VictorJuiz/thesis huggingface dataset:
Hedgehog Signaling Modulates Cholesterol Homeostasis in Chondrocytes and in Osteoarthritis

Osteoarthritis (OA) is a common degenerative disease of the joint that is characterized by degradation and calcification of articular cartilage, and subchondral bone changes. Hedgehog (Hh) signaling is known to be activated in human and murine OA. Since Hh signaling regulates Gli-mediated gene expression, we identified Hh target genes that are expressed in chondrocytes. Microarray analyses were performed to detect changes in gene expression when the Hh pathway was modulated in human OA cartilage samples. Results from the Affymetrix Human Gene 1.0 ST microarray were analyzed for differentially expressed genes from three patient samples. Using Ingenuity® Pathway analysis, several genes known to be involved in sterol homeostasis were found to be modulated with Hh inhibition. We hypothesized that Hh signaling regulates cholesterol biosynthesis in chondrocytes, and that modulating cholesterol homeostasis impacts the severity of OA. To investigate the function of cholesterol in the cartilage, mice with chondrocyte-specific cholesterol accumulation were generated. This was achieved by excising Insig1 and Insig2, major negative regulators of cholesterol homeostasis. Over time, mice with chondrocyte-specific cholesterol accumulation exhibited impaired growth of the long bones. With aging or surgically induced joint instability, these mice developed more severe OA than control littermates. They expressed typical OA markers, such as type X collagen, indicating chondrocyte hypertrophy in the articular cartilage. Genetic manipulation of Hh signaling in these mice suggests that Hh signaling is modulating the phenotype by regulating sterol homeostasis. Hh reduction and statin treatment both lowered cholesterol production and rescued the phenotype, reducing the severity of OA. Here we identified novel Hh target genes in chondrocytes which regulate intracellular cholesterol levels, and found that cholesterol dysregulation in the chondrocytes predisposes to OA. These data suggest that pharmacologic correction of intra-articular sterol imbalance can be used as a treatment for osteoarthritis.

Keywords: cartilage
cholesterol
Hedgehog signaling
microarray
osteoarthritis
statin
Advisor: Alman, Benjamin A
The Fundamental Roles of the Tissue Inhibitor of Metalloproteinase Family in Mammalian Biology

The metalloproteinases are a family of extracellular proteases responsible for degrading components of the extracellular matrix as well as shedding growth factors, cytokines and their receptors from cell surfaces, impacting signaling, tissue remodeling and homeostasis. The four mammalian tissue inhibitors of metalloproteinases (TIMP1-4) regulate metalloproteinase activity in the tissues. While the TIMPs exhibit some target specificity, functional redundancy exists due to overlapping expression patterns and shared proteinase targets. It is known that the TIMP-metalloproteinase network influences a vast spectrum of biological process and is implicated in most human diseases. Despite this, the fundamental roles of the TIMP family in mammalian development remained unidentified. This thesis describes the generation and characterization of quadruple knockout TIMPless mice deficient for

Keywords: chondrocyte
CXCL12
IHH
metalloproteinase
skeleton
TIMP
Advisor: Khokha, Rama
Polarized Light Imaging for Assessment of Anisotropy in Turbid Media: Instrumentation and Application in Urology

Assessment of anisotropy has many applications in tissue engineering and early detection of disease such as cancer or stroke. One of the emerging optical technologies for quantifying anisotropy in biological tissues is polarized light imaging. In this technique, the full Mueller matrix of the tissue is measured and then decomposed to yield optical retardance, which is proportional to the tissue anisotropy. The theory of polarized light imaging, its biomedical application and instrumentation are the subject of this thesis. To retrieve more information from the Mueller matrix, a quantitative analysis of generic turbid media's Mueller matrices beyond their decompositions was proposed. Two new metrics based on Mueller matrix were established in this thesis: 1) Tissue depolarization, calculated from the Mueller matrix, can be used to estimate its optical properties, and 2) Symmetry of the off-diagonal elements of a turbid medium's Mueller matrix can be used to detect the axial heterogeneity of anisotropy. Polarized light imaging, followed by Mueller matrix decomposition, was then successfully applied to locate the structural disorders induced by bladder outlet obstruction disease, in ex vivo functioning rat bladders. Motivated by the result of this study and to enable in vivo polarized light measurements of the bladder, a novel thin fiber based polarimetric probe which can measure the full Mueller matrix of the turbid media was suggested. Finally, to enhance the speed of the ex vivo examinations of biological tissues and avoid artifacts, a new rapid benchtop polarized light imaging system based on photoelastic modulators (PEM) and a charge-coupled device (CCD) was proposed and implemented. The demonstrated scheme does not involve using mechanically moving components and thus reduces systematic errors. This imaging system proved to be the fastest high resolution polarimetric characterization tool for imaging turbid media to date.

Keywords: anisotropy
bladder
imaging
polarization
turbid media
Advisor: Vitkin, Alex
Surface Enhanced Raman Scattering Nanoparticles as Optical Labels for Imaging Cell Surface Proteins

Assaying the expression of cell surface proteins has widespread application for characterizing cell type, developmental stage, and monitoring disease transformation. Immunophenotyping is conducted by treating cells with labelled targeting moieties that have high affinity for relevant surface protein(s). The sensitivity and specificity of immunophenotyping is defined by the choice of contrast agent and therefore, the number of resolvable signals that can be used to simultaneously label cells. Narrow band width surface-enhanced Raman scattering (SERS) nanoparticles are proposed as optical labels for multiplexed immunophenotying. Two types of surface coatings were investigated to passivate the gold nanoparticles, incorporate SERS functionality, and to facilitate attachment of targeting antibodies. Thiolated poly(ethylene glycol) forms dative bonds with the gold surface and is compatible with multiple physisorbed Raman-active reporter molecules. Ternary lipid bilayers are used to encapsulate the gold nanoparticles particles, and incorporate three different classes of Raman reporters. TEM, UV-Visible absorbance spectroscopy, DLS, and electrophoretic light scattering were used characterize the particle coating. Colourimetric protein assay, and secondary antibody labelling were used to quantify the antibody conjugation. Three different

Advisor: Walker, Gilbert C
The Role of Transcription Factor 7-Like 2 in Hepatic Glucose Metabolism

Transcription factor 7-like 2 (TCF7L2) is a principal downstream transcription factor that mediates the function of the developmental canonical Wnt signaling pathway. When partnered with -catenin, TCF7L2 stimulates Wnt target gene expression and mediates certain effects of other signaling cascades such as cAMP and insulin in cell type-specific manners. Recent genome-wide association studies have reproducibly revealed that common single nucleotide polymorphisms in TCF7L2 have the strongest genetic association with type 2 diabetes risk in a multitude of ethnic backgrounds. Following this hallmark discovery in 2006, the role of TCF7L2 in regulating metabolism and glucose homeostasis has been intensely investigated. Recent studies have shown that TCF7L2 regulates pancreatic -cell function and survival as well as the production and function of the incretin hormone glucagon-like peptide-1 (GLP-1). As human carriers of TCF7L2 diabetes risk polymorphisms also exhibited increased hepatic glucose production, we aimed to determine the role of TCF7L2 in hepatic glucose metabolism. We revealed that hepatic TCF7L2 expression is regulated by nutrient availability as feeding increased TCF7L2 levels in mouse livers while insulin treatment stimulated TCF7L2 expression in hepatic cell lines. Treatment of hepatocytes with the Wnt ligand Wnt-3a decreased, while TCF7L2 knockdown increased gluconeogenic gene expression and glucose production, suggesting that TCF7L2 and Wnt signaling repress gluconeogenesis. To further examine the

Keywords: Gluconeogenesis
Glucose production
Liver
TCF7L2
Wnt signaling
Advisor: Jin, Tianru
Characterization of Protein Tyrosine Kinase 7 (Ptk7) in Development and Disease

Protein Tyrosine Kinase 7 (Ptk7) is a transmembrane pseudokinase implicated in Wnt signal transduction during embryonic development and in cancer. Ptk7 is a known regulator of mammalian neural tube closure and Xenopus convergence extension (C) movements; however, conflicting reports have indicated both positive and negative roles for Ptk7 in both non-canonical Wnt/PCP and canonical Wnt/beta-catenin signaling pathways. To clarify the function of Ptk7 in vertebrate embryonic patterning and morphogenesis, I generated maternal-zygotic (MZ) ptk7 mutant zebrafish and found that early loss of zebrafish Ptk7 leads to defects in axial C, neural tube morphogenesis, and planar cell polarity (PCP). MZptk7 mutant embryos establish normal Wnt-dependent dorsoventral patterning at the onset of gastrulation; however, post-gastrulation MZptk7 mutant embryos display significant up-regulation of beta-catenin target gene expression. MZptk7 mutants show expansion of the mesodermal compartment within the tail bud, suggesting an important role for Ptk7 in regulating Wnt/beta-catenin-dependent cell fate specification. Furthermore, a plasma membrane-tethered Ptk7 extracellular fragment is sufficient to rescue both PCP morphogenesis and Wnt/beta-catenin patterning defects in MZptk7 mutant embryos, indicating that the extracellular domain of Ptk7 acts as an important regulator of both non-canonical Wnt/PCP and canonical Wnt/beta-catenin signaling in multiple developmental contexts. Zygotic ptk7 mutant zebrafish display no obvious embryological defects and develop to adulthood; however, as juveniles these fish develop severe spinal curvatures analogous to human idiopathic scoliosis (IS). Scoliosis is a complex genetic disorder, characterized by three-dimensional rotations of the spine associated with underlying vertebral malformations (congenital scoliosis, CS) or with no identifiable underlying abnormalities (idiopathic scoliosis, IS). Vertebral abnormalities are not associated with spinal curvature in zygotic ptk7 mutant zebrafish; however, MZptk7 mutants display vertebral malformations analogous to those found in humans with congenital scoliosis (CS). These defects are linked to abnormalities in embryonic segmentation, suggesting an important role for maternal ptk7 in axial patterning. Therefore, MZptk7 and zygotic ptk7 mutant zebrafish represent novel models of CS and IS (respectively) and suggest that both types of deformity share genetic mechanisms that relate to altered Wnt signal transduction.

Keywords: disease modelling
embryogenesis
scoliosis
zebrafish
Advisor: Ciruna, Brian
TIMPs in Mammary Stem Cell Homeostasis and Breast Cancer Progression

The mammary gland repeatedly undergoes reorganization and cellular turnover in the adult female. Ductal invasion and branching morphogenesis during puberty, cyclical expansion during reproductive cycles, functional differentiation following pregnancy and long-term maintenance of the ductal tree all require mammary stem cell activity. Through the shedding of signaling molecules and turnover of structural matrix proteins many of these remodeling processes are regulated by metalloproteinases and their inhibitors, the TIMPs (tissue inhibitors of metalloproteinases). Here I report on the role of TIMPs during mature mammary gland homeostasis and breast cancer progression. Across individual and compound

Keywords: aging
breast cancer
mammary gland
mammary stem cell
stem cell
TIMP
Advisor: Khokha, Rama
Union Strategies and Potential Targets for New-Member Organizing in the United States

This dissertation focuses on attempts by labor unions in the United States to prioritize new-member organizing as a means of reversing the decline in union density. In three papers, I look at strategic organizing efforts and opportunities at three distinct levels of analysis: the federation level, the national and local-union levels, and the level of the individual potential member. In the first paper, I look at efforts by seven unions that split from the AFL-CIO in 2005 to form a new union federation, Change to Win. I estimate the effect of Change to Win policies on whether the union won the certification election and the number and percentage of workers successfully organized, using data from the National Labor Relations Board and the National Mediation Board from September 2000 through September 2010 and a difference-in-difference estimator. The results indicate no statistically significant difference in organizing success, following Change to Win's formation and implementation of new organizing strategies and practices, relative to the AFL-CIO. The second paper of my dissertation analyzes recent attempts to organize the growing number of professional workers into historically blue-collar unions using a combination of data from the National Labor Relations Board and data from a national survey that I designed and administered to national and local unions throughout the country. Using a series of interactions, I test whether the effect of key strategies and tactics differ across professional-worker status. My results show that the effect of some typical union and employer strategies and characteristics does differ for professionals versus nonprofessionals. Finally, the third paper examines youth attitudes towards unions, since young workers are underrepresented in union membership. I examine how youth attitudes towards unions have changed over time using a generational approach and data from the 1976-2010 nationally representative Monitoring the Future survey of twelfth graders. I find that beginning with the Baby Boomers, each generation (i.e., Gen X and Gen Y) has had more favorable attitudes towards unions than the previous generation. Furthermore, I find that the antecedents of youth attitudes towards unions, including work values, socio-political beliefs, background, and employment history and expectations, have changed over each generation.

Advisor: Gunderson, Morley
Understanding the Unwritten Rules: Examining the use of Ontario Parliamentary Convention to Guide the Conduct of Elected Officials in Ontario

Government ethics legislation in Canada guides and restricts the conduct of parliamentarians. Ontario established an independent officer of the legislature in 1988 who is responsible for administering its government ethics legislation. In 1994, an undefined behaviour-guiding standard called “Ontario parliamentary convention” was added to the legislation. This paper explores the history of Ontario’s government ethics regime and examines its response to specific scandals, in order to describe the emergence of Ontario parliamentary convention as a standard of conduct. It then provides a full discussion and complementary summary of the specific parliamentary conventions that Ontario’s legislative ethics officers have determined must guide the conduct of Ontario’s parliamentarians. This discussion and summary illuminate the problematic and inconsistent use of this standard by Ontario’s legislative ethics officers. Two sets of recommendations are then offered to help modernize and strengthen the legislation for the benefit of Ontario’s parliamentarians.

Keywords: Accountability
Conflict of Interest
Ethics
Government
Integrity
Transparency
Advisor: Stern, Simon
Licence to Spill? Developing a Framework for International Liability and Compensation for Transboundary Pollution Arising From Offshore Drilling Activities

As new drilling technology enables exploitation of more and more previously inaccessible areas, there is renewed concern over the risk of catastrophic oil spills. Drilling in deeper waters increases the difficulties of remedying a blowout. Thus, there is a greater risk of extensive oil pollution damage. The Montara and Deepwater Horizon incidents illustrate the potential damage that catastrophic oil spills from offshore platforms may cause. Under the no-harm rule, states have an obligation of due diligence to ensure that offshore drilling activities within their jurisdiction do not cause harm to the environment of another state. However, even if a state has exercised its obligation of due diligence under the no-harm rule, a catastrophic oil spill may still occur. Under such circumstances, there is a gap in the law where liability and compensation is concerned. Hence, there is a need for an international civil liability convention for offshore drilling activities.

Keywords: compensation
international law
liability
offshore drilling
oil pollution
polluter-pays principle
Advisor: BrunnĂŠe, Jutta
Judicial and Political Decisions from a Critical Psychology Perspective

Judicial and Political Decisions from a Critical Psychology Perspective Kristine Arnet Connidis Doctor of Juridical Science Faculty of Law University of Toronto 2015 ABSTRACT I examine conflicting judicial and political decisions from the critical psychology perspective of Jung's theory of different psychological functions and corresponding types of conscious viewpoints. I apply that theory as a realistic approach to refining judicial and political processes and the relationship between them. I do so in a thoroughly interdisciplinary way, aiming for accuracy and fullness in both the psychological and the institutional functions. Judicial decision-making can uniquely provide a rational viewpoint of `concrete thinking' (as Jung probingly defined it), guided by an ideal of Justice, well-developed by judges as experts in this task, within court processes designed to facilitate it. Political decision-making (legislative and executive) can uniquely provide a well-developed rational viewpoint of citizens' shared `feeling evaluation' (as Jung defined it), guided by any of a number of ideals, led by politicians, who have resources designed for carrying it out, and who should also practice as experts in their exclusive role. Their two distinct viewpoints (reflecting familiar `hallmarks') are specialized, one-sided, `complementary opposites': Potentially oppositional and inherently complementary, the brilliance of one precisely compensates a blind-spot in the other. An `interplay' (or dialogue) between them on a contested topic enables them to refine each other's viewpoints and together differentiate and extend the overall rational grasp of the topic, in their own decisions and, through them, in the conscious attitudes and actions of the society as a whole. This shifts the perspective on difficult issues in positive and practical ways. It explains the importance of appreciating and refining what is distinct about judicial and political decisions, and about their dialogue. Among its helpful applications are the fresh reinforcements it gives to judicial decision-makers, to develop and apply a reasonable standard of care and skill in political practice, and to political decision-makers, to help make and meet such a standard.

Keywords: C.G. Jung
critical psychology
democracy
judicial decision-making
political decision-making
rational consciousness
Advisor: Nedelsky, Jennifer
Protein Non-Folding: A Molecular Simulation Study of the Structure and Self-Aggregation of Elastin

Elastin is the protein responsible for the elastic recoil of skin, arteries, and lungs. In order to function, elastin, as well as other self-assembling elastomeric proteins, must remain disordered even when aggregated, and must therefore avoid the formation of amyloid fibrils. Elastin undergoes phase separation and self-organization into a fibrillar structure upon increasing temperature. In order to investigate the molecular basis for elastin self-aggregation, we performed extensive atomistic molecular dynamics simulations of both monomers and aggregates. To obtain statistical convergence of average structural properties, it was necessary to use massive sampling in combination with simulated tempering distributed replica sampling. The development and testing of this method is an important contribution of this thesis. The first key finding of this thesis is that the sequences of all known rubber-like elastomeric proteins are separated from amyloidogenic sequences by a threshold in the combined content of proline and glycine. Our results suggest that avoiding the formation of a water-excluding core involving extensive self-interactions is not only a fundamental requirement, but may very well constitute the single most essential design principle of self-assembling elastomeric proteins. The conformational ensemble of an elastin-like aggregate resembles that of a polymer melt. In the aggregate, individual chains retain significant hydration and do not form a water-excluding hydrophobic core, but are also completely entangled with each other and form significant intermolecular interactions. As a result, the overall chain dimensions approach the expected dimensions of chains in an ideal solvent, a state in which chain entropy is maximized. This is the prediction of the Flory theorem for generic polymer chains within a polymer melt, but has never, to our knowledge, been observed before for an aggregate of polypeptide chains in atomistic detail. Finally, we note that our results are not consistent with the current model of elastin self-aggregation, which involves a conformational transition of a monomer towards a more ordered, aggregation-prone state. Instead, we propose a model in which both the hydrophobic effect and the enhanced chain entropy afforded by the interactions with other peptides within the aggregate favour elastin self-aggregation.

Keywords: elastin
molecular dynamics simulations
protein folding
disordered proteins
hydrophobicity
peptides
molecular simulation
biochemistry
Advisor: Pomès, Régis