VictorJuiz/thesis huggingface dataset:
Air-Surface Exchange of Persistent Organic Pollutants in North America

This thesis examines the air-soil and air-water gas exchange of persistent organic pollutants (POPs) with emphasis on organochlorine pesticides (OCPs). The current status of net exchange, factors which influence the exchange process, and different approaches used to estimate the surface exchange were explored. The net exchange of chemicals was evaluated using the fugacity approach, with the aid of chemical tracers (congener profiles of complex mixtures and enantiomer proportions of chiral chemicals) to infer current use vs. legacy sources to the atmosphere. DDT in southern Mexico was undergoing net deposition from air to soil. Occurrence of fresher DDT residues in the south was indicated by a higher proportion of p,p’-DDT relative to p,p’-DDE and racemic o,p’-DDT in air and soils. Congener profiles of toxaphene suggested soil emissions as the source to air. The influence of chemical aging on soil-air exchange and bioaccessibility was studied in a high organic soil. The use of nonexhaustive extraction with hydroxypropyl-beta-cyclodextrin (HPCD) to predict bioaccessibility was optimized for OCPs and polychlorinated biphenyls (PCBs). Reduced volatility of spiked chemicals correlated with reduced HPCD extractability for soil that had been aged under indoor and outdoor conditions for 730 d and infers volatility could be used as a surrogate for bioaccessibility. Measured soil-air partition coefficients (Ksa) were lower than those predicted from the Karickhoff relationship, which considers octanol as a surrogate for soil organic matter. The role of soil moisture, organic carbon, temperature, depth of soil surface horizon and dissolved organic carbon in the fate of organic contaminants in soil were assessed using chemical partitioning space maps. These maps allow instant visual prediction of the phase distribution and transport process of a chemical among the three major phases in soil; i.e., air, water and solid. Net volatilization of alpha-hexachlorocyclohexane from water to air was found in the southern Beaufort Sea using fugacity calculations and flux measurements. The influence of ice cover on volatilization was indicated by a winter-summer shift from racemic to nonracemic alpha-HCH in boundary layer air.

Keywords: persistent organic pollutants
soils
air
enantiomers
Arctic
Mexico
organochlorine pesticides
bioaccessibility
chemical partitioning space
volatiltiy
Advisor: Wania, Frank
Bidleman, Terry F.
Structural and Functional Regulation of the Human Chloride/Proton ClC-5 by ATP and Scaffold NHERF2 Interactions

The chloride/proton antiporter ClC-5 is primarily expressed in the kidney where it aids in re-absorption of proteins from the glomerular filtrate. Functional disruption of ClC-5 causes Dent’s Disease – a renal condition characterized by proteinuria and kidney failure in a third of all cases. The majority of disease-causing mutations translate into premature truncations of the carboxy-terminal (Ct) region of ClC-5 and are predicted to disrupt the protein-protein interactions mediated by this domain. In this thesis, direct ATP binding to the two cystathionine β-synthase (CBS) domains of ClC-5 was demonstrated. ATP binding enhanced the global compactness of the ClC-5 Ct region likely through a clamping motion of the CBS domains around the nucleotide. Along with ATP, the sodium proton exchange regulatory factor 2 (NHERF2) also binds ClC-5; however, the molecular mechanism behind this interaction was unknown as ClC-5 lacked the PDZ binding motif traditionally localized at the Ct end of bait proteins. Here, we also identified a class I PDZ binding motif (657-660; TSII) within the internal sequence of ClC-5. Despite the buried position of this motif in the Ct peptide’s X-ray crystal structure (PDB: 2J9L), the high propensity of this region for dynamic flexibility prompted us to test whether it could mediate NHERF2 interactions. In support of this hypothesis, we demonstrated that the motif is transiently available to interact directly with NHERF2 in vivo and to enable an enhancement in receptor-mediated endocytosis in mammalian cells. Collectively, these results gave further evidence that the intracellular Ct region of ClC-5 serves as a hub to mediate interactions essential for its maturation, stability, and trafficking in renal epithelium, as well as providing further insights into the molecular basis of Dent’s Disease.

Keywords: ClC-5
CBS Domains
ATP Binding Site
NHERF2
SAXS
Thermal Stability
Photoaffinity Labelling
Endocytosis
Internal PDZ Binding Motifs
Advisor: Bear, Christine
Identification and Characterization of Cancer Stem Cells in Mouse Medulloblastoma and Glioma

According to the cancer stem cell hypothesis a subpopulation of cells within a tumour has the capacity to sustain its growth. These cells are termed cancer stem cells, and are most simply defined as the cells within a primary tumour that can self-renew, differentiate and regenerate a phenocopy of that cancer when transplanted in vivo. Cancer stem cells have now been prospectively identified from numerous human tumours and are actively sought in many cancer types, both clinical and experimental. The cancer stem cell hypothesis remains controversial, with evidence both supporting and challenging its existence in human tumours and in animal models of disease. Here we prospectively identify and study brain cancer stem cells in clinically representative mouse models of the medulloblastoma and glioma. Cancer stem cells from both mouse brain tumour types are prospectively enriched by fluorescent activated cell sorting freshly dissociated cells for the surface antigen CD15, display a neural precursor phenotype, exhibit the hallmark stem cell characteristics of self-renewal and multilineage differentiation, and regenerate a phenocopy of the original tumour after orthotopic transplantation. Additionally, novel mouse medulloblastoma and glioma cancer stem cell lines were established and studied in vitro as adherent cultures in the same serum-free media conditions that support the growth of normal neural stem cells. When mouse and human glioma stem cell lines were compared, many novel molecular mediators of the tumour phenotype were identified, as were chemical compounds that selectively inhibit their growth. Our results have important implications regarding the cancer stem cell hypothesis, the mechanisms that drive brain tumour stem cell growth and the therapeutic strategies that may prove effective for the treatment of glioma and medulloblastoma.

Keywords: Medulloblastoma
Glioma
Cancer Stem Cell
Mouse Model
Advisor: Dirks, Peter Benjamin
A Review of Transformational Leadership Research: A Meta-analytic Approach

This research is a meta-analytic review of the effects of transformational school leadership (TSL)-- a systematic, comprehensive synthesis of the quantitative research on transformational school leadership. The review method used in this research is standard meta-analysis supplemented by narrative synthesis and vote-counting methods. The types of effect sizes involved in meta-analytical calculations are correlation coefficients rs. The evidence reviewed was provided exclusively by unpublished theses or dissertations that were completed between 1996 and 2008. This study identified 33 dimensions of transformational leadership as developed by various scholars and captured by a variety of leadership measures, which were synthesized into 11 core leadership dimensions. This study meta-analyzed the effects of transformational school leadership and its dimensions on a large range of school outcomes, including 17 school conditions (e.g., school culture, shared decision-making processes), 23 teacher-related outcomes (e.g., teacher satisfaction), and five types of student outcomes. Transformational school leadership was most influential on teachers’ emotions and inner states. TSL had large effects on teachers’ individual inner states and their practices while it had small effects on their group inner states. Leaders effectively influence teachers’ psychological inner states and practices mainly through modeling good practices themselves, providing support and intellectual stimulation to teachers individually and setting shared school goals. TSL was also very influential on school conditions. It had large effects on four key school conditions. This review detected significant, positive small direct effects of TSL on student achievements. The indirect effects of TSL on student learning vary when different school or teacher variables are controlled. This review identified seven important moderators and three mediators that significantly contributed to student learning along with TSL. Specific leadership practices that effectively influenced school and student outcomes were also examined and discussed. Regarding the moderating effects of contextual and methodological factors, school level and leadership measures were found to moderate leadership impacts significantly in some cases. The findings of this study provide guidance for school administrators and policy makers who want to improve school leadership as a means of improving school quality.

Keywords: School Leadership
Meta-analysis
transformational leadership
review
Advisor: Leithwood, Kenneth
From Elusive Conceptions to Arrested Developments: Leadership for Social Justice

The general question guiding this research is: how do equity minded administrators lead for social justice? The following specific questions are addressed in this study: How have participants become oriented to social justice? How do educational administrators conceptualize leadership for social justice? What are the barriers and supports that participants experienced in leading for social justice in diverse contexts? What are some (participant-identified) examples of how they lead for social justice? From a critical perspective this study examines the experiences of educational administrators leading for social justice. Vital to this examination are analyses of power relations and the locatedness of participants within those relations. At the core of these power relations are participant experiences of social justice as contingent on the interconnectedness between their lived realities and the “doing” of social justice as espoused by and evidenced in their approaches to leadership for social justice. For this study I have interviewed ten administrators from Southern Ontario, who self-identify as being committed to and leading for social justice and have been in formal positions of leadership for at least five years. Interviewees were able to identify and articulate the interconnected experiences of lived realities and their commitments to leadership for social justice; critical examples of social justice praxis; and facets of the educational systems which supported and, conversely, erected barriers to their leading for social justice. Conclusions, implications and recommendations can be broadly organized as issues related to systemic and structural processes, support and accountability for the hiring, retention and promotion of diverse school personnel who have evidenced commitments to social justice, the retraining and retooling of educators and leaders through curriculum centred on social justice, the dramatic restructuring of educational administrative thought by practitioners and researchers, and the critical inclusion of the community, students, parents and trustees in roles that substantively impact the decision making power within the educational system (from the overall governance of the educational system to everyday activities).

Keywords: educational administration
leadership
Advisor: Portelli, John P.
Genomic DNA Copy Number Variations and Cancer: Studies of Li-Fraumeni Syndrome and its Variants

Copy number variations (CNVs) are a major source of inter-individual genetic difference, accounting for a greater proportion of the human genome than other forms of variation. Recently, the identification of benign and pathogenic CNVs has improved due to arrays with increased coverage. Nevertheless, most CNVs have not been studied with great precision and questions persist regarding their exact breakpoint, gene content, frequency and functional impact. This is especially true in cancer, in which a role for CNVs as risk factors is under-explored. Li-Fraumeni syndrome (LFS) is a dominantly inherited disorder with an increased risk of early-onset breast cancer, sarcomas, brain tumors and other neoplasms in individuals harboring germline TP53 mutations. Known genetic determinants of LFS do not fully explain its clinical phenotype. In this thesis we describe the association between CNVs and LFS. First, by examining DNA from a healthy population and an LFS cohort using oligonucleotide arrays, we show that the number of CNVs per genome is well conserved in the healthy population, but remarkably enriched in these cancer-prone individuals. We found a significant increase in CNVs among carriers of germline TP53 mutations with a familial cancer history. Second, we find that ii specific CNVs at 17p13.1 are associated with LFS or developmental delay, depending on the exact breakpoint with respect to TP53. Using a purpose built array with 93.75% accuracy, we fine-mapped these microdeletions and find that they arise by Alu-mediated non-allelic homologous recombination, and contain common genes, whose under-expression distinguishes the two phenotypes. Third, we explore somatic CNVs in choroid plexus carcinoma tumor genomes. We show that this tumor is over-represented in LFS, and the number of somatic CNVs is associated with TP53 mutations and disease progression. These studies represent the first genomic analyses of LFS, and suggest a more generalized association between CNVs and cancer.

Keywords: Cancer
Genomics
Copy number variations
Copy number variants
Li-Fraumeni syndrome
p53
TP53
Advisor: Malkin, David
A Complexity Analysis of Noise-like Activity in the Nervous System and its Application to Brain State Classification and Identification in Epilepsy

Complexity lies halfway between stochasticity and determinism, suggesting that brain activity is neither fully random nor fully predictable but lives by the rules of nonlinear high- and low-complexity dynamics. One important aspect of brain function is noise-like activity (NLA), defined as background, electrical potential fluctuations in the nervous system distinct from spiking rhythms in the foreground. The objective of this thesis was to investigate the neurodynamical complexity of NLA recorded at the cellular and local network scales in in vitro preparations of mouse and human hippocampal tissue, under healthy and epileptiform conditions. In particular, it was found that neuronal NLA arises out of the physiological contributions of gap junctions and chemical synaptic channels and is characterized by a spectrum of complexity, ranging from high- to low-complexity, that was measured using methods from nonlinear dynamical systems theory. Importantly, the complexity of background, neuronal NLA was shown to depend on the degree of cellular interconnectivity to the surrounding local network. In addition, the complexity and multifractality of NLA was further studied at the cellular and local network scales in epileptiform transitions to seizure-like events, identifying emergent low-complexity and reduced multifractality (bordering on monofractal-type dynamics) in the pathological ictal state. Finally, dual intracellular recordings of hippocampal epileptiform activity were analyzed to measure NLA synchronicity, showing evidence for increased same- and cross-frequency correlations and increased phase synchronization in the pathological ictal state. Convergence towards increased phase synchrony manifested in lower frequency regions including theta (4-10 Hz) and beta (12-30 Hz), but also in higher frequency bands (gamma, 30-80 Hz). In summary, there is evidence to suggest that background NLA captures important neurodynamical information pertinent to the classification and identification of brain state transitions in healthy and epileptiform hippocampal dynamics, using sophisticated neuroengineering analyses of these physiological signals.

Keywords: Noise-like activity
Brain
Complexity
Hippocampus
Signal analysis
Membrane potential
Electrophysiology
Network dynamics
Phase synchrony
Nonlinear dynamics
Fractal
Advisor: Carlen, Peter Louis
Bardakjian, Berj
Valiante, Taufik
Assessment of Missense Alterations in MLH1 and their Pathogenic Significance

Germline mutations in mismatch repair genes predispose individuals to Lynch Syndrome, the most common colorectal cancer predisposition syndrome. MLH1 is a key mismatch repair gene that is mutated in Lynch syndrome and about a third of the genetic alterations identified in MLH1 are missense variants of unclassified clinical significance. We hypothesize that missense alterations in distinct domains of MLH1 likely affect its expression and function(s) to varying degrees. To address this we utilized several approaches to investigate the molecular basis of the pathogenicity of a panel of unclassified variants. Our results demonstrate that the MLH1 variants p.R265C and p.K618A significantly decrease the stability of the MLH1 protein, while the variant p.L749Q compromises heterodimerization of the MLH1-PMS2 complex. Given the limitations and complexity of in vitro assessment strategies, we conducted a proof-of-principle study to investigate whether missense variants in MLH1 lead to allelic imbalances at the transcriptional level. Our analysis using the PeakPicker software indicated that the missense variants c.350C>T, c.793C>T, c.1852_1853AA>GC, as well as the truncating variant c.1528C>T were associated with significantly unbalanced allelic expression. This illustrates a novel method of investigating the pathogenicity of unclassified genetic variants, which has the potential to be applied in the diagnostic setting. Previous genetic epidemiology studies from our laboratory have demonstrated that the MLH1 c.-93G>A promoter variant is strongly associated with the microsatellite instability phenotype in colorectal tumours. Additionally, this promoter variant was associated with an elevated risk of endometrial cancer in case-control studies. Results from our functional studies indicate that the c.-93G>A variant significantly alters the promoter activity of MLH1. The MLH1 promoter is bi-directional with the EPM2AIP1 gene located on the antisense strand. Interestingly, we observed that this variant significantly affected EPM2AIP1 transcription as well. Furthermore, our experiments suggest that c.-93G>A variant affects transcription by altering the affinity of nuclear factors that bind this region. Combined, these findings shed light on the possible mechanisms by which missense variants affect MLH1 expression and function, which in conjunction with results from other functional assays will help increase the accuracy and efficiency of genetic testing of inherited cancers.

Keywords: Mismatch Repair
DNA repair
Cancer
Colorectal cancer
Cancer Genetics
unclassified variant
DNA alterations
Lynch syndrome
Advisor: Bapat, Bharati
Manipulating the Mechanical Microenvironment: Microdevices for High-throughput Studies in Cellular Mechanobiology

Determining how biological cells respond to external factors in the environment can aid in understanding disease progression, lead to rational design strategies for tissue engineering, and contribute to understanding fundamental mechanisms of cellular function. Dynamic mechanical forces exist in vivo and are known to alter cellular response to other stimuli. However, identifying the roles multiple external factors play in regulating cell fate and function is currently impractical, as experimental techniques to mechanically stimulate cells in culture are severely limited in throughput. Hence, determining cell response to combinations of mechanical and biological factors is technically limited. In this thesis, microfabricated systems were designed, implemented and characterized to screen for the effects of mechanical stimulation in a high-throughput manner. Realizing these systems required the development of a fabrication process for precisely-aligned multilayer microstructures, and the development of a method to integrate non-traditional and clinically-relevant biomaterials into the microfabrication process. Three microfabricated platforms were developed for this application. First, an array was designed for experiments with high mechanical throughput, in which cells cultured on a surface experience a range of cyclic, uniform, equibiaxial strains. Using this array, a novel time- and strain-dependent mechanism regulating nuclear β-catenin accumulation in valve interstitial cells was identified. Second, a simpler system was designed to screen for the effects of combinatorially manipulated mechanobiological parameters on the pathological differentiation of valve interstitial cells. The results demonstrate functional heterogeneity between cells isolated from different regions of the heart valve leaflet. Last, a microfabricated platform was developed for high-throughput mechanical stimulation of cells encapsulated in a three-dimensional biomaterial, enabling the study of mechanical forces on cells in a more physiologically relevant microenvironment. Overall, these studies identified novel biological phenomena as a result of designing higher-throughput systems for the mechanical stimulation of cells.

Keywords: Microdevices
Cellular Mechanobiology
Microfabrication
Mechanical stimulation
High-throughput screening
Bioreactors
Advisor: Simmons, Craig Alexander
Sun, Yu
Shiga-like Toxin 1: Molecular Mechanism of Toxicity and Discovery of Inhibitors

Ribosome-inactivating proteins (RIPs) such as Shiga-like toxin 1 (SLT-1) halt protein synthesis in eukaryotic cells by depurinating a single adenine base in the sarcin-ricin loop of 28S rRNA. The molecular details involved in the ER lumenal escape and subsequent site-specific depurination are lacking, despite a general understanding of the biochemical basis of SLT-1 toxicity. Using a combination of yeast-2-hybrid and HeLa lysate pull-down followed by LC-MS/MS we have discovered yeast and human proteins that interact with the catalytic A1 chain of SLT-1. Yeast-2-hybrid library screens followed by the expression of full-length protein candidates and pull-down experiments yielded Cue2 as the only yeast cellular component that binds to the SLT-1 A1 chain. Further truncational analysis revealed that the known protein domains (two Cue domains and a Smr domain) within the primary sequence of Cue 2 were not essential for the interaction. Cue2 is a yeast monoubiquitin binding protein of no known function that is structurally homologous to the human ubiquitin-associated domain which has been implicated in intracellular routing and ER-associated degradation. Pull-down experiments indicated that the mechanism by which the catalytic domain of RIPs cleaves its substrate involves initial docking interactions with the ribosomal stalk by virtue of a conserved acidic C-terminal peptide domain common to all three stalk proteins P0, P1, and P2. The A1 chain of SLT-1 transiently binds to this peptide with a modest binding constant and rapid on and off rates. Mutagenesis of charged residues within the A1 chain identified a cationic surface that interacts with the peptide motif. In addition, phage-display was used to rapidly probe the importance of each residue within this C-terminal ribosomal peptide. The analysis revealed a complementary acidic surface and an additional hydrophobic motif involved in the interaction. Moreover, deletion mutagenesis performed on the ribosomal protein P0 revealed that the A1 chain binds to an alternate site on P0 in proximity to the contact sites for P1/P2 heterodimers. These results demonstrate that the catalytic chain of RIPs such as SLT-1 dock on ribosomes using two classes of binding sites located within the ribosomal stalk which may aid in orienting their catalytic domain in close proximity to the depurination site.

Keywords: ribosome inactivating protein
toxin
ribosomal stalk
proteomics
Advisor: Gariepy, Jean