. Thus, these findings suggest exon 5 may selectively control the stability of cell-surface NMDARs and expands our understanding on GluN1 splice variants and their impact on intracellular signaling.

Keywords: alternative splicing
NMDA receptor
Advisor: Salter, Michael W
Functional Characterization and Molecular Evolutionary Analyses of Dim-Light Adaptations in Visual Pigments and Interactions with Arrestin

Rhodopsin and cone opsins are responsible for dim-light and colour vision, respectively, and mediate photon absorption, resulting in retinal chromophore isomerization and visual pigment activation. This triggers the visual transduction cascade, which is subsequently inhibited by the binding of arrestin. First, I investigated arrestin-rhodopsin complex formation relevant to adaptive mechanisms underlying phototransduction. Substitutions identified in comparative analyses of dim-light animals showed enhanced ability of arrestin-rhodopsin complexes to sequester retinal chromophore when assayed in vitro. The second study analyzed the selective pressures across the cone opsin gene RH2 of teleosts and identified a positively selected site with unusual amino acid substitutions in the deep-sea fish. These substitutions showed altered kinetics when assayed experimentally. Overall, my findings provide insight into the less-well studied aspects of dim-light adaptation and show the significance of investigating the visual system as an interdisciplinary study involving evolution, biochemistry and molecular biology.

Advisor: Chang, Belinda S.W.
The Influence of Ensemble Processing on Visually Guided Motor Behaviour

The current study examined whether ensemble perception would bias grasping for an ambiguous grasp dimension. Participants performed a precision grip to a circular target which had an explicit size but importantly no explicit orientation that the visuomotor system could attend to. The target was embedded within an ensemble of ellipses that varied in size and orientation. On separate blocks of trials, participants made explicit perceptual judgments of the average size or orientation of the ensemble or grasped the target presented alone or within the ensemble, without any explicit perceptual judgment. Maximum grip aperture and grip orientation were not biased by ensemble statistics, despite participants being able to report average size and orientation in the perceptual task. This suggests that the visuomotor system is resistant to perceptual biases induced by ensemble perception, and further contrasts the context-sensitive nature of perception with the emphasis the visuomotor system places on the veridical properties of objects.

Keywords: Cognitive Neuroscience
Ensemble Perception
Human movement
Vision
Visuomotor control
Advisor: Cant, Jonathan S
Niemeier, Matthias