VictorJuiz/thesis huggingface dataset:
Potential of Cyanobacterial Carbonate Precipitation for Concrete Restoration

Concrete is a widely used construction material with a global production growing by 2.5% annually. However, concrete can easily be cracked and has a limited lifespan. Among strategies for healing cracks and recycling concrete, microbial carbonate precipitation (MCP) by nitrogen-involved heterotrophic bacteria showed great potential. In this study, an alternative technology using autophototrophic cyanobacteria is proposed to overcome the pollution generated by urea-based MCP. This study investigated cyanobacterial carbonate precipitation (CCP) in concrete and mortar, and its impact on their performance. Solution composition and cell viability were monitored, morphology of precipitates and the relation of precipitate-cell-substrate was observed with scanning and transmission electron microscopy as well as atomic force microscopy and epifluorescence microscopy. Chemical components were analyzed by energy dispersive X-ray spectroscopy, X-ray diffraction and Raman spectroscopy. The performance of concrete/mortar were evaluated using water absorption tests, sonication tests, compressive strength tests and mercury intrusion tests. Results show that cyanobacteria were able to survive in cement solution for a certain period, the biotic-formed precipitates were different in morphology and achieved higher amount compared to abiotic-formed precipitates. In addition, the calcite-cell aggregate layer was more cohesive on concrete/mortar than the calcite layer formed in the abiotic condition. The durability of concrete/mortar was greatly enhanced by CCP through decreasing the water absorption and porosity, and increasing the compressive strength. Nevertheless, the capability of cyanobacteria improving concrete/mortar properties is strain-dependent, and varies according to environmental conditions. This study concluded that Synechocystis PCC6803 works better than Synechococcus PCC8806 and Synechococcus LS0519. Generally, UV pretreatment of cyanobacteria contributes to better results by producing higher amount of EPS. Consequently, cyanobacteria, especially UV-killed cells, show a great potential for restoring concrete/mortar.

Keywords: Carbonate Precipitation
Concrete Restoration
Cyanobacteria
Mortar
Advisor: Dittrich, Maria
Regulation of Mucosal T cell Activation and Inflammation by NLRC3 and Tritrichomonas muris

The mucosal immune system in the gut is specialized to protect the host from infection by pathogenic microbes while maintaining tolerance towards the antigen-rich microbiota. T cells are a major component of the mucosal immune system that help to respond to pathogenic microbial invasion while maintaining a tolerogenic environment during times of homeostasis. These T cells can be regulated by genetically inherited factors as well as factors from the environment. Since defects in T cell function can contribute to the development of inflammatory bowel diseases, it has become increasingly important to understand how these factors are regulating T cell function. In this thesis we seek to explore how an extrinsic microbe, Tritrichomonas muris and an intrinsic factor, NLRC3, separately contribute to T cell function and disease regulation in various models of colitis.

Keywords: Immunology
Inflammatory Bowel Disease
NLRC3
NOD-like Receptor
T cell
Tritrichomonas muris
Advisor: Philpott, Dana J
Mallevaey, Thierry
Effect of solute-solvent interactions on protein stability and ligand binding

My doctoral thesis is aimed at characterizing the effect of solute–solvent interactions on protein stability and ligand binding events. To quantify non-specific protein–solvent interactions, we measured and analyzed partial molar volume and compressibility of proteins within a framework of statistical thermodynamic formalisms. We characterized the binding of tri-N-acetylglucosamine [(GlcNAc)3] and cAMP to lysozyme and cAMP-binding domain of EPAC1, respectively. Our volumetric measurements reveal that the protein–ligand complexes are less dynamic compared to their unbound states while complex formation is accompanied by the release of water of hydration to the bulk. To characterize protein–urea interactions, we determined and analyzed volumetric properties of four globular proteins at urea concentrations ranging from 0 to 8 M. We interpreted urea-dependent volumetric measurements in terms of the solvent exchange model in which the binding of urea to a protein proceeds with a release of two waters of hydration. Comparison of urea-dependent volumetric data for a folded protein with the similar data obtained on small molecules mimicking protein groups suggests the lack of cooperative effects involved in protein–urea interactions. Changes in volumetric properties associated with urea-induced unfolding transitions are consistent with solvent-accessible surface areas of unfolded proteins being roughly twice as large as those of their respective native states. Specifically, we reported the first experimental characterization of the thermodynamic profile of urea binding to a native protein. We measured the volumetric parameters of lysozyme as a function of urea within a temperature range of 18 to 45 ◦C. Based on the van’t Hoff analysis of the temperature dependence of the equilibrium constants for protein–urea binding events we evaluated the full thermodynamic profile of protein–urea interactions. Finally, we combined the experimental and theoretical approaches to investigate the influence of the urea on the binding of (GlcNAc)3 to lysozyme. Analysis of urea dependence of the binding free energy reveals that the protein–ligand binding reaction is governed by a close interplay between the free energy contributions of the excluded volume effect and direct solute–solvent interactions.

Advisor: Chalikian, Tigran
Cognitive Correlates of Anterolateral Entorhinal Cortex Volume Differences in Older Adults

Alzheimer’s disease pathology first appears in the medial temporal lobe (MTL): in particular, in the anterolateral region of the entorhinal cortex (alERC). However, the scientific community has only recently begun to appreciate the importance of the subdivision of the human entorhinal cortex, and as such, our understanding of the alERC’s cognitive roles and how it fits into models of MTL function remains limited. In this dissertation, I describe a series of studies inspired by findings from the animal literature, which shed light on the cognitive functions supported by the alERC. Using structural volumetry, I quantified the volumes of the alERC and other MTL regions in a group of ostensibly healthy older adults with varying degrees of cognitive decline. I compared participants’ structural differences to their performance on behavioral tasks that we hypothesized represented cognitive functions supported by the alERC. Specifically, I investigated how alERC structural differences were related to performance on the Montreal Cognitive Assessment (MoCA), a standard neuropsychological assessment used in the diagnosis of AD (Chapter 2), as well as eyetracking-based behavioral tasks assessing intra-item configural processing (Chapter 3) and object-in-place memory (Chapter 4), cognitive functions which the rodent literature suggest are supported by the alERC. I found that participants who scored below the MoCA threshold score (indicating possible AD) had smaller alERC volumes (Chapter 2), demonstrating that alERC volume is related to cognitive decline. Further, intra-item configural processing – regardless of an object’s novelty – was strongly predicted by alERC volume, but not by the volume of any other MTL subregion (Chapter 3). Finally, alERC (and parahippocampal cortex) volume was also related to object-in-place memory for items in everyday scenes, but no such relationship was found for object-trace memory (Chapter 4). Together, these studies suggest that the alERC may support aspects of the spatial processing of objects, advancing our understanding of the cognitive correlates of the alERC. More pragmatically, the alERC-specific tasks I developed may prove useful in early screening for AD and evaluating its progression.

Keywords: Alzhiemer's disease
Anterolateral entorhinal cortex
Cognitive Decline
Eyetracking
Memory
Structural volumetry
Advisor: Barense, Morgan D
Political-Financial Scandal, Political Disaffection, and the Dynamics of Political Action

This thesis examines whether and to what extent political-financial scandals shape public attitudes toward the political system and citizensâ patterns of participation in political action. The investigation employs a combination of Canada-focused case studies and large-N cross-national analyses. The findings indicate that while political-financial scandals do seem to contribute to an erosion of specific and intermediate forms of political support, they also suggest that scandals do not vitiate public support for broader democratic principles. With respect to the impact of scandals on political participation, the thesis highlights and investigates a puzzle. The Canadian case studies presented here suggest that revelations of political actorsâ ethical transgressions serve as a catalyst for both traditional and non-traditional forms of political participation in the short and medium-term. Even so, multi-level analyses of cross-national individual and aggregate-level data suggest that persistently high perceptions of corruption in government undermine citizensâ intrinsic motivation to vote, and that political-financial scandals might well suppress voter turnout over longer time horizons.

Advisor: Nevitte, Neil
The Prion Protein Controls Polysialylation of Neural Cell Adhesion Molecule 1 during Cellular Morphogenesis

The cellular prion protein (PrPC) is one of the most studied mammalian proteins. Despite the ongoing efforts and the ubiquitous expression of PrPC in vertebrate cells, the main function of this protein has remained enigmatic to date. Several lines of evidence pointed towards the involvement of PrPC in the morphogenetic reprogramming underlying the epithelial-tomesenchymal transition (EMT). To address this, we applied CRISPR-Cas9 genome engineering technique to establish multiple PrPC knockout cell models (Chapter 2). The follow-up studies uncovered a critical role of PrPC in EMT and showed that PrPC controls the polysialic acid (polySia) modification of neural cell adhesion molecule 1 (NCAM1). Surprisingly, this effect of PrPC on NCAM1 polysialylation relies on a novel signaling loop that modulates expression of ST8SIA2, one of the two polysialyltransferase enzymes responsible for adding polySia on NCAM1 (Chapter 3). Intriguingly, a comparative analysis revealed that PrPC levels correlate directly or inversely with ST8SIA2 levels in different cell models. Deep global proteome analyses of multiple PrP-deficient models not only uncovered surprising cell model-specific proteome shifts but also showed robust changes in the levels of MARCKS and BASP protein families at the plasma membrane. Further investigation of their involvement in a biology that controls NCAM1 polysialylation revealed that reduced levels of MARCKSL1 also led to a significant reduction of polySia-modified NCAM1 (Chapter 4). Data from this study emphasize a iii thus far underappreciated coordinated biology of PrP and NCAM1. A close comparison of knockout phenotypes in mice is consistent with a model, whereby several of the known phenotypes in PrP-deficient mice might be explained by the contribution of PrPC to NCAM1 polysialylation. Attempts to validate this model and to assert its significance for determining if perturbed PrPC signaling contributes to toxicity in prion diseases are ongoing and have not been included in this thesis at this time.

Keywords: Neural cell adhesion molecule 1
polysialylation
Prion protein
ST8siaII
ZIP6
Advisor: Schmitt-Ulms, Gerold
Extending the Atlas of Variant Effects in Human Disease Genes

Although we now routinely sequence human genomes, we cannot yet confidently identify functional variants. Here a deep mutational scanning framework is developed that combines random codon-mutagenesis and multiplexed functional variation assays with computational imputation and regularization to yield exhaustive functional maps for human missense variants. The framework is applied to five proteins corresponding to seven human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), NCS1 (neuronal calcium sensor 1), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting functional impact scores correspond to known protein features, and serve to confidently identify pathogenic variation.

Keywords: Calmodulin
Deep Mutational Scanning
Sumoylation
Variants of Uncertain Significance
Advisor: Roth, Frederick P
Phenomenology of Heavy Lepton and Heavy Higgs Decays at the LHC

Strongly interacting chiral fermions, present for example in fourth family or technicolour models, induce electroweak symmetry breaking. If the effective low energy theory is identified with a multi-Higgs model, the heavy chiral fermions can be consistent with a light Higgs ( h). The SM-like Higgs rates for h → VV,gg,γγ are then used to constrain the Higgs potential and the heavy fermions h couplings in technicolour and fourth generation models. The phenomenological consequences of these models are explored, and neglected LHC signals are identified. The particle content of interest is heavy quarks (t',b'), heavy leptons (τ',ν') and heavy Higgs (H,A,H±). Existing LHC searches are recast to put limits on heavy lepton decays to third generation leptons, heavy Higgs decays to heavy leptons (H → τ'τ') and heavy Higgs decays A/H → H/AZ. These limits are then combined with LHC heavy quark and heavy Higgs limits to explore heavy quark decays to heavy Higgs. The allowed range of heavy lepton masses in fourth family and technicolour models are determined by taking into account the calculated mass limits, the h couplings and the oblique parameters.

Advisor: Holdom, Bob
Elucidating the Molecular Mechanisms Involved in Assembly/Folding and Targeting V-ATPase a-subunit Isoforms to their Functional Destinations

Vacuolar H+-ATPases (V-ATPases) are proton pumps distributed across membranes of specialized cells and luminal compartments. V-ATPases in the plasma membrane of osteoclasts are responsible for acidifying the surface of bone, essential for bone resorption. V-ATPases in the plasma membrane of metastatic cells acidify the extracellular space to facilitate invasion. The V-ATPase a subunit has four isoforms (a1-a4) that localize to distinct compartments. In invasive cancer, plasma membrane expression of a3 and a4 are required for metastasis while a3 is specific for the plasma membrane of osteoclasts. Thus, both isoforms are potential therapeutic targets. Sequences of a isoforms reveal putative N-glycosylation sites within extracellular loop II (ELII). Upon PNGase F and Endo H treatment, all a isoforms showed faster mobility on SDS-PAGE indicating the presence of N-linked oligosaccharide. Using site-directed mutagenesis, I showed that deglycosylated a1â a4 had shorter half-lifes, more rapid proteasomal degradation, endoplasmic reticulum (ER) retention, defective Golgi trafficking, and an inability to associate with ER assembly factor, VMA21. In addition, deglycosylated a4 showed defective cell-surface expression and assembly. Cutis laxa type II, osteopetrosis and distal renal tubular acidosis (dRTA) result from mutations within the a2, a3 and a4 subunits, respectively. To further map critical domains essential for V-ATPase structure and function, I studied human disease-causing missense mutations that affect conserved residues of a isoforms, specifically: a2P405L, a4R449H and a4G820R. a4R449H and a2P405L were unstable and degraded by the proteasomal pathway. The data also indicated that a2-P405 is required for Golgi trafficking while a4-R449 is essential for ER exit and cell-surface expression. a4R449H shows increased association with the assembly factor, VMA21. Molecular modeling of a4 predicts a4G820R would interfere with proton translocation through the cytoplasmic half channel formed by the a subunit. This work enhances our knowledge of a isoforms structure and informs possible therapeutic interventions against cancer metastasis and lytic bone diseases.

Keywords: ER-associated degradation
Membrane protein
N-glycosylation
Protein degradation
Trafficking
V-ATPases
Advisor: Manolson, Morris F
Reithmeier, Reinhart AF
The quantification of the online control of goal-directed movement using frequency domain analysis

The field of motor control has devoted a lot of attention to the use of sensory information during movements for the maintenance of accuracy. This sensorimotor processing has been colloquially termed online control. Its accurate quantification and identification has posed a continual challenge to motor control researchers. Consequently, many measures of online control have been developed and have shaped the concurrent state of the field. Recent theories of online control have posited the existence of multiple distinct feedback processes. The current dissertation sought to gain insights into the multi-faceted nature of online control by evaluating the utility of frequency domain analyses as a tool for its quantification. Frequency domain analyses were hypothesized to be sensitive to the aforementioned distinct feedback processes given the assumption that they operate at unique timescales. Four experiments were conducted and evidence was obtained in favour of the utility of frequency domain analyses for the quantification of online control. Specifically, frequency domain analyses were found to be both one of the most sensitive measures to online control and the most robust measure to offline contamination. Thus frequency domain analyses represent an excellent choice for the evaluation of online control processes. Additionally, theoretical insights were attained through the sensitivity of frequency domain analyses to the contribution of two distinct processes contributing to reaching performance. The first was an iterative visuomotor process that influenced reaching performance at relatively stable rates. Notably, the specific rate of influence was found to be flexible based on the spatio-temporal requirements of reaching movements. Additionally, frequency domain analyses were found to be sensitive to a second, non-visual process. This process was promoted in the absence of online vision and likely represented the contribution of a peripheral proprioceptive process. Importantly, contemporary alternative methodologies for the quantification of online control were not sensitive to the unique contributions of this secondary process. Altogether, the current dissertation reaffirmed and expanded upon the multi-faceted nature of online feedback utilization and provided a novel approach to its quantification.

Keywords: Frequency domain analysis
Online control
reaching
Advisor: Tremblay, Luc
Transformative Learning in an Interculturally-Inclusive Online Community

My dissertation addresses the question of how foreign language (FL) students’ perspectives and attitudes about their target language (TL), target culture (TC), first language (L1) and L1 culture changed through communicating with each other during an online exchange project. Specifically, the research focused on the personal narratives of ten FL learners who participated in an online project between an English language class at a Japanese university and a Japanese language class at a Canadian university. The objective was to examine perspectives and attitudes about the students’ experiences during the online exchange project. The literature review showed that telecollaborative language exchanges enhance language learning and intercultural knowledge. Through the concept of community of practice (CoP) (Wenger, 2014), language learners improve their skills and become empowered. This study used Wenger’s notion of CoP as a theoretical framework in the context of university FL classroom settings. A narrative approach captures students’ experiences during their online communication. The findings demonstrate that students gained confidence and increased their motivation for learning the TL while expanding their language skills and cultural knowledge. Some students showed transformative processes. In both Canada and Japan, the participants appreciated their partners and the community members for friendship, shared interests and learning support, and were able to overcome linguistic challenges during the online communication. However, the findings also suggest that Japanese and Canadian students perceived their online community a little differently. These differences seem to be caused by the notion that the learning process was situated in a local CoP. The study concludes by offering theoretical as well as pedagogical implications to suggest how FL classes can better support the telecollaborative language exchanges.

Keywords: Action research
Community of practice
English as a foreign language
Japanese as a foreign language
Narrative approach
Telecollaboration
Advisor: Kerekes, Julie
Great Sexpectations: How Implicit Theories of Sexuality Shape Sexual and Relationship Well-being

How do people believe they can best maintain sexual satisfaction in their romantic relationships? In the current research, I draw upon the literature on implicit theories of relationships to develop and validate a scale examining two types of lay beliefs about how sexual satisfaction can be maintained over time. Individuals high in sexual growth beliefs think that sexual satisfaction is attained from hard work and effort, whereas individuals high in sexual destiny beliefs think that sexual satisfaction is attained through finding a compatible sexual partner. Across six studies (two cross-sectional online studies, a 21-day daily experience study, two dyadic studies, and an experimental manipulation; N = 1,896), I find evidence that those higher in sexual growth beliefs experience higher relationship and sexual satisfaction, and have partners who are more satisfied. Conversely, the effects of sexual destiny beliefs on satisfaction are contingent upon signs of partner compatibility: When individuals high in sexual destiny beliefs experience greater sexual disagreements in their relationship, they experience lower relationship quality. These results are independent of general relationship implicit beliefs, providing evidence for the uniqueness of these two constructs and the importance of examining implicit beliefs in the domain of sexuality. Overall, these results provide novel evidence that individualsâ lay beliefs about maintaining sexual satisfaction are important for understanding the quality of their sex lives and relationships.

Keywords: destiny beliefs
expectations
growth beliefs
implicit theories
relationship satisfaction
sexual satisfaction
Advisor: MacDonald, Geoff