VictorJuiz/thesis huggingface dataset:
Synthesis and Biological Evaluation of Antibacterial Small Molecule Activators of Caseinolytic Protease P and the Synthetic Utility of Metal Carboxylate Salts in Amidation Reactions with Amines
Keywords: Amidation
Antibacterial
Carboxylate Salts
Depsipeptides
Small Molecules
Synthesis

This thesis is presented in two parts and summarizes work carried out in the laboratory of Professor Robert A. Batey at the University of Toronto from September 2009 through March 2016. Part 1 of this thesis covers the synthesis and biological evaluation of two types of small molecules which target bacterial Caseinolytic Protease P (ClpP); these are the cyclic acyldepsipeptide (ADEP) class of antibiotics and related analogues (Chapter 2) and the ACP1 analogues (Chapter 3). Part 2 of this thesis outlines work related to the synthetic utility of metal carboxylate salts in amide bond-forming reactions with amines. Part 1 of this thesis begins with an introductory chapter (Chapter 1) on antibiotics to familiarize the reader with antibiotic classes, bacterial mechanisms of drug resistance as well as strategies for antibacterial drug discovery. Next, Chapter 2 details the total synthesis and biological evaluation of the A54556 ADEP natural products and related analogues. In the course of our investigations on this class of compound, a rapid two-step synthetic approach was developed that utilized a combination of solid-phase peptide chemistry and a novel lanthanide salt-promoted macrolactonization reaction. Importantly, this methodology was used to prepare several structurally diverse analogues. Chapter 3 then describes the synthesis and biological evaluation of ACP1 and related analogues. In contrast to the ADEPs, ACP1 was discovered using a high-throughput screen and several structurally unique analogues were synthesized in an attempt to improve potency and understand the structural features that impart biological activity. Part 2 of this thesis covers amidation reactions from the direct coupling of metal carboxylate salts with amines or ammonium salts in the presence of the coupling reagent HBTU (Chapter 4). A wide variety of carboxylate salts were examined and the methodology was later extended to multistep, one-pot variants using carboxylate salts that were generated in situ.
Inhibition of eIF2α Kinases by Viral and Small Molecule Inhibitors
Keywords: antimalarial kinase inhibitor
eIF2α kinase
lobe-swap
PK2
PKR
HRI
PK4
viral mimicry

Phosphorylation of the alpha subunit of the eukaryotic initiation factor 2 (eIF2α) on Ser51 is a key event in the eukaryotic stress response pathway. Specifically, this phosphorylation signal potently blocks protein synthesis, which allows cells to conserve energy under stress conditions, to upregulate genes that promote stress remediation, or alternatively, to induce apoptosis should the triggering insult become insurmountable. Phosphorylation of eIF2α is carried out by the eIF2α family kinases comprised of four prototypical members in mammals: the heme-regulated inhibitor kinase (HRI), the RNA-dependent protein kinase (PKR), the PKR-like endoplasmic reticulum kinase (PERK) and the general control nonrepressible 2 kinase (GCN2). Due to the importance of maintaining protein homeostasis under stress conditions, misregulation of eIF2α kinases underlies the pathophysiology of many human diseases including diabetes, neurodegeneration and cancer, and has thus propelled these kinases as attractive targets for pharmacological intervention in the clinical setting. Moreover, since conserved or all together novel eIF2α kinases have also been identified in pathogenic protozoans such as Plasmodium and Toxoplasma, targeting these kinases have also gained traction for the treatment of malaria and related infectious diseases. While much work has been done to elucidate the catalytic switching mechanism of eIF2α kinases as well as the activated state of their catalytic domains, little is known about how eIF2α kinases become inhibited. The work described in this thesis was conducted with the aim of exploring the inhibition of eIF2α kinases by viral or small molecule inhibitors using a combination of structural biology, biochemistry, and cell biology approaches. In chapter 2 a biochemical and biological framework is described detailing how a baculovirus-encoded protein kinase mimic called PK2 inhibits human PKR and insect HRI eIF2α kinases by a novel lobe-swap mechanism of action. In chapter 3, a high-throughput kinase activity screen was performed, which led to the discovery of five small molecule inhibitors of the plasmodium eIF2α kinase PK4. These inhibitors were then validated in vitro and in vivo with respect to both mechanism of action as well as therapeutic potential in malaria. These results have broad implications for understanding catalytic switching and inhibitor design for eIF2α family kinases and their therapeutic application in disease.
Loss of Sbds in Shwachman-Diamond Syndrome Murine Model Leads to Reduction of 80S Ribosomes and Altered Transcript Binding
Keywords: altered mRNA binding
non-translating ribosomes
polysome profile
Shwachmanâ Diamond syndrome
transcript length

Shwachman-Diamond syndrome (SDS) is an autosomal recessive disease characterized by growth retardation, exocrine pancreatic dysfunction, skeletal dysplasia, cognitive impairment and bone marrow failure. SDS is caused by mutations in SBDS (Shwachman-Bodian-Diamond syndrome). A recent model proposes that SBDS/Sbds functions together with EFL1/Efl1 to release EIF6/Eif6 from the pre-60S complex, enabling ribosomal subunit joining for translation initiation. To assess the protein synthesis deficiency that has been detected in SDS, I examined ribosomal profiles of murine fetal organs with the SDS-associated missense mutation, R126T (SbdsR126T/R126T). The SDS organ extracts revealed reduced 80S monosomes and preserved polysomes, with no ribosomal subunit imbalance compared to matched controls. Further, Eif6 was found to bind to both the 60S and 80S ribosome complexes in mutants in contrast to only 60S complexes in controls. To investigate these changes and to learn how the SDS translatome is affected, total and polysomal mRNAs of mutant and control samples were studied using cDNA microarray analyses. By comparing individual polysomal transcripts to respective total transcript levels, I found 799 transcripts (of 18,936 analyzed) with altered polysome loading in mutant fetal livers, with 634 being increased. Changes in polysome loading did not correspond with steady state protein levels, as indicated by proteome analysis using label-free mass spectrometry. Rather, these changes correlated with physical features of the transcripts, including 5' untranslated region composition as well as the lengths and nucleotide contents of the open reading frame and the 3' untranslated regions. Together, I conclude that the untimely release of Eif6 due to Sbds deficiency results in ribosomes with compromised translation initiation and that SDS disease phenotypes reflect protein synthesis insufficiency and the formation of sub-populations of â SDS ribosomesâ with non- or poor- translating capability.
Impact Behaviour of Hybrid Long Fibre Thermoplastic Composites
Keywords: Composite
Extrusion
Impact strength
surface treatment
Work of fracture

Impact strength is a critical property of composites in the auto industry by way of product service life, safety, and liability. The aim of this project is to arrive at a hybrid biocomposites of hemp-glass fibre-PP with high toughness. Long glass fibres are believed to increase impact strength of composites, and current literature has mainly focused on hand layup process of laminates and mats to achieve long fibres, whereas this work investigates the use of extrusion and GF roving. The hypothesis being tested is that the energy absorption of hybrid composites can be improved by increasing glass fibre length using an extrusion process. Process optimization resulted in a hybrid composite with notched impact strength of 131 Âą 12 J/m, tensile strength of 92 Âą 7 MPa, and flexural strength of 160 Âą 15 MPa produced at an optimum shear rate of 62 sec-1 while feeding glass fibre into a port before the vent. To enhance interaction of fibres and matrix, 5% MAPP coupling agent was added to the composite since the other examined surface treatments for natural fibres did not yield significant improvement of impact properties. The last objective for this thesis was to relate the work of fracture of hybrid composites to fibre and matrix properties using a theoretical model, since there is no experimental validation for the available models in literature. The model presented here uses the Rule of Mixtures model to incorporate matrix failure, fibre debonding and fibre pull out for short fibres, in addition to fibre stress redistribution for long fibres. Good agreement between the presented model predictions and experimental data was observed. For the case of hybrid composites with long fibres, the dominant failure mechanisms were fibre stress redistribution and matrix failure, while for the case of short fibre composites fibre pull-out and matrix failure were dominant. In order to produce hybrid composites with high work of fracture, the focus should be on fibre processing to arrive at an optimum length, aspect ratio, volume fraction, and good dispersion.
Digital Materialisms: Information Art In English Canada, 1910-1978
Keywords: Canadian art
Conceptual art
Harold A. Innis
Henri Bergson
Information art
Marshall McLuhan

Digital Materialisms: Information Art In English Canada, 1910-1978 Adam Lauder Doctor of Philosophy Department of Art University of Toronto 2016 Abstract Information art has a long history in English Canada. The multidisciplinary production of Bertram Brooker (1888-1955) is paradigmatic of early-twentieth-century English-Canadian artists’ distinctive responses to, and interventions within, the channels of an emergent social formation characterized by an unprecedented circulation of “information.” Brooker’s counter-hegemonic renderings of information as a corporeal and qualitative alternative to the mathematical frameworks embraced by American peers cleared a path for a subsequent generation of information artists inspired by the percepts of Marshall McLuhan (1911-1980), notably the Vancouver-based N.E. Thing Co. Ltd. (1966-1978). Like Brooker before them, NETCO’s co-presidents would attribute somatic and ontological meanings to information that trouble the cognitive, linguistic and structuralist frameworks conventionally mobilized by discussions of Conceptual art. In tracing the sources of this discourse network to the Canadian-born British proto-media theorist Wyndham Lewis (1882-1957), as well as its subterranean legacy in the Postminimalism of Robert Smithson (1938-1973), this study simultaneously troubles essentializing narratives of English-Canadian identity that problematically project representations of Canadianicity onto the territorial borders, and terrain (or “landscape”), of the nation state. Inspired in equal measure by recent developments in media archaeology and a resurgent scholarly interest in McLuhan, detailed investigations of discrete information media and instrumentalities are woven into a trajectory of progressive “informationalization” coterminous with the rise of an information society. Through original readings of archival materials and other primary sources, this dissertation argues for a revised understanding of information art produced in and beyond the borders of English Canada as articulating a critique of transcendence. Artists and thinkers implicated in the common “discourse network” delineated in these pages harnessed information concepts and information media to express shared visions of immanence. This dissertation historicizes and marterializes these non-technological visions of information by undertaking an archaeology of specific media and discourses.
User-centered Design Approach to the Development and Pilot Testing of a Smartphone App To Support Real-time Pain Management for Adolescents with Cancer
Keywords: Adolescent
Cancer
mHealth
Pain management
Pilot study
Usability

It is estimated that 49-96% of adolescents with cancer will experience pain related to the disease and/or associated invasive procedures and treatments. Pain negatively impacts adolescent health-related quality of life (HRQL) and is associated with long-term morbidity. In response, a smartphone-based pain app, called Pain Squad+, capable of providing adolescents with real-time pain management support was developed and evaluated. Using user-centered methods, research aims were to utilize iterative cycles of usability testing with adolescents with cancer to refine the app (Study 1), to evaluate the ability to implement the Pain Squad+ app in a hypothesis-testing trial (Study 2), and to obtain estimates of treatment effects on adolescent health outcomes (Study 2). In Study 1, iterative cycles of usability testing with 16 adolescents were used to refine the Pain Squad+ app to ensure it was easy to use, easy to understand, efficient, and acceptable to adolescents. In Study 2, 33 adolescents used the app for 28-days, receiving real-time self-management advice and clinical support from a nurse dependent on self-reported pain. Acceptability of the intervention assessed quantitatively and qualitatively was high. The study accrual percent was 75% and the withdrawal percentwas 3%. Technical malfunctioning of the app was rare. The nurse received pain-related emails from 39% adolescents with a mean time to follow-up of 62.5 hours (SD=55.5). Outcome assessment piloting was successful with a mean of 94.9% (SD=4.3) of baseline and 84.3% (SD=31.0) of post-study questions completed. Adherence to pain reporting was 69.0Âą40.8%. Significant trends in improvement in pain intensity and HRQL were observed (p
Principles and Practices of Ontology Reuse
Keywords: design
logic
ontology
requirements
reuse

Reusability has always been a defining characteristic of ontologies; it is the key to their supposed benefit of shareability, and the answer to the difficulty of their development. Consequently, reuse is a crucial aspect in the paradigm of ontologies. The vision for reuse is a state in which design via reuse occurs whenever it is possible. In such a state, no unnecessary design work is ever performed, and the supposed benefits of ontologies will naturally result. Unfortunately, the vision for reuse is not feasible at the time of this writing. Reuse is currently a difficult, somewhat ad-hoc process with unpredictable results, therefore it is often not a viable alternative to designing an ontology from-scratch. This thesis addresses these issues by reducing the barriers and increasing the motivation for reuse. These objectives are achieved by way of 3 key contributions: (1) rigorous techniques for reuse, (2) a formal definition of reuse, and (3) a comprehensive architecture for reuse. Rigorous techniques are designed and presented in such a way as to minimize the demands on the developer, thereby reducing the barriers resulting from the difficulty of the task. The formal definition of reuse is applied to make the benefits of shareability and reduced design work more tractable for the developer, thereby increasing the motivation to design via reuse when appropriate. Finally, the comprehensive architecture describes the infrastructure necessary to apply the collection of solutions presented here in order to simplify their adoption. Beyond this, we consider ways in which the solutions presented here might be extended as the practice of ontology reuse evolves. The work contained here provides a solid foundation upon which the vision for reuse may be achieved and sustained.
Listening to Unheard Voices: Muslim Canadian Perceptions and Experiences of Domestic Violence and Seeking Help
Keywords: Acculturation
Attitude toward Women
Help Seeking
Intimate Partner Violence
Muslim Immigrants
Religiosity

This research was designed to contribute to an understanding of intimate partner violence perpetration and help-seeking behaviours among Muslim immigrants. The mandate of this study is not to ostracize Muslims or cast judgement for or against religious beliefs, but to better understand how religion and culture might interact with other factors to influence domestic violence perpetration. This understanding is critical for the development and implementation of effective intervention. In this study, I used a mixed-method to explore how religious perspectives, patriarchal attitudes toward women, cumulative childhood abuse and acculturation might be related to domestic violence and help-seeking at both attitudinal and behavioural levels. In a quantitative study, survey data was collected from 131 Muslim students. In a qualitative study, semi-structured interviews were conducted with 8 abusive Muslim men. The results of both studies were converging: religiosity predicted acceptance of violence and intimate partner violence via non-egalitarian attitudes toward women. Contrary to intergenerational theories of family violence, cumulative childhood experiences of abuse were not related to either acceptance or experiences of violence or help-seeking behaviours. In the quantitative study, acculturation also moderated the relationship between non-egalitarian attitudes towards women and domestic violence. The relationships were stronger for participants who were at lower levels of acculturation, compared with those at higher levels. Similarly, in the qualitative study, abusive men indicated that women acculturated faster to Canadian society and were empowered by Canadian regulations. Different levels of acculturation were considered threatening to men's positions as heads of the family and seemed to contribute to conflict and violence in the relationship. Non-egalitarian attitudes toward women also predicted beliefs toward help-seeking through acceptance of violence. Participants with higher levels of acculturation showed more egalitarian attitudes and tendencies toward help-seeking behaviours. The qualitative study also revealed that Muslim men were reluctant to seek formal help due to their traditional gender role ideology, their lack of familiarity with available services and their doubts about the effectiveness of those services. Findings around both domestic violence and help-seeking behaviours have applications for effective prevention, as well as community-based and culturally-based intervention programs for Muslim immigrants.
Understanding How Life-history Traits and Environmental Gradients Structure Diversity
Keywords: climate change
dispersal
dormancy
latitude
metacommunity
zooplankton

Determining how diversity is distributed through space and time is a fundamental goal of ecology. My research tested how speciesâ life-history traits structure diversity at landscape and broader scales and over time. I first asked how traits related to seed dispersal shape plant diversity in a naturally fragmented landscape by testing the relationship between diversity and patch characteristics (size and isolation) for species with different dispersal modes. Dispersal mode altered outcomes predicted from theory â while fragment isolation had a negative effect on wind-dispersed species, it did not influence the diversity of animal-dispersed species. I then examined how zooplankton traits (body size and dormancy) correlate with species distributions at a large scale using lakes across an 1800 km north-south gradient in western Canada. Despite predictions that body size should decrease with latitude and low temperatures, I found only weak evidence for any effect of latitude on inter- and intra- specific body size. Zooplankton dormancy dynamics are virtually impossible to test through sampling, yet dormancy underpins seasonal fluctuations in abundance and long term persistence, and it is expected to vary with climate. I therefore used an experimental approach to test how temperature and photoperiod affect hatching rates of dormant eggs from lakes across the latitudinal gradient. My results suggest that mismatches between temperature and photoperiod, as predicted to result from climate change, could drive latitude-dependent shifts in zooplankton emergence. Finally, I examined the temporal stability of diversity across the same latitudinal gradient by examining species colonization and extinction over 50 years. I found that low-latitude communities are increasingly diverse and comprised of small-bodied species despite more rapid temperature change at higher latitudes. Overall, my research has implications for how global changes, such as fragmentation and climate change, alter diversity by changing the viability of specific life-history strategies.
Characterization of the Microbial Community Composition and Benzene Activation Mechanisms in Anaerobic Benzene-Degrading Enrichment Cultures
Keywords: anaerobic biodegradation
benzene
bioremediation
metatranscriptome
microbial dark matter
petroleum hydrocarbon

Benzene is a carcinogenic petroleum hydrocarbon that is prevalent and particularly persistent in anoxic aquifers. It can be biodegraded under anaerobic conditions; however, this process is relatively slow compared to aerobic conditions, and the microorganisms and the pathways involved therein remain poorly understood. The objectives of this thesis were to accelerate the microbially-mediated benzene degradation, to characterize benzene-metabolizing microbial communities, and to identify the biochemical mechanisms involved in anaerobic benzene activation. The growth rate and substrate range of the laboratory enrichment cultures were investigated. Conclusive evidence was also obtained to support that a Deltaproteobacterium sp. (ORM2) and a Peptococcaceae sp. are the microorganisms directly involved in benzene activation. The Deltaproteobacterium ORM2 was observed to dominate under methanogenic conditions while Peptococcacceaea sp. dominated only under nitrate-reducing conditions. Syntrophic partners in these cultures were also identified. Organisms belonging to Parcubacteria were identified in all analyzed cultures and observed to grow up to 15% of the total bacteria. This is the first time a member of this clade has been observed to grow in the laboratory. In nitrate-reducing cultures, transcripts related to a putative anaerobic benzene carboxylase (abcDA) were specific to benzene, supporting carboxylation as the benzene activation mechanism in these cultures. The benzene-activating genes and mechanism in the methanogenic cultures remain unknown. Methods to extract protein from the cultures for biochemical assays were developed, and lysis using a French pressure cell press yielded crude extracts with the highest biochemical activity. Assays were developed to test various enzymatic steps, including benzoyl-CoA ligation, benzene carboxylation and carbonylation. Benzoyl-CoA ligase activity was detected in nitrate-reducing, but not in methanogenic cultures, consistent with the absence of this gene in ORM2 genome. Further assay development is required for detecting benzene transformation; however, these first experiments have provided some guidance for the next steps in functional analysis.