VictorJuiz/thesis huggingface dataset:
The Role and Regulation of the Exchange Factor GEF-H1 in Tubular Cells

The Rho family small GTPases are key regulators of the cytoskeleton, through which they impact and control many vital cellular functions, including growth, vesicle trafficking, intercellular junctions, transepithelial transport, migration, and gene transcription. Activation of Rho GTPases is induced by Guanine Nucleotide Exchange Factors (GEFs). We have previously shown that Tumour Necrosis Factor-α (TNF), plasma membrane depolarization, and immunosuppressive drugs activate RhoA through a specific exchange factor, GEF-H1. However, the question of whether other stimuli, such as hyperosmolarity, that activate RhoA, act through GEF-H1 and whether GEF-H1 activates other RhoGTPases was not known. The overall objective of this research project has been to gain insights into the complex mechanism through which the Rho GTPases, Rac and RhoA, are regulated in tubular cells. Specifically, we wished to explore the role and pathway-specific regulation of GEF-H1 in hyperosmotic stress- and TNF-induced signalling in tubular cells. In order to accomplish our goals, we optimized and used affinity precipitation assays to detect GEF-H1 activation (RhoA(G17A) and Rac(G15A)). We found that 1) GEF-H1 is activated by hyperosmotic stress and mediates the hyperosmolarity-induced RhoA activation, as well as nuclear translocation of the Myocardin-Related Transcription Factor (MRTF); 2) TNF induces activation of both Rac and RhoA through GEF-H1, but via different mechanisms. Epidermal Growth Factor Receptor (EGFR)- and Extracellular signal Regulated Kinase (ERK)-dependent phosphorylation at the Thr678 site of GEF-H1 is a prerequisite for RhoA activation only, while both Rac and RhoA activation require GEF-H1 phosphorylation on Ser885. Interestingly, Rac is required for TNF-induced RhoA activation. Together these findings highlight a role for GEF-H1 as an osmosensitive molecule that regulates cellular reprogramming through MRTF. Importantly, we have also uncovered a novel mechanism explaining hierarchical activation of Rac and RhoA by TNF. Such a mechanism could be key in coordinating GEF function and fine-tuning Rac and RhoA activation.

Keywords: Rho GTPases
Tumour Necrosis Factor-alpha (TNF)
Guanine Nucleotide Exchange Factors
GEF-H1
Cytoskeletal remodelling
Hyperosmotic stress
Advisor: Szaszi, Katalin
Children's Acquisition of Values within the Fmily: Domains of Socialization Assessed with Autobiographical Narratives

The transmission and internalization of values are the primary processes that occur during socialization. A recent approach integrates existing theories and research findings into a comprehensive model of socialization. According to the domains of socialization approach, there is no general principle governing socialization but rather it occurs in different domains of caregiver-child interactions. Grusec and Davidov (2010) outlined five socialization domains, which involve controlling children’s behaviour by external means (control domain), protecting children from harm and relieving their distress (protection domain), teaching children information or skills outside of the discipline or distress setting (guided-learning domain), managing children’s environment to increase desirable role models (group participation domain), and accommodating each other’s wishes (mutual reciprocity domain). Previous work demonstrated the utility of the domains of socialization approach for the study and understanding of value acquisition (Vinik, Johnston, Grusec, & Farrell, 2013). The present study expanded on this work by focusing on processes within the family. A modified narrative methodology was used to explore aspects of the value acquisition process. Autobiographical narratives of 294 emerging adults about a time they learned an important value from a caregiver were analyzed. The sample included participants from four ethnic backgrounds. Findings provided further support for the usefulness of the domains of socialization approach to the study of value development, as events recalled in narratives were categorized into all domains but reciprocity. Values learned in the control domain were most frequently reported but were associated with the lowest levels of internalization. The highest level of value internalization was found to occur in the group participation domain, drawing attention to the importance of observing the behaviour of others. Socialization domains were associated with particular types of lesson content. The guided learning and group participation domains were associated with more positive and less negative emotional valence compared to the other domains. In turn, absence of negative valence was significantly related to better confidence in accuracy of memory reported in narratives, indicative of quality of information processing and learning. Most effects were not moderated by demographic variables providing support to the universal applicability of the domains of socialization approach.

Keywords: value acquisition
narratives
Advisor: Grusec, Joan
Seeing What Remains: On the Enigma of the Look Between Mourning and Melancholia

Walter Benjamin, in Thesis IX of his “Theses on the Philosophy of History,” wrote of the angel of history looking back at the past from the now-time of the present moment, at the historical wreckage, a single catastrophe as it were, piling in front of its feet, as it gets pulled forward facing back into the temporality of the future and the space of modernity’s violent excesses, heralded by the promise of apparent progress. As the title to my dissertation suggests, my study begins, following the angel’s look, with these three words, seeing what remains, and as such it is structured around the very nature of this arresting “look back” and that which is being regarded, the ruins, or the remains and remainders that exist after, and in the aftermath of, traumatic loss. Working with and across a variety of mediums, I conduct a series of exegetical studies of recent “texts” – literary, photographic, and cinematic – within which, I argue, this look back figures as central to the concern of how we might understand the simultaneous existence of the forces of remembrance and forgetting, and of mourning and melancholia in memory-work. The various “texts” within which I explore this look back are Anne Michaels’s novel Fugitive Pieces, the photographic series titled Library of Dust by David Maisel, the movies Hiroshima, mon amour by Marguerite Duras and Alain Resnais and Amour by Michael Haneke. I situate my exploration of the enigmatic nature of the look back in these different textual scenes alongside Sigmund Freud’s critical work on transference and transference love and Kaja Silverman’s rigorous expansion of the psychoanalytic objective of the “cure by love.” Here, it is my intention, as such, to work toward and expand on my thesis that this look, of the angel (or the materialist historian or the artist as witness), is a look of redemptive love, both against erasure and against the possibility of invisibility, “to awaken the dead” as it were, so as to address the loss inscribed in historical experiences with catastrophic temporality and to thereby redeem the ethical from within the scene of trauma.

Keywords: psychoanalysis
history of philosophy
ruin studies
memory
remembrance
forgetting
look
gaze
trauma
Walter Benjamin
Sigmund Freud
Advisor: Walcott, Rinaldo
A Novel Reciprocal Regulatory Circuit Between Caspase-8 and c-Src

Apoptosis and cell survival are two seemingly opposing fate-determining processes that are regulated by distinct and complex signaling pathways. Caspase-8, an apical caspase, plays a pivotal regulatory role in initiating apoptosis. c-Src, a prototypical member of the Src family kinases (SFKs), regulates a myriad of cellular processes including cell mitogenesis, proliferation, growth and migration. Although the regulation of caspase-8 by c-Src has been suggested, the reciprocal regulation of these two seemingly opposing signaling molecules, caspase-8 and c-Src, has never been explored. To study this reciprocal regulation, we asked three questions. (1) Can active caspase-8 negatively regulate c-Src activity to allow the propagation of apoptosis? (2) Can c-Src negatively regulate caspase-8 activity to prevent the propagation of apoptosis? (3) Can caspase-8, when its enzymatic activity is inhibited, further promote c-Src activity to allow the propagation of cell survival? To address these questions, we first investigated the effect of active caspase-8 on the activation and activity of c-Src. We discovered that active caspase-8 inhibited c-Src activation and some of its downstream effectors. Next, we investigated whether c-Src could tyrosine phosphorylate caspase-8. We discovered that c-Src could phosphorylate caspase-8 at multiple tyrosine sites. We then examined whether tyrosine phosphorylated caspase-8 prevents apoptosis. We found that phosphorylation of caspase-8 at Y465 prevented its cleavage, and activity towards activating caspase-3 and towards causing cell morphological changes associated with apoptosis. Finally, we studied whether tyrosine phosphorylation of caspase-8 could further promote the activation of c-Src. We showed that phosphorylation of caspase-8 at both Y465 and Y397 resulted in the activation of c-Src and extracellular signal-regulated kinase 1/2 (Erk1/2). In conclusion, this work demonstrated the reciprocal regulation of two opposing signaling molecules, caspase-8 and c-Src. These results also suggest an elegant mechanism for a cell to commit efficiently and rapidly to a fate-determining process, either apoptosis or survival, by further suppression of the opposing signaling pathway.

Keywords: Survival
Apoptosis
Caspase-8
c-Src
Advisor: Marshall, John C
Nonlinear Optical Properties of Carotenoid and Chlorophyll Harmonophores

Information regarding the structure and function of living tissues and cells is instrumental to the advancement of cell biology and biophysics. Nonlinear optical microscopy can provide such information, but only certain biological structures generate nonlinear optical signals. Therefore, structural specificity can be achieved by introducing labels for nonlinear optical microscopy. Few studies exist in the literature about labels that facilitate harmonic generation, coined "harmonophores". This thesis consists of the first major investigation of harmonophores for third harmonic generation (THG) microscopy. Carotenoids and chlorophylls were investigated as potential harmonophores. Their nonlinear optical properties were studied by the THG ratio technique. In addition, a tunable refractometer was built in order to determine their second hyperpolarizability (γ). At 830 nm excitation wavelength, carotenoids and chlorophylls were found to have large negative γ values however, at 1028 nm, the sign of γ reversed for carotenoids and remained negative for chlorophylls. Consequently, at 1028 nm wavelength, THG signal is canceled with mixtures of carotenoids and chlorophylls. Furthermore, when such molecules are covalently bonded as dyads or interact within photosynthetic pigment-protein complexes, it is found that additive effects with the γ values still play a role, however, the overall γ value is also influenced by the intra-pigment and inter-pigment interaction. The nonlinear optical properties of aggregates containing chlorophylls and carotenoids were the target of subsequent investigations. Carotenoid aggregates were imaged with polarization-dependent second harmonic generation and THG microscopy. Both techniques revealed crystallographic information pertaining to H and J aggregates and β-carotene crystalline aggregates found in orange carrot. In order to demonstrate THG enhancement due to labeling, cultured cells were labeled with carotenoid incorporated liposomes. In addition, Drosophila melanogaster larvae muscle as well as keratin structures in the hair cortex were labeled with β-carotene. Polarization-dependent THG studies may be particularly useful in understanding the structural organization that occurs within biological structures containing carotenoids and chlorophylls such as photosynthetic pigment-protein complexes and carotenoid aggregates in plants and alga. Further, artificial labeling with carotenoids and chlorophylls may be useful in clinical applications since they are nontoxic, nutritionally valuable, and they can aid in visualizing structural changes in cellular components.

Keywords: third harmonic generation
labels
carotenoid
chlorophyll
Advisor: Barzda, Virginijus
Fekl, Ulrich
District Leaders as Members of a Professional Learning Community: Changing Approaches to Leasdership Practices

The term professional learning community is generally defined as a group of people sharing and critically interrogating their practice in an “ongoing, reflective, collaborative, inclusive, learning-oriented, growth-promoting way and operating as a collective enterprise” (Stoll, Bolam, McMahon, Wallace & Thomas, 2006, p. 223). The professional learning community is increasingly being used as an explicit change strategy for generating, sharing and managing knowledge in educational organizations. Improving the performance of a district requires district supervisory officers to build their capacity for learning how to improve leadership practices. In this retrospective qualitative study, I investigate to what extent leadership practices change for a group of district supervisory officers, that is, the senior leaders responsible for the district leadership functions, while they responded to provincial reform mandates between 2000 and 2006. I also examine whether this group of supervisory officers in one Ontario English Public School District, renamed Green Ridge District School Board (GRDSB) for anonymity, functions as a professional learning community. Data sources used in this investigation were developed through a university partnership between GRDSB and an Ontario Institute for Studies in Education field center known as the Midwestern Centre. Data were gathered from six research reports, written annually between 2001 and 2006; interviews from seven supervisory officers conducted in 2006; and interviews from 12 school administrator interviews held in 2005. One limitation of the study is that participants were selected from school sites that chose to become involved with the district change strategies and therefore tended to take a positive orientation when responding to semi-structured questions. The data gathered did not reflect the views of those who chose not to be actively involved in the district change strategies. This investigation’s findings inform leadership theory and practice with respect to the descriptions of evolving leadership practices of a group of supervisory officers as they worked to re-culture the GRDSB. Findings provide empirical support for the contention that a socially constructed environment, such as a professional learning community, provides a context for supporting changes to leadership practices through collective professional learning, problem solving, knowledge creation and knowledge sharing (Anderson, 2006; Honig, 2008; Louis, 2008).

Keywords: supervisory officers
administrators
professional learning community
leadership practices
district change
school improvement
Advisor: Rolheiser, Carol
Brett, Clare
Mascall, Blair
Non-rigid Structure from Locally Rigid Motion

The non-rigid structure from motion problem typically involves recovering the 3D trajectories of a set of scene points, from their corresponding image trajectories. In this thesis, the assumption of locally-rigid motion is used to regularize this otherwise underconstrained problem. The key idea is that even when a scene undergoes complex global deformations, the trajectories of local triplets of scene points can often be approximated by the vertices of a rigidly moving triangle. This intuition informs our bottom-up reconstruction procedure, which discovers such triplets through a hypothesis and test framework. To this end, a rigid triangle model is fit to the proposed image trajectories and evaluated using a procedure that we call 3-SFM. The recovered triangle models are then integrated into a global solution, by resolving their orthographic depth ip and translation ambiguities. Lastly, we consider using this solution to initialize an energy based model, subject to a set of soft isometric constraints, in order to allow each observation to constrain the global scene structure. Results on several sequences, both our own and from related work, suggest that these models are applicable in diverse and challenging scenes, such as those including multiple deforming bodies.

Keywords: computer vision
structure from motion
Advisor: Jepson, Allan D.
Kutulakos, Kiriakos N.
The Mortality and Morbidity of Alcohol-attributable Injury

Alcohol is a recognized cause of over 60 injuries and diseases and is consistently in the top 5 most important risk factors for global burden of disease. It is important to be able to measure how drinking alcohol affects our health, and how our risk of getting injured or acquiring diseases caused by alcohol is dependent on how much alcohol we drink. This type of information allows us to make personal choices about our health and is an integral piece of public health evidence to inform how alcohol policy is informed, implemented, or monitored. This analysis will, for the first time, model the effects of alcohol for injury outcomes over the entire drinking lifetime for men and women separately using a new method that aims to improve upon existing calculations by accounting for different patterns of drinking – both acute consumption and average daily drinking. In both cases, both the amount consumed and the number of times it is consumed is taken into account. Within acute consumption, the number of occasions and the amount ii consumed at each occasion was counted. What’s more, for the first time in this field, a lifetime approach was adopted – risks will no longer be seen as discrete, individual events that occur independently of each other. In this study, risks are combined much like other exposures to environmental substances or contaminants – in a cumulative manner over a lifetime of drinking. The method combines data sources from experimental data, from meta-analyses, Canadian mortality and hospital data, and survey data, making this a rich, yet complicated analysis. Its products were dose-response risk curves for each injury outcome, by sex, and age group, and alcohol-attributable fractions and their variance estimation for mortality and morbidity for injury. This study has important implications for forming and planning health policy, represents advancements in absolute risk calculation, and will result in important consumer-level information that will enable development of limits around healthy drinking.

Keywords: Alcohol
Injury
Advisor: Rehm, Juergen
Expertise and Policy Learning - The Case of the European Union's Research Policy

This thesis examines policy learning and expertise in the European Union research policy by focusing on the Open Method of Coordination (OMC) initiative. The research is guided by the overarching question - How do experts’ individual policy learning experiences relate to the EU’s research policy? First, background of the European Union’s research policy is presented, clarifying the need for policy learning. Second, the theoretical approaches on expertise and theories of policy learning are analyzed. The synthesis of the two streams of literature leads to a conceptual framework for the study, featuring two distinct perspectives of policy learning – the evidence-based approach and the value-based approach. This framework brings the individual experiences of the OMC participants into focus, allowing an examination of policy processes that do not always result in direct policy changes. For data collection three distinct OMC working groups are selected, each focusing on a different topic related to European research policy – research funding (Group 1), research cooperation with Third Countries (Group 2) and research activities in universities (Group 3). A case study approach is employed, involving document analysis, a pilot study and thirty-four interviews with member-states’ experts and European Commission policy-makers. The findings suggest that individual policy learning shapes the development of European research policy. Through the OMC policy learning initiatives participants gain new knowledge on policy approaches, programs, best practices and policy failures. In addition, learning experiences involve knowledge on individual relationships, decision-making styles, organizational cultures and power-relationships that diverse stakeholders bring with them to the process. Such knowledge helps to update the policy beliefs of participants, providing a strong foundation for developing mutual ownership of decisions that lead to policy coordination. The findings emphasize the importance of a value-based perspective in policy analysis, where results emerge gradually, over a long time period and contribute to policy change.

Keywords: policy learning
research policy
Advisor: Sa, Creso
Chlamydia Trachomatis Disrupts Cytokinesis to Accelerate Nutrient Acquisition from Host Cells

Chlamydia trachomatis is the leading cause of bacterial sexually transmitted infections worldwide and it has been linked to increased risks of cervical cancer. Our study aims to understand the mechanisms by which chlamydia infection contributes to higher risks of tumorigenesis. We discovered in over 90% of infected human epithelial cells that chlamydia inclusions localized to the host cell centre during mitosis and prevented the completion of cleavage furrow ingression. Infected cells that failed to divide into two daughter cells re-entered interphase as tetraploid multinuclear cells, which are known initiators of tumorigenesis. In order to address whether chlamydia actively sought the host cell centre during mitosis, we created vacuoles using internalized latex beads and our findings indicated that chlamydia inclusions localized to the host cell centre much more frequently than similarly sized vacuoles. In addition, we demonstrated that metabolically inactive chlamydia inclusions localized to the cell centre less frequently than inclusions under normal conditions. Together, these results suggested that chlamydia actively localized to the host cell centre to efficiently block host cell mitosis. We took advantage of the microtubule-displacing capability of the C. trachomatis inclusions and demonstrated that astral microtubules could promote furrow initiation independent of the central spindle microtubules. Microdomains on chlamydia inclusions play important roles in inclusion localization and chlamydia replication. We discovered that these structures were surprisingly resistant to bacterial protein synthesis and host Src family kinase inhibitors. Finally, we demonstrated that multinuclear cells that resulted from unsuccessful mitosis contained significantly higher Golgi content, an important nutrient source for chlamydia. Our results indicated that C. trachomatis in multinuclear cells intercepted Golgi-derived lipids faster than in mononuclear cells. Together, my results reveal that C. trachomatis inclusions robustly localize to the cell centre to block host cell mitosis in order to acquire host Golgi nutrients more quickly in multinucleated cells.

Keywords: Chlamydia
cytokinesis
Advisor: Rene, Harrison