VictorJuiz/thesis huggingface dataset:
Molecular Mechanisms of p63-Derived Ectodermal Dysplasia

Molecular defects in the p63 gene give rise to severe physiological abnormalities in patients with ectodermal dysplasia, however the mechanisms by which p63 mutations disrupt p63 function are unknown. In this study we examined four ΔNp63α mutants; Ectrodactyly-Ectodermal Dysplasia with Clefting (EEC) R204W, R304W and Ankyloblepharon-Ectodermal Dysplasia with Clefting (AEC) mutants, L514F and G530V, and characterized DNA binding, transcription factor activity, oligomerization with wild-type p63 and changes in protein stability/nuclear localization. We also investigated the putative OD-SAM interaction in p63 and p73. We demonstrated that both the EEC and AEC mutants cannot transcriptionally activate the PERP promoter and can hetero-oligomerize forming dominant negative complexes with wild-type p63. We show that both EEC mutants and AEC L514F mutants are more stable which is not due to aberrant degradation by the E3 ligase Itch. Finally, we discovered that a novel interaction between the p73 OD and SAM domain is absent in p63.

Keywords: p63
Ectodermal Dysplasia
p53 Family
Protein Stability
Transactivation
Itch
PERP
EEC
Advisor: Irwin, Meredith
Inhibitory Actions of Gastrin-releasing Peptide in Mouse Anterior Cingulate Cortex

The anterior cingulate cortex (ACC) expresses high density of Gastrin-releasing peptide (GRP) and GRP receptor mRNA. To address possible function, this investigation used patch clamp recordings in mouse brain slice preparations to evaluate intrinsic properties of ACC neurons and neuronal responses to bath-applied GRP peptide. The ACC neurons were divided according to their morphology, the properties of action potentials and their firing pattern in response to depolarizing current pulses. Two physiological groups of interneurons and three groups of pyramidal neurons were defined. Application of the GRP induced depolarization and increased firing of the interneurons while hyperpolarization and reduced firing in pyramidal neurons. Moreover, activation of GRP receptor facilitated GABAergic neurotransmission via a postsynaptic mechanism. The results suggest that GRP receptor is an important regulator of neuronal circuits in the ACC and may consequently play an important role for ACC neurons in the central processing of high brain function.

Keywords: Gastrin-releasing peptide
Anterior cingulate cortex
Advisor: Wojtowicz, Jan Martin
Molecular Genetic Analysis of the Mouse Anorexia Mutation

The serotonergic system regulates numerous behaviours and disruptions in this system have been associated with disorders of mood and mind. Although molecular genetic analysis has dissected many of the genes involved in the specification of the serotonergic system, relatively little is known about the mechanisms that promote axonal outgrowth from serotonin-producing neurons and how these projections are directed to innervate and form synapses with their appropriate targets. The mouse anorexia mutation causes hypersprouting of serotonergic projections in target fields and has provided us the unique opportunity to examine the crucial events that lead to the establishment of these complex serotonergic networks. Through positional cloning, I have identified a candidate gene that is upregulated during a time in which innervation and synaptogenesis of serotonergic neurons are maximal. I have assessed the expression of this candidate gene in the brain and have found striking differences in the pattern of expression between the normal and the mutant mouse. Furthermore, by using transgenic methods, I have partially rescued several hallmark behavioural phenotypes in the mutant mouse. Thus, this candidate almost certainly represents the “Anorexia” gene.

Keywords: serotonin
mouse
Advisor: Cordes, Sabine
Acting and Second Language Pragmatics: Pedagogical Intersections

The study sheds light on the interrelations between interlanguage pragmatics and the use of a popular acting method, the Stanislavsky System, for second language (L2) acquisition. The theoretical investigation explores various uses of acting in second language education. The empirical enquiry represents an exploratory case-study of two adult EFL learners attending a theatre course in English. Through teacher journals, interviews, and the analysis of the students’ pragmatic performance as captured by a video camera, the researcher hypothesizes that the pragmatic development of the students involved in drama comes from three main sources: the script, the acting exercises, and the necessity to communicate in English during the theatre course. In all three cases, the zone of proximal development in relation to pragmatic competence emerged as a result of a teacher-generated impetus to use L2, numerous opportunities for imitation and repetition, continuous peer-support, and the collaborative spirit created in the classroom.

Keywords: drama
second language
education
L2
acting
performance
pedagogy
case study
sociolinguistics
pragmatics
pragmatic competence
sociolinguistic competence
intonation
theatre
foreign language
musical
adult education
second language education
Advisor: Kerekes, Julie
Refining Positional Identity in the Vertebrate Hindbrain

The vertebrate hindbrain is divided early in embryogenesis along its anterior-posterior axis into eight segments known as rhombomeres. This provides an excellent model for studying early segmentation and region-specific transcriptional domains. MafB, a basic domain leucine zipper transcription factor, is the first gene known to be expressed in the presumptive rhombomere 5 and 6 domain (r5-r6). MafB expression is directly activated by the homeodomain protein vHnf1. vHnf1 and MafB share an anterior expression limit at the r4/r5 boundary but vHnf1 expression extends beyond the posterior limit of MafB and, therefore, cannot establish the posterior expression boundary of MafB. Through the use of in situ hybridization, immunofluorescence, and chromatin immunoprecipitation analyses, I have determined that the caudal-related homeodomain protein Cdx1 establishes the posterior boundary of MafB by directly inhibiting expression beyond the r6/r7 boundary. My results indicate that MafB is one of the earliest direct targets of Cdx1.

Keywords: hindbrain development
segmentation
Advisor: Cordes, Sabine
Protecting Group-free Synthesis of Glycosides

Carbohydrates play major roles in many biological processes. Therefore, the synthesis of oligosaccharides is of considerable interest for biological, medicinal, and pharmacological studies. Many approaches have been developed for the synthesis of oligosaccharides, in which the main focus is often the formation of the glycosidic bonds. Traditional approaches use protecting group strategies that can be time consuming and can result in poor overall yield. This thesis describes the protecting group-free synthesis of a series of glycosyl donors of a range of mono- and disaccharides. These donors can be used to synthesize unprotected glycosyl chlorides, observed in situ. Reaction of the glycosyl chlorides with a variety of nucleophiles afforded the expected displacement products, giving access to a range of O-, N-, and S-linked glycosides, without resorting to the use of protecting groups.

Keywords: Protecting group-free glycosidations
Unprotected glycosyl chlorides
Glycosyl donors
Advisor: Nitz, Mark
Investigating the Neurobiological Role of Tubby, a Protein Involved in Obesity

Tubby mice succumb to blindness, deafness, and obesity. Vision and auditory deficits are attributed to neurodegeneration and tubby-associated obesity has been postulated to result from neuronal deficits in brain regions controlling weight regulation. TUB has been implicated in Gq signaling and 2 isoforms of TUB, found exclusively in the brain, may have opposing effects on transactivation. Toward this end, I developed several cell culture assays to interrogate TUB function and found that TUB directs neuronal outgrowth in an isoform-specific manner. One isoform directs stable and polar outgrowth while the other directs multiple process outgrowths and branching. These effects can occur via Gq signaling and require nuclear localization. Furthermore, I have found that the serotonergic system of tubby mice displays morphological and innervation deficits. Since the serotonergic system is implicated in modulating moods and behaviours, including appetite, these deficits may result in the obesity and motivational issues observed in tubby mice.

Keywords: Tubby
Advisor: Cordes, Sabine
Group 4 Metal Complexes with Ferrocenyl Amidinates

Bis(amidinate) dichloride complexes of the type M(L)2Cl2 (M=Zr, 2a; M=Ti, 2b; L=CyNC(C5H5FeC5H4)NCy) were synthesized by treating 2 equiv of ferrocenyl amidine, H(L), with M(NMe2)2Cl2 (M=Ti, Zr.2THF). Half sandwich mono(amidinate) complexes, Cp’ZrLCl2 (Cp’=Cp, 2c; Cp’=Cp*, 2d), were prepared by the reaction of Cp’ZrCl3 with 1 equiv of Li(L). The dialkyl complexes, M(L)2Me2 (M=Zr, 3a; M=Ti, 3b), CpZr(L)(CH2Ph)2 (3c) and Cp*Zr(L)Me2 (3d) were prepared by treatment of the dichloride complexes (2a-2d) with an appropriate alkylating agent. The dichloride complexes (2a-2d) activated with MAO, and dialkyl complexes (3a-3d) activated with B(C6F5)3 and [Ph3C][B(C6F5)4] show low to moderate ethylene polymerization activities. Cyclic voltammetry studies on the metal complexes containing ferrocenyl amidinates reveals quasi reversible oxidation and reduction waves for the ferrocene/ferrocenium couple.

Keywords: organometallics
polymerization catalysis
Advisor: Stephan, Douglas
Evidence of Mobility in the 3-chlorobenzoate Degradative Genes in a Pristine Soil Isolate, Burkholderia phytofirmans OLGA172

The genome of B. phytofirmans OLGA172 has been sequenced by Next Generation sequencing methods. Over 42 kbp of its genome surrounding its 3CBA degradative genes, tfdCIDIEIFI, was assembled and annotated. The most important method used was the synteny method, which implies homology between the genes, and descent from a common ancestor (Guttman, 2008). The conserved gene order between B. phytofirmans PsJN, B. xenovorans LB400, and OLGA172 was used as a confirmation of annotation through BLASTn, enabled closing of the gaps in the sequencing data, and allowed prediction of genes further downstream. Though the whole genome is not yet assembled, a very significant region carrying a concentrated area of mobile genetic elements (MGE) has been found to surround the degradative genes in OLGA172. This thesis details the sequence evidence that, upon examination of closely related strains, OLGA172 and its related strain from pristine soils may be the ancestral chlorobenzoate degraders.

Keywords: chlorobenzoate
burkholderia
horizontal gene transfer
Advisor: Fulthorpe, Roberta
Genetic Variation in Bitter Taste Perception, Food Preference and Dietary Intake

The role of variation in the TAS2R50 bitter taste receptor gene is unknown, but may influence taste perception and dietary habits. Individuals (n=1171) aged 20 to 29, from the Toronto Nutrigenomics and Health Study, completed a food preference checklist and a semi-quantitative food frequency questionnaire to assess their preference and intake of potentially bitter foods and beverages. DNA was isolated from blood and genotyped for 3 polymorphisms in the TAS2R50 gene (rs2900554 A>C; rs10772397 A>G; rs1376251 A>G). Taste intensity was examined using taste strips infused with 3µg of naringin. The rs2900554 SNP was associated with naringin taste intensity, grapefruit preference and grapefruit intake in females. Homozygotes for the C allele reported the highest frequency of experiencing a high naringin taste intensity, disliking grapefruit and not consuming grapefruit. The rs10772397 and rs1376251 SNPs were associated with disliking grapefruit. These results suggest that naringin may be a ligand for the T2R50 receptor.

Keywords: Bitter taste
Nutrigenomics
TAS2R50
Taste
Advisor: El-Sohemy, Ahmed
Understanding the geography of Industry Canada's Community Access Program in Toronto

Industry Canada’s Community Access Program (CAP) aims to provide affordable public access to the Internet and the skills that people need to use it effectively. In fact, the CAP is an Industry Canada effort to bridge the digital divide (rural-urban, intra-urban). In the City of Toronto Industry Canada funding is used to support CAP sites managed by two organizations, the Learning Enrichment Foundation and the Toronto District School Board. CAP was implemented through the establishment of community-based public Internet access facilities. The implementation of the CAP in Toronto has resulted in the use of a wide range of organizations and locations including: libraries, schools, community centres, employment and social service agencies, and language development centres. This research asks the question, is the current network of CAP locations adequately geographically organized to meet the demand for service provision? Adequate supply means that the neighbourhood CAP supply is not over-served and under-served. Data from Industry Canada’s CAP database and the Canada census are input to a modeling process that combines multi-attribute decision analysis with a location-allocation model. The results suggest that there is likely a need to reevaluate the geographical structure of the current CAP network, with a view to achieving a more equitable allocation of supply.

Keywords: Digital Divide
Community Access Program
Geography
GIS
Advisor: Buliung, Ron
The Effect of using Book Clubs to Improve Literacy and Build a Learning Community Among Under-performing Elementary Students

Although literature has extensively documented the stereotypes of developing learning communities in schools through book clubs— especially to improve literacy— little is revealed about varied indicators of improvements, such as student self-identification, authentic dialogues, and transforming small groups into learning communities. In this respect, formal efforts on adopting book clubs to improve literacy in Saudi Arabia are simply absent. This thesis presents research findings that seek to explore the effect of book clubs on improving literacy and building a learning community among seventh-grade, under-performing students in Canada. This thesis is contextualized through a thorough review of related literature and discussion of findings from classroom observations, and students’ interviews. The completion of this thesis indicates positive, causal relationships between using a book club as a learning tool and building a learning community, thus improving literacy. The research concludes with implications for using book clubs in Saudi Arabia.

Keywords: Saudi Arabia
Literacy
under-performing students
elementary
reading
writing
learning community
identity
authentic dialogue
academic performance
book clubs
Advisor: Kooy, Mary
LINCing Literacies: Literacy Practices among Somali Refugee Women in the LINC Program

This thesis investigated the literacy practices of a group of Somali refugee women participating in Canada’s federally‐funded ESL program LINC (Language Instruction for Newcomers to Canada). Assuming that many Somali women arrive in Canada with limited experience with print literacy, and so encounter novel challenges in their settlement and learning experiences, I interviewed 4 Somali women about their uses and perceptions of the value of literacy in their lives and their experiences of learning to read and write in Canada. A cross‐case analysis revealed how social forces constrain and enable the women’s literacy practices, shaping both how they access and use literacy, as well as the ways in which they understand and value literacy. Implications are outlined for ESL educators, researchers and policy makers.

Keywords: ESL education
language instruction
Somali refugees
literacy practices
LINC program
Advisor: Cumming, Alister
Shear Resistance of High Strength Concrete I-beams with Large Shear Reinforcement Ratios

Experiments were performed to examine the shear resistance of heavily reinforced I-beams. Six I-beams with identical cross sections were constructed using high strength self-consolidating concrete, and were tested under monotonic anti-symmetric loading. All specimens had almost the same amount of longitudinal reinforcement, which provided sufficient flexural capacities. There were two variables: shear span and shear reinforcement ratio. Test results showed that ACI code was too conservative in predicting the shear strengths of heavily shear reinforced I-beams, and the shear strength limit for deep beams should be increased to account for the benefit of high strength concrete. However, doubling the amount of stirrups did not improve the ultimate shear resistance much. The three beams that contained around 2.45% stirrups showed over-reinforced shear failures. Longitudinal flange cracking occurred to every specimen due to lack of cross tie reinforcement in the flanges, and it was believed to have reduced the ultimate shear strength.

Keywords: high strength concrete
shear resistance
heavily shear reinforced
I-beams
anti-symmetric loading
Advisor: Bentz, Evan
Collins, Michael P.
An In Vitro Investigation of the Spatial Control Involved in Collagen Mineralization

An in vitro model system utilizing de-mineralized periodontium tissues was developed for investigating the molecular controls involved in the spatial deposition of minerals on collagenous tissues. Preferential mineral deposition was observed when the de-mineralized tissue sections were incubated in solutions containing a supersaturation of calcium and phosphate ions with respect to hydroxyapatite (HA). Energy dispersive X-Ray (EDX) analysis demonstrated that these minerals are likely to be octacalcium phosphate (OCP) or dicalcium phosphate dihydrate (DCPD); further characterization with a secondary technique is required to draw a more definitive conclusion. The role of collagen fibrils in mineralization was tested by removing all the non-collagenous components from the tissue sections with proteolytic enzymes and exposing them to similar mineralization conditions as the control samples. A substantially less amount of minerals were formed in these samples; this correlates well with the hypothesis in the literature that collagen fibrils alone cannot initiate mineral formation.

Keywords: In vitro model system
biomineralization
periodontal ligament
hydroxyapatite
Advisor: Sone, Eli D.
Non-invasive Assessment of Pulmonary Wave Reflection Using Phase Contrast Magnetic Resonance Imaging

Pulmonary arterial hypertension (PAH) alters pulmonary hemodynamics by changing the vascular wall mechanics. Currently, pulmonary vascular resistance is used clinically to assess the disease. However, the invasive nature of pressure measurements, needed for calculating the resistance, prevents longitudinal monitoring of patients during therapy. This work employs wave reflection as an alternative measure of the downstream stiffness and proposes a new method for wave reflection assessment using only non-invasive phase contrast magnetic resonance (PCMR) flow data. The feasibility of the proposed method was investigated in a numerical model of blood flow in the right pulmonary artery. Furthermore, it was validated experimentally using a flow phantom and compared with an existing invasive technique. Finally, the feasibility of the method was tested in a study of the right pulmonary artery of a volunteer. This approach may provide a non-invasive method to evaluate PAH and its response to therapy.

Keywords: Cardiovascular Imaging
Magnetic Resonance Imaging
Pulmonary Arterial Hypertension
Advisor: Macgowan, Christopher K.
Why Are You “Active”? -Voices of Young Muslim Women Post-9/11

Contributing to the literature on the Muslim experience post-9/11, the purpose of this study was to engage with a group that is often talked about, but not with: Muslim youth. Using an integrative anti-racist and anti-colonial approach with an emphasis on a spiritual way of knowing, this study gives voice to young Muslim activists in Toronto who have made the choice to “do something”. The study aims to understand what motivates these young activists, particularly in the context of post-9/11 Islamophobia, with the goal being to challenge stereotypical perceptions of Muslims, while contributing to the body of knowledge that aims to disrupt dominant notions of what “Canadian” identity is. The following analysis helps answer this question, which includes the role of spirituality, the attachment to Canadian identity and the desire to educate. Key challenges and what these youth prescribe for Canada’s future are also discussed.

Keywords: Muslim youth
post 9/11 Canada
Islamophobia
Muslim youth activism
spirituality and education
anti-racism
identity
Islam
Advisor: Wane, Njoki
Zine, Jasmin
The Role of Bacteriophage Lambda gpK in Tail Assembly and Host Cell Entry

The bacteriophage lambda tail protein gpK is required for tail assembly. The activity of the protein can be found at the assembling tail tip and is believed to be localized to this structure. GpK is a 27 kDa protein that has sequence identity to two families of proteins: the Mov34 family of peptidases and the NlpC/P60 family of peptidoglycan endopeptidases. Point substitutions and complementation data confirm that gpK possesses each of these domains and that they can function in trans. When the Mov34 domain is inactivated tail assembly is disrupted whereas when the NlpC/P60 domain is inactivated tails assemble but are inactive. Evidence is presented here that the C-terminal domain possesses lytic activity in isolation but not when part of the full-length protein.

Keywords: bacteriophage lambda
gpK
NlpC/P60
tail assembly
Advisor: Davidson, Alan R.
Edwards, Aled M.
The Temporal Trends of Contaminants in Lake Erie Fish Communities

The Great Lakes has been impaired by elevated concentrations of contaminants, and different regulatory actions are taken to decrease theses concentrations. Recent research of Dr. Azim suggests a decline in mercury levels in the Lake Erie, and an increase in the Hg concentration in the fish communities. This research is a follow up study to examine whether the contaminant levels are indeed increasing. In the first chapter we evaluate the temporal trends of polychlorinated biphenyls (PCBs) in Lake Erie fish over the last 30 years by conducting the Exponential and Dynamic Linear Modeling analysis. DLM analysis in the chapter two detects the PCB and Hg contaminant trends in a broader range. There is a high variability in two contaminants trends. These patterns may be because of factors such as fish physiological parameters, and the impact of invasive species. The results of my research will contribute to the Toxics Reduction Strategy.

Keywords: Fish contamination
Lake Erie
PCBs
Hg
Advisor: Arhonditsis, George
Life-cycle Cost Evaluation of Building Envelope Energy Retrofits

Improving the energy efficiency of our existing building stock is attainable by upgrading the building envelope through carrying out various retrofit measures. The objective of this thesis is to evaluate the life-cycle cost implications of energy retrofits for existing buildings. Measures examined include improving insulation and air-tightness with overcladding strategies. The life-cycle costs of the upgrades are determined for an existing building and compared with model energy performance. A life-cycle cost evaluation for the building envelope upgrades is provided, together with the payback period and the projected return on investment (ROI) for two energy escalation rate scenarios. A costbenefit matrix for various over-cladding strategies is provided to facilitate the evaluation of each option. Further, this thesis presents a simplified ROI algorithm to enable owners, architects and engineers to evaluate the cost-benefit of their building envelope retrofit options.

Keywords: Building Envelope
Energy efficiency
Advisor: Pressnail, Kim D.