VictorJuiz/thesis huggingface dataset:
Sac1 is required for Pigment Cell Morphogenesis and Function in the Drosophila Eye

Phosphatidylinositol (PI) phosphates (PIPs) are membrane lipids that regulate an array of cellular processes by recruiting effector proteins to specific membranes, as well as orchestrating membrane function and identity. Phosphatidylinositol 4-phosphase (PI4P) is one of the most abundant cellular PIPs. PI4P is produced by PI 4-kinases (PI4Ks) and kept in check by a sole, highly conserved phosphatase called Sac1. Studies in yeast and cultured mammalian cells have implicated Sac1 in a variety of cellular processes, including membrane trafficking, cytoskeletal dynamics, sphingolipid production and lipid homeostasis. However, because Sac1 is essential in multicellular organisms, it has been difficult to determine its contribution to development and homeostasis in vivo. To this end, I used a temperature-sensitive allele of sac1 (sac1[ts]) in Drosophila melanogaster to study the role of Sac1. Using this allele, I discovered that Sac1 is required for proper Drosophila eye formation and function, as well as for normal oogenesis. In the developing pupal retina, Sac1 is essential for patterning and specification of retinal cell precursors. Within these cells, Sac1 is important for microtubule (MT) stability and organization, transmembrane protein distribution and degradation, as well as endoplasmic reticulum (ER) homeostasis. Moreover, Sac1 loss leads to increased intracellular PI4P and decreased plasma membrane (PM) PI 4,5-bisphosphate [PI(4,5)P2]. The elevated pool of PI4P in sac1[ts] mutants is likely produced by the type II PI4K (PI4KII), since deletion of PI4KII can suppress Sac1 loss of function phenotypes, including defects in retinal cell patterning and eye formation. This indicates that Sac1 and PI4KII regulate a pool of PI4P that is required for Drosophila eye development. Proper regulation of PI4P by Sac1 and PI4KII is also required for eye pigmentation in adult flies. PI4KIIÎ or sac1[ts] mutants exhibit reduced pigment levels and fewer pigment granules (PGs) per ommatidium. Thus, PG biogenesis is highly sensitive to alterations in PI4P. Together, my results highlight the importance of Sac1 during development and provide a sensitized model for future studies.

Keywords: cell adhesion
Drosophila melanogaster
ER homeostasis
eye development and pigmentation
membrane trafficking and regulation
phosphoinositides
Advisor: Brill, Julie A
A Tale of Two Tails: Characterization of R-type and F-type Pyocins of Pseudomonas aeruginosa

Pseudomonas aeruginosa causes a broad spectrum of infections with high mortality rates. There is significant interest in development of alternative therapeutics due to the rise in multidrug-resistant infections. One such alternative is the use of protein-based antimicrobials called pyocins, which are produced by P. aeruginosa to kill related strains. This study focuses on R-type and F-type pyocins. R-type pyocins are evolutionarily related to contractile bacteriophage tails and F-type pyocins to non-contractile tails. Most previous work has focused on R-type pyocins, under-emphasizing F-type pyocins. In this study both pyocins are characterized, with a specific focus on F-type pyocins and their potential to be developed as a therapeutic. To understand their diversity and bactericidal activity, I characterized R-type and F-type pyocins of 32 P. aeruginosa strains. I found R-type pyocin gene clusters in 24 genomes and F-type in 23. R-type pyocins could be categorized into previously known groups (R1, R2 and R5). I confirmed that the O-specific antigen could act as a receptor or shield for R-type pyocins. I categorized the F-type pyocin clusters into seven groups, F1, F2 and F4-F8 (only F1 and F2 were previously known). The differences between these groups lay in the 3â end of the gene clusters that constituted of nine, six or five genes, referred herein as the â putative specificity regionâ . I showed that every F-type pyocin possesses bactericidal activity. The putative specificity region determines killing spectrum of each group of F-type pyocin and this specificity can be genetically engineered to target resistant strains. O-specific antigen could also act as a receptor or shield for F-type pyocins, however F-type pyocins can kill strains that R-type pyocins cannot. Finally, I developed a platform to rapidly clone F-type pyocin clusters into E. coli plasmids and demonstrated that functional F-type pyocins could be produced in a safe and cost-effective manner.

Keywords: antibiotic resistance
bacteriocin
novel therapeutics
Pseudomonas aeruginosa
Pyocin
tailocin and phage-tail-like-bacteriocin
Advisor: Davidson, Alan R
Maxwell, Karen L
Policing in Unsettled Times: An Analysis of Culture in the Police Organization

This dissertation examines how actors within a public sector institution - a police organization - use culture to make sense of a shifting occupational landscape. Interviews with 100 police officers and field notes from 50 ride-along hours were collected over the course of 18 months in the police service of a medium-sized city. Rather than conceive "police culture" as an ideal-type of values and attitudes, this project engages with concepts from sociological literature on culture and organizations to re-conceptualize police culture as a "resource" officers deploy to navigate what can be risky work in a contentious organization. First, contrasting traditional cultural depictions of police officers as unremittingly mission-oriented and indivisible, findings reveal the fragility of officer solidarity and unwillingness to engage with risky situations. Expanding surveillance outside the reach of law enforcement (e.g. cellphone videos, social media, etc.) contribute to uncertainty as officers carry out their duties. Second, police engage with a combination of myths and generational scripts in ways that both defend and challenge the status quo in their organization. "Old-school" scripts sustain the prominence of paramilitarism, camaraderie and athleticism. And while "new-generation" scripts are mainly deployed ceremonially to signal legitimacy to external policing constituents, some officers also use them to express the importance of education, the banality of military mindsets, and the need for equitable practices to be implemented on a more routine basis. Finally, results show that police rely on jointly established understandings about their local community to both perform and justify their organization's non-conformity with certain industry standards. Overall, insofar as change in policing is the objective in the current era of wavering public confidence and fiscal crisis, this study suggests that mere top-down policy reform is insufficient: organizational policy and actual practices are only loosely-linked and those charged with implementing a new course of action (i.e. senior officers) are often the staunchest supporters of non-change. Without a disruption to the lock-step hierarchical structure of the police organization, institutional reform is likely only to emerge generationally, as the most promising energy for transformative change rests among cohorts entering the occupation at a particularly unsettled time.

Keywords: Organizations
Police Culture
Policing
Sociology of Culture
Advisor: Levi, Ron
The Fate of Organic Matter in Biochar-amended Soil

Biochar, an aromatic carbon-rich biomass pyrolysis product, has been proposed as a soil amendment to enhance soil properties and fertility. Biochar production also converts labile biomass carbon to a recalcitrant aromatic form, slowing CO2 emissions from biomass decomposition. However, biochar may stimulate soil microbial activity, potentially enhancing soil organic matter (OM) degradation. A laboratory incubation study was conducted to assess biochar-induced changes in microbial activity and soil OM molecular composition in a temperate forest soil using biomarker and nuclear magnetic resonance (NMR) techniques. Increased soil bacterial activity and enhanced degradation of plant waxes and polysaccharides were detected after 24 weeks, while lignin was more degraded after 32 weeks. NMR analysis of water- and base-extractable OM showed a reduction of labile components and an accumulation of recalcitrant soil OM constituents. The laboratory findings were tested at the field-scale via a three-year amendment study which examined changes in soil microbial activity and native OM composition following biochar, phosphorus (P) and biochar + P addition. P fertilization stimulated soil bacterial activity, whereas biochar and biochar + P addition increased both bacterial and fungal activity and shifted the soil microbial community toward fungi. P fertilization induced soil priming, resulting in an accumulation of primarily recalcitrant OM. Biochar and biochar + P shifted the soil OM composition toward a greater proportion of aliphatic lipids and lignin and a reduction in carbohydrates. The microbial community and native OM compositional shifts observed with biochar amendment may alter soil OM turnover and nutrient cycling rates in the long-term. Higher microbial activity following biochar addition may increase the production of dissolved organic matter (DOM) in soil. The role of OM-OM interactions in DOM sorption and layering on organo-clay complexes was examined through the repeated sorption of DOM onto three minerals with contrasting properties (kaolinite, montmorillonite and gibbsite). DOM sorption was initially controlled by mineral properties, but with increased DOM loading, OM-OM interactions also influenced the composition and concentration of DOM sorbed. Aliphatic-aliphatic and aromatic-aliphatic interactions were observed for organo-clay complexes containing all three minerals, and may represent important mechanisms by which DOM sorbs to minerals with diverse properties.

Keywords: biochar
biomarker
clay mineral
organic geochemistry
organic matter
soil
Advisor: Simpson, Myrna J
Jean-Luc Nancy and the Deconstruction of Christianity

This dissertation is a study of the origins and development of the French philosopher Jean-Luc Nancy’s work on the “deconstruction of Christianity.” By situating Nancy's work in light of the broader Continental philosophical analysis of religion in the 20th Century, it argues that what Nancy calls the "deconstruction of Christianity" and the "exit from religion" is his unique intervention into the problem of metaphysical nihilism in Western thought. The author explains that Nancy’s work on religion does not provide a new “theory” for the study of religion or Christianity, but shows how Western metaphysical foundations are caught up in a process of decomposition that has been brought about by Christianity. For Nancy, the only way out of nihilism is to think of the world as an infinite opening unto itself, for this dis-encloses any transcendent principle of value or immanent notion of meaninglessness in the finite spacing of sense, and he finds the resources to think this opening within Christianity. By reading Christian notions like "God" and "creation ex nihilo" along deconstructive lines and connecting them with the rise and fall of this civilization that once called itself "Christendom," he attempts to expose "the sense of an absenting" that is both the condition of possibility for the West and what precedes, succeeds, and exceeds it.

Keywords: Christianity
Deconstruction
Derrida
Metaphysics
Nihilism
Religion
Advisor: Ricco, John Paul
Depression in People Living with HIV and Their Unmet Needs in Mental Health Care in Ontario: A Prospective Cohort Study

Nearly 50% of HIV-positive patients have a history of suffering from depression. Although the condition is treatable, depression in these patients is under-recognized and under-treated, resulting in poorer clinical and quality-of-life outcomes. There are also gaps and disparities in accessing mental health care among these patients, but current evidence is limited to U.S. studies. The primary objectives of this thesis work were to: (1) establish the validity and reliability of self-report measurement instruments in identifying depression against DSM-IV criteria; (2) examine the burden of current depression and the underlying factors driving the burden; (3) estimate the rate of publicly-funded mental health service use and unmet needs for mental health care among HIV-positive patients with depression; and (4) examine the impact of depression on costly and preventable acute health services use in the Canadian health care system. A prospective cohort study was conducted by following a cohort of HIV-positive patients from October 1, 2007 to March 31, 2013 in the province of Ontario, Canada. I adopted a novel longitudinal linked data approach. Various regression models were employed for the analysis. Three self-report instruments (CES-D20, K10, and PHQ9) performed equally well and accurately when compared against DSM-IV criteria. With regards to the burden of depression, one in four HIV-positive patients was depressed. Half of depressed HIV-positive patients had a recurrent episode. In addition, there were delivery gaps in mental health care for depressed HIV-positive patientsâ one-half used mental health services and of these, one-half received minimally adequate care. Furthermore, HIV-positive patients with depression and/or substance use issues were associated with a 19â 70% elevated rate of emergency department (ED) admissions and a 17-67% elevated rate of potentially preventable ED admissions compared to those without these conditions. In sum, depression is highly prevalent in HIV-positive patients and is likely to be chronic and recurrent over time. There are delivery gaps in mental health care for depressed HIV-positive patients. More effective mental health care policies and better access to mental health care services are required to address the unmet needs of HIV-positive patients and reduce the impact of depression on their lives.

Keywords: Canada
Delivery of care
depressive disorder
HIV
Mental Health Services
Advisor: Rourke, Sean B.
Remembering Past(s), Imagining Futures: The Politics of Hope in Palestine

Using hope as a category of experience, this dissertation explores the ways Palestinians and their Israeli-Jewish allies undermine urban spatial expropriations under Israeli-settler-colonialism. Focusing on the city of Jaffa, I analyze the ways in which the Israeli state and the Tel Aviv municipality succeeded in ‘burying’ histories of mass expulsions, organized violence and appropriations of private and public spaces. I then follow the fortunes of Palestinians – those who remained in Jaffa and became a minority under regimes of neoliberalization and Judaicization, and those who were expelled, found themselves de-nationalized and precarious refugees, some confined to decrepit camps, while others pursued opportunities for meaningful political engagement and armed struggle. The dissertation ends with a powerful gesture towards a future that undermines the colonial present and its attendant sense of hopelessness: I explore how both Palestinians and Israeli-Jews engage with the ideas of reconciliation and “living together” in the “Jaffa of tomorrow.” My focus on hope as a category of experience hinges on two main intersecting axes: temporality and place. Just as political identities are rooted in the refugee camp experience and informed by the quotidian and the present, on the one hand, and memory and absence on the other, so, I argue, is Palestinians’ understanding of the local. Rather than accepting normative assertions that define the local as a bounded place that is both community-making and exclusive of those outside of it, I wish to suggest that locality, and attachment to it, is much more multi-directional, dispersed in time and space. This understanding brings to our line of sight those people who are geographically external to place, in this case Jaffa, but have nonetheless powerful attachment to it. In many ways, then, Palestinians are fighting for the right to belong against submerged histories of ethnic cleansing and entrenched colonial denial of their attachments to places they were expelled from.

Keywords: Colonialism
Hope
Memory
Palestine
Urban
Advisor: Hanssen, Jens
The Role of Macrophages in Bone Development, Repair, and Aging

With age, the risk of sustaining a fracture increases, yet bone repair becomes a slower and more fibrotic process. This fracture healing process recapitulates the process of bone development, except that fracture repair is initiated with an inflammatory response to injury resulting in the recruitment of various immune cells, including macrophages. Interestingly, macrophages are present during early bone development, yet their function during this process is not well understood. Hence, the purpose of this study was to determine the functions of macrophages during bone development, repair and aging. Using transgenic mice to constitutively ablate macrophages, we demonstrated that macrophage deficiency impaired bone marrow progenitor cell differentiation resulting in decreased bone mineral density. Constitutive or temporal depletion of macrophages during fracture repair led to decreased callus formation and bone deposition resulting in impaired bone union. When we compared fracture healing between young and old mice, we found that old animals developed a slower and more fibrotic response to healing. To determine whether the age-related delays in fracture repair are associated with changes in this macrophage population with age, we performed parabiosis and cell transplantation experiments. We found that young macrophages rejuvenated fracture repair in older animals by suppressing fibrosis and promoting bone mineralization. Furthermore, conditioned media from young, but not old, macrophages rescued osteoblast differentiation of old bone marrow progenitor cells, and analysis of these cells indicated that old cells polarized towards a pro-inflammatory phenotype. Mass spectrometry analysis of young and old macrophage secretomes identified 56 â youth factorsâ . One of these factors, LRP1, was found to promote osteoblast differentiation of old progenitor cells. Taken together, these findings demonstrate a functional role for macrophages in bone formation and fracture repair, and that substitution of old macrophages with young macrophages rejuvenates fracture healing in older mice.

Keywords: Aging
Fracture repair
Macrophages
Advisor: Alman, Benjamin A
Functional Dynamics of the β2-Adrenergic Receptor and Fluoroacetate Dehalogenase by 19F NMR

Proteins represent 1/3 of the macromolecular constituents of cells and are responsible for key aspects of structural support, signal transduction, and catalysis. Protein function is controlled largely by dynamics. This is particularly true in the case of signal transduction and catalysis, where a protein is more aptly described in terms of an ensemble of key states associated with the signaling process or the reaction coordinate pathway. This thesis explores two proteins – namely, a G protein-coupled receptor, β2AR and a homodimeric enzyme, fluoroacetate dehalogenase (FAcD) - in terms of their functional ensembles and the dynamic processes which contribute to function. Chapter 2 of this thesis addresses aspects of GPCR dynamics in different detergents, as measured by 19F NMR. 19F NMR spectra of β2AR measured in dodecyl maltoside (DDM) and maltose-neopentyl glycol (MNG-3) detergent showed dramatic differences in receptor dynamics. The difference in detergent off-rates of the micelles was linked to the conformational exchange rates between functional states. Chapters 3 and 4 show that β2AR can be represented by four states (two inactive, an activation intermediate, and a fully active state). The two inactive states are in a fast exchange on an NMR time scale with lifetimes of hundreds of microseconds. The activation intermediate is found to be the most dynamic state and is entropically favored with a lifetime of ~660 milliseconds. Moreover, the full active state is only stabilized with G protein, or G protein mimetic nanobody (Nb80), and an agonist. The last part of this thesis details the role of asymmetric structure and dynamics along the reaction coordinate pathway of the bacterial dimeric enzyme, FAcD. NMR and time-resolved X-ray crystallography show that dynamic collective motions across the dimer drive its catalysis via allostery between protomers. The apo-enzyme is characterized by a subtle asymmetry, which is averaged by millisecond timescale conformational exchange between protomers. Asymmetric binding of substrate stabilizes an excited state in the apo-enzyme and increases the dynamics of protomer exchange. The stabilized excited state shows dramatic changes in local protein dynamics and the number of water molecules around the empty protomer which facilitates the catalysis in the bound protomer.

Keywords: Enzyme
GPCR
NMR
X-ray crystallography
Advisor: Prosser, Robert Scott
Mixed Reality Gaming for Older Powered Chair Users: A Human Factors Model of Well-being and Engagement

Older adults who develop mobility impairments and begin to use powered chairs, such as mobility scooters and electric wheelchairs, are at risk of experiencing parallel declines in well- being. Yet, most interventions focus on training, chair function, and environmental factors. To address this gap, a cooperative dyadic mixed reality platform was developed to improve the well-being of older powered chair users along two lines: internal, in terms of performance mastery; and external, in terms of empathy training of an able-bodied other. Four studies were conducted: (1) a needs and requirements analysis study using human factors focus group methodology; (2) a usability evaluation of the game prototype, which also captured baseline well-being data; (3) a usability evaluation of the facilitating display for mixed reality during powered chair use; and (4) a semi-longitudinal, exploratory evaluation of the mixed reality gaming platform. Psychological measures of well-being, particularly eudaimonia (personal growth, self-determination and self-expression) and hedonia (pleasure, enjoyment) were captured and analyzed in combination with measures of game engagement and usability. The main contribution is a theoretically- and empirically-supported human factors model of well-being, game engagement, and usability based on established measures and validated with older powered chair users within a human- computer interaction context.

Keywords: engagement
game design
mixed reality
older adults
power mobility
well-being
Advisor: Chignell, Mark
Fels, Deborah I