VictorJuiz/thesis huggingface dataset:
Mapping Specificity Profiles and Protein Interaction Networks for Peptide Recognition Modules

Protein-protein interactions are of vital importance to the cell as they mediate the assembly of protein complexes that carry out diverse biological functions. Many proteins involved in cellular signaling are built by the combinatorial use of peptide recognition modules (PRMs), which are small protein domains that bind to their cognate ligands by recognizing short linear peptide motifs. Thousands of PRMs are found in nature, requiring improved methods to better elucidate their molecular determinants of binding and to allow accurate mapping of their interaction networks. In this thesis, I describe the development and application of phage-displayed peptide libraries to map the binding specificities of two common PRMs. First, I generated specificity profiles for 82 C. elegans and human PDZ domains that could be organized into a specificity map. The map revealed that PDZ domains have far greater substrate sequence specificity than previously believed, providing significant insights into the relationships between PDZ structure and specificity, and allowing specificity prediction for uncharacterized domains. My results were used to predict both endogenous and pathogenic PDZ interactions. This analysis revealed that viruses have evolved ligands that specifically mimic PDZ domains to subvert host cell immunity. Second, I analyzed the binding specificity for the SH3 domain family in S. cerevisae. I found that, like PDZ domains, SH3 domains have binding specificities that are more detailed than the conventional classification system. The phage-derived specificity profiles were combined with data from oriented peptide and yeast two-hybrid screening to generate a highly accurate SH3 domain interaction network. Given the prominent role of SH3 domains in endocytosis, the SH3 domain interaction data was used to predict the dynamic localization of several uncharacterized endocytosis proteins, which was subsequently confirmed by cell-based assays. The application of the techniques described here to other PRM families will significantly improve protein interaction maps for signaling pathways, which will illuminate our understanding of the cell circuitry, allow the use of PRMs as general affinity reagent and detection tools, and guide the development of small molecule inhibitors that mimic their peptide ligands for therapeutic intervention.

Keywords: Phage display
Protein domain
Protein interaction network
PDZ domain
SH3 domain
endocytosis
Advisor: Boone, Charles
Option Pricing using Fourier Space Time-stepping Framework

This thesis develops a generic framework based on the Fourier transform for pricing and hedging of various options in equity, commodity, currency, and insurance markets. The pricing problem can be reduced to solving a partial integro-differential equation (PIDE). The Fourier Space Time-stepping (FST) framework developed in this thesis circumvents the problems associated with the existing finite difference methods by utilizing the Fourier transform to solve the PIDE. The FST framework-based methods are generic, highly efficient and rapidly convergent. The Fourier transform can be applied to the pricing PIDE to obtain a linear system of ordinary differential equations that can be solved explicitly. Solving the PIDE in Fourier space allows for the integral term to be handled efficiently and avoids the asymmetrical treatment of diffusion and integral terms, common in the finite difference schemes found in the literature. For path-independent options, prices can be obtained for a range of stock prices in one iteration of the algorithm. For exotic, path-dependent options, a time-stepping methodology is developed to handle barriers, free boundaries, and exercise policies. The thesis includes applications of the FST framework-based methods to a wide range of option pricing problems. Pricing of single- and multi-asset, European and path-dependent options under independent-increment exponential Levy stock price models, common in equity and insurance markets, can be done efficiently via the cornerstone FST method. Mean-reverting Levy spot price models, common in commodity markets, are handled by introducing a frequency transformation, which can be readily computed via scaling of the option value function. Generating stochastic volatility, to match the long-term equity options market data, and stochastic skew, observed in currency markets, is addressed by introducing a non-stationary extension of multi-dimensional Levy processes using regime-switching. Finally, codependent jumps in multi-asset models are introduced through copulas. The FST methods are computationally efficient, running in O(MN^d log_2 N) time with M time steps and N space points in each dimension on a d-dimensional grid. The methods achieve second-order convergence in space; for American options, a penalty method is used to attain second-order convergence in time. Furthermore, graphics processing units are utilized to further reduce the computational time of FST methods.

Keywords: option pricing
Fourier Space Time-stepping
partial integro-differential equation
fast Fourier transform
Advisor: Jackson, Kenneth
Jaimungal, Sebastian
Crosstalk between Insulin and Wnt Signaling Pathways

Type II diabetes and hyperinsulinemia are associated with increased risks of developing colorectal cancer (CRC). Detailed mechanisms underlying this correlation, however, are yet to be explored. The present study demonstrates that insulin increases the expression of proto-oncogenes c-Myc and cyclin D1 via both translational and transcriptional mechanisms. We show here that insulin stimulates c-Myc gene translation via an Akt/PKB-dependent mechanism involving the mTOR signaling pathway. More importantly, we show for the first time that transcriptional stimulation of c-Myc and cyclin D1 expression by insulin involves a novel Akt/PKB-independent signal crosstalk between insulin and canonical Wnt signaling pathways. We then identified p21-activated protein kianse 1 (PAK-1) as a novel mediator for insulin and Wnt/beta-catenin (b-cat) molecular crosstalk, involving MEK/ERK signaling. Furthermore, we found that insulin treatment leads to increased b-cat phosphorylation at Ser675, and this is associated with increased b-cat nuclear content and increased b-cat interaction with Tcf/Lef-binding elements (TBEs) of the human c-Myc gene promoter. Lastly, we demonstrated that insulin signaling directly alters the expression levels of components of the Wnt signaling pathway, including fizzled homology 4 (Fdz-4) and TCF7L2 (=TCF-4). This study not only demonstrated the existence of signaling crosstalk between insulin and canonical Wnt signaling pathways at multiple levels, it reveals molecular mechanisms for observed correlation between CRC and hyperinsulinemia. The growing evidence implicating PAK-1 in various human tumorigenesis has emerged PAK-1 as a potential therapeutic target. Our discovery of PAK-1 functioning as a novel central mediator for insulin and Wnt signaling crosstalk in intestinal cells suggests that PAK-1 may potentially be a good target candidate for treating patients with CRC, especially those who have Type II diabetes or experience hyperinsulinemia.

Keywords: colorectal cancer
Type 2 Diabetes
beta-catenin
insulin
Advisor: Jin, Tianru
The Tie2 RTK: Regulation and Downstream Signaling

Tie2 is a receptor tyrosine kinase (RTK) involved in numerous aspects of both normal and pathological angiogenesis. Proper functioning of this receptor is essential for normal development of the vasculature in the embryo as well as vessel maintenance and at sites of active angiogenesis in the adult. A growing list of pathological states has been attributed to a disruption of the angiogenic ‘balance’ including psoriasis, arthritis, atherosclerosis and diabetic retinopathy. Elucidating the molecular mechanisms behind this important biological process will provide insight into the various molecules involved as well as provide potential targets for novel angiogenic therapies. In an attempt to better understand the signaling pathways downstream of the Tie2 receptor we have studied tyrosine residues on the receptor believed to play an important role in Tie2 function. Of these, we have identified Y1111 as a negative regulatory site on Tie2. Mutation of this site affects receptor phosphorylation and kinase activity. Furthermore, protease digestion studies indicate that mutation of Y1111 may alter receptor conformation and potentially relieve negative inhibition imparted by the C-tail of Tie2. As well, we examined potential Tie2 downstream binding partners, specifically the novel Grb7 family of proteins. This work describes for the first time tyrosine phosphorylation of Grb14, an adaptor molecule previously shown to bind Tie2 in vitro. Moreover, our data suggests a role for this adaptor in Tie2 signal transduction involving two tyrosine residues in the receptor C-terminal tail; Y1100 and Y1106. These studies provide important insight into both signal transduction downstream of Tie2 as well as help us understand some of the molecular mechanisms behind the intrinsic ability of this RTK to regulate its own activity.

Keywords: Tie2
signal transduction
Advisor: Dumont, Daniel Joseph
Stem Cells of the Neural and Pancreatic Lineages

In this thesis, I describe studies identifying and characterizing two putative stem cell populations of the neural and pancreatic lineages. The mechanisms governing the emergence of the earliest mammalian neural cells during development and the ontogeny of neural stem cells remain incompletely characterized. A default mechanism has been suggested to underlie neural fate acquisition, however an instructive process has also been proposed. I utilized mouse ES cells to explore the fundamental issue of how an uncommitted, pluripotent mammalian cell will self-organize in the absence of extrinsic signals, and what cellular fate will result. Individual ES cells were found to rapidly transition directly into neural cells by a default mechanism, a process shown to be independent of suggested instructive factors. Further, I provide evidence that the default neural identity is that of a primitive neural stem cell, the earliest identified stem cell of the neural lineage. The exiguous conditions used to reveal the default state were found to present primitive neural stem cells with a survival challenge, which could be mitigated by survival factors or genetic interference with apoptosis. I also report the clonal identification of multipotent precursor cells, PMPs, from the adult mouse and human pancreas. These cells proliferate in vitro to form clonal colonies and display both pancreatic and neural cell multipotentiality. Importantly, the newly generated beta cells demonstrate glucose-dependent calcium responsiveness and regulated insulin release. PMP colonies do not express markers of embryonic stem cells, nor genes suggestive of mesodermal or neural crest origins. Moreover, genetic lineage-labeling experiments excluded the neural crest, and established the embryonic pancreatic lineage, as the developmental source of PMPs. The PMP cell was further found to express insulin in vivo, and insulin+ stem cells were shown to contribute to multiple pancreatic and neural cell populations in vivo. These findings demonstrate that the adult mammalian pancreas contains a population of insulin+ multipotent stem cells, capable of contributing to the pancreatic and neural lineages. In the final section of this thesis, I consider the relationships between neural and pancreatic tissues, as well as discussing the relevance of these two novel stem cell populations.

Keywords: stem cells
pancreas
neural
diabetes
brain
PMPs
Advisor: Kooy, Derek van der
Disruption of Epigenetic Regulatory Elements and Chromosomal Alterations in Patients with Beckwith-Wiedemann Syndrome

Genomic imprinting refers to the parent-of-origin specific monoallelic expression of a gene. Imprinted genes are often clustered in the genome and their expression is regulated by an imprinting centre (IC). ICs are regions of DNA that propagate the parental specific regulation of gene expression, which are usually characterized by differential DNA methylation, histone marks and the presence of non-coding RNAs. Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome associated with the dysregulation of imprinted gene expression on human chromosome band 11p15.5. The 11p15.5 imprinted region has two imprinting centres, IC1 and IC2. IC1 is telomeric and regulates the imprinted expression of the genes H19 and IGF2. IC2 is ~700kb centromeric and is associated with a cluster of nine imprinted genes including CDKN1C, KCNQ1 and an imprinted non-coding RNA associated with IC2, KCNQ1OT1. Loss of differential DNA methylation at IC2 is seen in 50% of patients with BWS with loss of imprint of the non-coding RNA KCNQ1OT1 and associated with a decreased expression of the putative tumour suppressor CDKN1C. Patients with BWS also have a thousand-fold increased risk of pediatric cancer. The focus of this thesis involves investigation of dysregulation of imprinting in three groups of BWS patients. Firstly, I show that BWS patients with alveolar rhabdomyosarcoma have constitutional loss of methylation at IC2 and biallelic expression of KCNQ1OT1. Secondly, loss of methylation at IC2 has been previously associated with female monozygotic twins discordant for BWS. In male monozygotic twins with BWS, however, the molecular lesions reflect the molecular heterogeneity seen in BWS singletons. Thirdly, BWS patients associated with translocations and inversions that have breakpoints within the KCNQ1 gene near IC2 show regional gain of DNA methylation around the breakpoint and decreased expression of CDKN1C. Therefore, using a rare collection of BWS patients, I have attempted to determine the various roles of the imprinting centres IC1 and IC2 and their involvement in tumourigenesis, monozygotic twinning and structural chromosomal rearrangements causing BWS.

Keywords: Genomic Imprinting
Epigenetics
Beckwith-Wiedemann syndrome
DNA Methylation
Cytogenetics
Rhabdomyosarcoma
Monozygotic Twins
Advisor: Weksberg, Rosanna
Undoing Wit: A Critical Exploration of Performance and Medical Education in the Knowledge Economy

Over the past decade, there has been a turn in applied health research towards the use of performance as a tool for knowledge translation. The turn to performance in applied health sciences has emerged as researchers have struggled to find new and engaging ways to communicate complex research findings regarding the human condition. However, the turn to performance has occurred within the political landscape of the knowledge economy, and thus conforms to contemporary practices of knowledge production and evaluation. Recent studies about health-based performances exhibit two hallmarks of economized modes of knowledge production. First, these studies focus their attention on the transmission of knowledge to health care professionals through an exposure to performance. Knowledgeable, and thus more useful or efficient, health care providers are the end-product of this transaction. Second, many of these productions are created in the context of application, and thus are driven by an accountability and goals-oriented approach to knowledge acquisition. This thesis argues that economized and rationalized modes of knowledge production do great harm to performance’s pedagogical and ethical potential. By utilizing scientific evaluative methodologies to monitor performance’s ‘success’ as an evaluable, predictable and ends-oriented practice obscures performance’s libratory value, and thus misses performance’s potentially most potent and critical contributions. To mount this argument, I present a case study of Margaret Edson’s play Wit, which has been used widely in medical education. Drawing from the philosophy of Emmanuel Levinas, I critically explore the impact of the knowledge economy on arts-based pedagogical models within health research and education. Further, I seek to redress potential harms inflicted by the knowledge economy by developing the notion of ethical “response-ability.” Through this concept I argue that performance challenges normative conceptions of reason, rationality and scientific evaluation, making the use of theatre in contemporary educational settings at once troublesome and vital.

Keywords: medical education
knowledge economy
performance
ethics
Advisor: Robertson, Ann
Priority Setting for Expensive Biopharmaceuticals: An Analysis of Six Drug Case Studies

Priority setting for expensive biopharmaceuticals is one of the most important challenges for publicly funded health systems. One of the drivers of rising healthcare expenditures is pharmaceuticals (i.e., drugs). Moreover, people are living longer and their expectation of, and demand for, health care, drugs, and services are continually increasing. The overall aim of this research was to describe and evaluate reimbursement decisions for six expensive biopharmaceuticals across five countries in order to ascertain if the processes were legitimate and fair. I conducted qualitative case studies of six expensive biopharmaceuticals in order to describe and evaluate the priority setting activities of eight committees across five countries, including Canada, England and Wales, Australia, Israel and the United States. Data sources included: 1) 32 documents and 2) 56 interviews with informants. The recommendations process of each committee partially met the four conditions of ‘accountability for reasonableness’. My main finding is that, while a number of values were considered by committees when making reimbursement decisions, committees tended to focus on values of evidence, effectiveness and efficiency, but not the full range of relevant values. Thus, these contexts did not fully meet the conditions of legitimacy and fairness. I have provided an in-depth description of the eight committees’ priority setting activities regarding the study drugs, as well as committee members’, patients’ and industry representatives’ views regarding the process. I developed practical guidance for leaders for improving reimbursement decisions for expensive biopharmaceuticals, the implementation of which would enhance the fairness and legitimacy of priority setting. This study has demonstrated that in order to create a fair and legitimate drug reimbursement process, we need to ensure the incorporation of a wide range of values, and the involvement of multiple stakeholder groups within the deliberative and appeals/revisions processes.

Keywords: Priority Setting
Decision making
Accountability for reasonableness
Case studies
Advisor: Martin, Douglas K.
Development and Refinement of New Products from Multi-angle Remote Sensing to Improve Leaf Area Index Retrieval

Remote sensing provides methods to infer vegetation information over large areas at a variety of spatial and temporal resolutions that is of great use for terrestrial carbon cycle modeling. Understory vegetation and foliage clumping in forests present a challenge for accurate estimates of vegetation structural information. Multi-angle remote sensing was used to derive and refine new information about the vegetation structure for the purpose of improving global leaf area index mapping. A field experiment with multi-angle, high resolution airborne observations over modified and natural backgrounds (understory, moss, litter, soil) was conducted in 2007 near Sudbury, Ontario to test a methodology for the background reflectivity retrieval. The experiment showed that it is feasible to retrieve the background information, especially over the crucial low to intermediate canopy density range where the effect of the understory vegetation is the largest. The tested methodology was then applied to background reflectivity mapping over conterminous United States, Canada, Mexico, and Caribbean land mass using space-borne Multi-angle Imaging SpectroRadiometer (MISR) data. Important seasonal development of the forest background vegetation was observed across a wide longitudinal and latitudinal span of the study area. The previous first ever global mapping of the vegetation clumping index with a limited eight-month multi-angular POLDER 1 dataset was expanded by integrating new, complete year-round observations from POLDER 3. A simple topographic compensation function was devised to correct negative bias in the data set cause by topographic effects. The clumping index reductions can reach up to 30% from the topographically non-compensated values, depending on terrain complexity and land cover type. The new global clumping index map is compared with an assembled set of field measurements, covering four continents and diverse biomes. Finally, inclusion of the new vegetation structural information, including background reflectivity and clumping index, gained from the multi-angle remote sensing was then shown to improve the performance of LAI retrieval algorithms over forests.

Keywords: LAI
multi-angle remote sensing
Advisor: Chen, Jing Ming
Molecular Mechanisms Regulating Embryonic Cerebral Cortex Development

Cerebral cortex development is a complex process that integrates both extrinsic and intrinsic mechanisms. The surrounding cellular environment triggers receptor activation, which in turn initiates components of different signalling cascades and subsequently gene transcription, influencing cell survival, proliferation, and differentiation. Genetic mutations causing a loss-of-function or gain-of-function of signalling pathways elements can lead to cortical abnormalities and result in cognitive dysfunctions. In this thesis, I examined the receptor tyrosine kinase (RTK) TrkB and TrkC, the small GTPase Ras, and the C/EBP family of transcription factors, investigating their roles during cerebral cortex development. First, I looked at the role of C/EBPs during cortical cell fate determination. I determined that inhibition of C/EBPs decrease neurogenesis, keeping precursors in an undifferentiated state and later promoting their differentiation into astrocytes, while expression of an activated form of C/EBP promoted neurogenesis and reduced astrogenesis. Moreover, the inhibition of MEK, a mediator of C/EBPβ phosphorylation, also caused a decrease in neurogenesis. Thus, activation of the MEK-C/EBP pathway biases precursor cells to become neurons rather than astrocytes, thereby acting as a differentiation switch. Second, I examined the involvement of Trk signalling during cortical development. I showed that genetic knockdown using shRNA, or inhibition using dominant negative of TrkB and TrkC lead to a decrease in proliferation and later to postnatal precursor cells depletion. Moreover, it caused a reduction in number of neurons combined with mislocalization of the generated neurons to the different cortical layers. Thus, Trk signalling plays an essential role in the regulation of cortical precursor cell proliferation and differentiation during embryonic development. Third, I elucidated the effect of Costello syndrome H-Ras mutations during cerebral cortex formation. I determined that these mutations promoted cell proliferation and astrogenesis, while reducing neurogenesis. Together, these data support a model where proper Trks/Ras/MEK/C/EBP signalling is essential for normal genesis of neurons and astrocytes and show that cortical development perturbations can ultimately lead to cognitive dysfunction as seen in Costello syndrome patients.

Keywords: cerebral cortex development
cellular differentiation
in utero electroporation
cortical precursors
Advisor: Miller, Freda