VictorJuiz/thesis huggingface dataset:
Revealing Retention Mechanisms of Duplicated Genes and Surveying Triple Mutant Genetic Interaction Space in Yeast

Recent genome sequencing efforts have revealed astounding genetic diversity between individuals in the human population. The current challenge is to assign functions to the thousands of genes in our genomes and to understand how individual differences in genes contribute to disease. Much progress has been made in identifying causal loci of single gene disorders for both common and rare genetic diseases. However, many phenotypes are influenced by more complex genetic interactions involving larger sets of genes and genetic variants. Thus, deciphering the genotype-phenotype relationship requires that we expand our focus beyond pair- wise genetic interactions to include complex, higher-order genetic interactions involving more than two genes. In this thesis I used the simple model organism, the budding yeast, and a method for automated yeast genetics called Synthetic Genetic Array (SGA) analysis, to construct double and triple mutants, and to measure the resulting genetic interactions by using colony size as a proxy for cell fitness. I first applied this methodology to dissect and characterize the mechanisms of functional divergence of duplicated genes. I also applied it more generally to estimate the prevalence of complex genetic interactions in a eukaryotic cell. My results suggest that triple mutant genetic interactions occur frequently in the yeast genome and are therefore expected to have a major impact on our understanding of the relationship between genotype and phenotype. This map of complex genetic interactions provides a unique dataset for studying how the content of our genomes is shaped and how this relates to complex disease.

Keywords: complex genetic interactions
genetic interactions
genetics
genomics
higher-order genetic interactions
yeast
Advisor: Boone, Charles M
Andrews, Brenda J
Maternal One-carbon Nutrients Status and Effects on DNA Methylation and Hydroxymethylation in Newborn Infants

DNA methylation is an important epigenetic determinant in gene expression, aberrancies of which are mechanistically related to the development of several diseases. During embryogenesis, a new DNA methylation pattern of the fetus is established, rendering this period highly susceptible to environmental modifiers. Maternal dietary intake and status of one-carbon nutrients (folate, vitamins B6, B12, choline, and betaine) have the potential to modulate DNA methylation via the provision of S-adenosylmethionine. The primary objective of this study was to determine the effects of maternal one-carbon nutrient status on DNA methylation and hydroxymethylation in umbilical cord blood mononuclear cells. This study also characterized folate and pyridoxal 5â phosphate (vitamin B6) concentrations in Canadian pregnant women and in umbilical cord blood. Demographic and dietary information was assessed in 368 pregnant women. Maternal blood samples were collected in early pregnancy and at the time of delivery when an umbilical cord blood sample was also collected. Blood concentrations of one-carbon nutrients including serum and RBC folate, serum vitamin B12, plasma pyridoxal 5â phosphate, plasma choline and betaine were measured. Mononuclear cells from umbilical cord blood were extracted and total global DNA 5-methylcytosine and 5-hydroxymethylcytosine content was calculated. Folate concentrations in maternal and cord blood were high, while pyridoxal 5â phosphate concentrations were adequate. There were no strong associations between one-carbon nutrient concentrations and DNA methylation or hydroxymethylation, although maternal concentrations measured in early pregnancy seemed to have more association than later time point measurements. Further studies are warranted to elucidate the potential impact of maternal one-carbon nutrient status on DNA methylation and hydroxymethylation in the developing fetus, which has the potential to modulate disease risk, including cancer, osteoporosis, metabolic and cardiovascular diseases, in the offspring later in life.

Advisor: Kim, Young-In
O'Connor, Deborah L
Acceptability and Feasibility of Behavioural and Sweet-tasting Solution Interventions for Procedural Pain Treatment in Neonatal Units in Kenya

Acceptability and Feasibility of Behavioural and Sweet-tasting Solution Interventions for Procedural Pain Treatment in Neonatal Units in Kenya Oâ Brien Munyao Kyololo Doctor of Philosophy Graduate Department of Nursing Science University of Toronto 2016 Abstract Background Although, over the last decade, the frequency of procedures has decreased and pain treatment practices have improved in high-income countries, in most low- and middle-income countries (LMICs), the burden of pain remains very high and procedural pain is severely undertreated. The nature and frequency of procedures and pain treatment practices has not been comprehensively examined in Kenya. Additionally, acceptability and feasibility of behavioural and sweet-tasting solution interventions has not been comprehensively examined. Objectives To determine the: (a) nature and frequency of painful procedures, (b) use of behavioural and sweet-tasting solution pain treatment interventions and (c) acceptability and feasibility of behavioural and sweet-tasting solution interventions and factors influencing their acceptability and feasibility in Kenya. Methods A three-phase sequential mixed-methods study involving (a) review of medical charts, (b) prospective observations and (c) photo-elicitation semi-structured interviews was conducted in two neonatal units in Kenya. Descriptive analysis, t-tests, Mann-Whitney U test, chi-square tests, multiple regression and ecological comparative analysis were used to describe the frequency of procedures, use of pain treatment interventions and factors predicting frequency of procedures and use of interventions. Inductive content analysis was conducted for qualitative data. Results Neonates experienced 1.6 (SD = 1.1, range 1-12) painful procedures per day; more tissue-damaging (1.2Âą1.7) than non tissue-damaging procedures (0.3Âą0.6) were performed (p = .03). Term neonates were less likely to undergo procedures (RR 0.85, 95% CI [0.76, 0.95], p = .003) while neonates were 1.8 times and 1.6 times more likely to undergo procedures during the 3rd - 7th day of life and if admitted in the Level II unit respectively (p

Keywords: Acceptability
Behavioural
Feasibility
Neonatal units
Procedural pain
Sweet-tasting
Advisor: Stevens, Bonnie
Linking Laboratory Engine Studies to Real-world Observations: Assessing the Air Quality Implications of Gasoline Direct Injection Engines

In response to stringent regulations on fleet-average fuel economy, vehicle manufacturers have increasingly replaced port fuel injection (PFI) engines with gasoline direct injection (GDI) engines. These engines emit substantial quantities of ultrafine particulate matter (PM) and black carbon (BC) which is of concern due to their associated health and climate effects, respectively. This thesis investigated GDI emissions, with a focus on the particle phase, in both laboratory and real-world environments to help understand the air quality impacts of this engine technology. As part of the study, advanced PM measurement techniques were assessed, and a correction protocol for a popular high-time resolution particle sizing instrument needed to accurately measure vehicle exhaust size distributions was developed. A laboratory study to quantify phase-partitioned polycyclic aromatic hydrocarbon (PAH) concentrations was also conducted. Compared to PFI engines, GDI engines emitted elevated concentrations of heavy molecular weight PAHs, including benzo(a)pyrene, a PAH with established associations to negative health outcomes. The GDI engine exhaust also had elevated concentrations of the PAHs pyrene and fluoranthene; these PAHs also exhibited the greatest extent of particle-gas partitioning. A study of real-world GDI emissions in an urban environment showed that GDI particle number and BC emissions were in the upper end of the fleet distribution, and that exhaust plumes exhibited dynamic behaviour in the near-road region, with increasing particle number emission factors with increasing distance from the roadway. This behaviour was unique to GDI vehicles, the same effects were not observed for heavy-duty garbage trucks or a PFI-equipped vehicle. Comparing size distributions at different distances from the roadway, rapid particle growth of sub-5 nm soot cores due to condensation of low volatility organic gases, such as pyrene and fluoranthene, was proposed to be the dominant growth mechanism in GDI vehicle exhaust. Comparing laboratory and real-world emission factors, BC emission factors were in good agreement, while real-world particle number emission factors were up to an order of magnitude higher. An estimate of the climate impacts of increased BC relative to fuel savings from GDI also showed that fuel economy gains of up to 12% may be needed to offset the radiative forcing of BC.

Keywords: air quality
black carbon
emission factors
engine emissions
gasoline direct injection
ultrafine particles
Advisor: Evans, Greg J
Wallace, James S
Perceptions, Experiences and Management of Knee Symptoms in Adults Age 35-65 Years - A Qualitative Study

Background: Osteoarthritis (OA) is a highly prevalent and costly chronic condition which can begin as early as the third or fourth decade of life. To date, interventions have focused on older adults. There is an urgent need to focus on younger adults with OA symptoms to improve management and potentially limit progression of OA. However, there is an inadequate understanding of the perceptions, experiences and management of younger adults to begin to develop interventions which address peoples’ needs earlier in life. Objectives: To explore, in adults aged 35-65 years with knees symptoms: 1) the meaning of knee symptoms to people; 2) how people manage knee symptoms; and 3) the consequences of knee symptoms on peoples’ lives. Methods: Six focus groups and 10 one-on-one interviews were conducted with 51 participants (median age 49; 61% female) who self-reported knee OA or reported knee symptoms (i.e. pain, aching or stiffness) on most days of the past month. Constructivist grounded theory guided sampling, data collection and analysis. Data were analyzed using a constant comparative method, in which comparisons constituted each stage of analysis. Results: Central to participants’ understanding of their knee symptoms was a perception that symptoms were preventable, meaning there was the potential to prevent the onset of symptoms and to alter the course of symptoms. Their approach to management was not linear, but rather, a process that moved back and forth between searching for “solutions” and active management (ongoing use of strategies). During the process, participants consulted health care providers but often perceived that medical care offered limited options and guidance. Participants experienced a range of disruptions and changes in their lives due to knee symptoms. They described the consequences of symptoms on their physical activity, social life and emotions. Participants reported a new awareness of their knee, a lack of trust in their knee and that their sense of self was altered. Conclusions: This study provides new insights into the perceptions and experiences of adults age 35-65 years with knee symptoms. Findings have implications for the development of health policies and interventions to support primary and secondary prevention of knee symptoms.

Keywords: Disease management
Focus groups
Illness perceptions
Interviews
Osteoarthritis
Qualitative Research
Advisor: Davis, Aileen M
Josephs of the Country: James Jones's Thirty-year Men and the Image of the WWII Soldier in American Culture

This dissertation analyzes the war trilogy written by James Jones and argues that Jones’s GI characters are foundational sources of the American World War II soldier’s popular culture image in their own time and in the decades that followed. Not only do From Here to Eternity, The Thin Red Line, and Whistle demonstrate the influences of factors both historic and contemporary across the thirty years of their publication span, but they also serve as a generative medium in which the American soldier’s representative capacity, fluidity, and adaptability are highlighted. While a central goal of this thesis is to encourage new understandings of Jones’s characters as interstitial figures capable of expressing dissent within the channels of regulated society, the study also offers a critique of the ways that these same soldiers perpetuate certain values associated with a traditional American character. The dissertation begins by showing how Jones’s secondary soldiers rework the figure of the colonial yeoman in contemporary contexts, proceeds by explaining the characters’ reflection of Weberian influences in the organization of post-war American life, and finishes by examining their response to America in Vietnam. At stake in the study is a deeper understanding of the soldier’s image in American life and the ways that this malleable image both shapes and reflects the cultural imagination. By seeking to restore balance to the discourse currently surrounding the soldier, the study engages current scholarship in the fields of Jones scholarship, studies of the war novel, and veteran studies.

Keywords: American war fiction
WWII American novels
Advisor: Dolan, Neal
A Non-invasive Validation Method for Conductivity Imaging

Conductivity imaging is of great potential importance in many biomedical applications, such as in the early diagnosis of breast tumors and the diagnosis and therapy planning for cardiac arrhythmia. With significant progress in conductivity imaging, there is a growing need for a quantitative non-invasive validation method. A new non-invasive validation procedure has been developed to assess the accuracy of any low-frequency conductivity imaging method. This procedure is based on Current Density Imaging, a well-established procedure to measure currents inside an object. A testing current is applied to the object under study. The proposed validation protocol compares measurements of this testing current against that computed using a forward solver. The forward solver computes the current using the conductivity determined by the method under test and the boundary conditions for the measured current. We implemented the proposed procedure on three conductivity imaging methods. The first, Current Density Impedance Imaging (CDII), uses measurements of two currents to determine the isotropic conductivity of the structure under test. The second, Diffusion Tensor Current Density Impedance Imaging (DT-CD-II), was recently developed in our laboratory for imaging anisotropic conductivities and relies on the measurement of the diffusion tensor and of two currents. The third method requires only the magnitude of one current and of the corresponding voltage on the boundary of the object to determine an isotropic conductivity, and will be referred to as MCDII. The validation method was first tested on earlier experimental data for CDII. It was then used to assess the accuracy of DT-CD-II on experimental data for an anisotropic conductivity. We show that the results of the DT-CD-II reconstruction are better than those obtained using CDII on the same current measurements and assuming the conductivity to be isotropic. The validation procedure was also shown to be applicable to a third, and very different conductivity imaging method (MCDII), that requires only the magnitude of one current and the corresponding boundary voltage. The thesis includes the first three-dimensional numerical implementation of this method. The validation yields a quantitative comparison of its accuracy with that of CDII on the same simulated data.

Advisor: Joy, Michael LG
Nachman, Adrian I
Development of an automated and scalable lab-on-a-chip platform with on-chip characterization

Digital Microfluidics (DMF) is a fluid-handling technique that enables precise control of drops on an array of electrodes using electrostatic forces. In contrast to most other lab-on-a-chip technologies (e.g., channel-based microfluidics), DMF is highly reconfigurable (i.e., function is defined by software and not by the physical structure of the chips). Thus, DMF offers the possibility for a truly general-purpose lab-on-a-chip platform, where a wide variety of biological and chemical protocols may be implemented at the microscale, under automated control, and on a generic chip. Widespread adoption of this technology has thus far been limited by: (1) lack of access to control hardware/software, (2) the high-cost and specialized equipment required for fabricating DMF chips, (3) an incomplete understanding of DMF device physics, and (4) lack of methods for performing on-chip characterization. This thesis aims to address these limitations. We describe the development of a control instrument and software capable of applying a precise electrostatic force and measuring device capacitance, drop position, and drop velocity on-chip. We also demonstrate a low-cost method for fabricating DMF devices that does not require a cleanroom facility: inkjet printing of silver electrodes on paper. We present new on-chip methods for characterizing the resistive forces that oppose drop movement on DMF and report the results from an initial screen of conditions, establishing the effects of surface tension, conductivity, viscosity, protein content, and driving frequency on resistive forces. Finally, we demonstrate an extension of impedance-based drop sensing techniques (e.g., device capacitance, drop position, and drop velocity) to facilitate measurement across multiple electrodes in parallel. In combination, these advancements represent significant progress toward the goal of establishing a general-purpose lab-on-a-chip platform that is accessible to the wider biomedical and chemical research communities.

Keywords: digital micrfluidics
electrowetting
feedback
inkjet printing
microfluidics
resistive forces
Advisor: Wheeler, Aaron R
Monoamine Oxidase A in Relation to Subtypes and Treatment of Major Depressive Disorder

Identification of central biomarkers related to subtypes of major depressive episodes (MDEs) can contribute to a more personalized treatment approach of major depressive disorder (MDD). Monoamine Oxidase-A (MAO-A) is a replicated central biomarker of MDE and may represent a biomarker of MDE subtypes. The current body of research aimed to identify clinical predictors of elevated MAO-A total distribution volume (VT), to evaluate the relationship of MAO-A VT to replicated brain structural changes seen in MDD and to assess the targeting of MAO-A with monoamine oxidase inhibitors (MAOIs). Greater severity and reversed neurovegetative MDE symptoms were associated with elevated MAO-A VT in the prefrontal cortex (PFC) and anterior cingulate cortex (ACC) (Multivariate Analysis of Variance (MANOVA), severity: F(2,38)=5.44, p=0.008; reversed neurovegetative symptoms: F(2,38)=5.13, p=0.01). There was no significant relationship between hippocampal MAO-A VT and hippocampal volume or PFC and ACC MAO-A VT to PFC or ACC cortical thickness in MDD. Mean brain MAO-A occupancies ranged from 74-84% for moclobemide (300-1200mg daily dose) and was 87% for phenelzine (45-60mg daily dose). There was significantly greater MAO-A occupancy by phenelzine (45-60mg) and higher dose moclobemide (900-1200mg) compared to lower moclobemide doses (300-600mg) (F(7,16)=3.94, p=0.01). In conclusion, this research suggests elevated MAO-A VT as a distinct biomarker of MDE compared to structural brain changes that has the greatest elevation in MDEs with the highest severity or reversed neurovegetative MDE symptoms and this research has identified the optimal occupancy and treatment algorithm of MAOIs available to target MAO-A.

Keywords: Major Depressive Disorder
Monoamine Oxidase A
Monoamine Oxidase Inhibitors
Positron Emission Tomography
Advisor: Meyer, Jeffrey H
Kish, Stephen J
13C PEG as an In Vivo Macromolecular Probe for MRI and Biophysical Studies of Detergent-Peptide and Detergent-Detergent Interactions using NMR

In the first part of this thesis, a new platform technology is demonstrated for the direct in vivo observation and quantification of macromolecular constituents, such as proteins and drug delivery systems, using 1H MRI. To overcome sensitivity challenges, a 28 kDa non-immunogenic tag is employed, consisting of 13C-enriched polyethylene glycol (PEG), whose spectroscopically equivalent 1H nuclei provide a signal amplification of 2500. Passing the 1H PEG signal through the directly coupled 13C nuclei enables the removal of background water and fat signal. Imaging capabilities are demonstrated by monitoring the real-time clearance of PEG and pegylated albumin in the hind leg of a mouse. Improvements to the initial imaging methodology are subsequently proposed, which increase the sensitivity and extend the imaging capabilities to abdominal and cranial regions. Ex vivo detection of pegylated constituents is also possible using NMR spectroscopy. Using blood as a sample biological fluid, clearance profiles of both unlabeled and 13C labelled PEG, as well as a pegylated protein were determined in rats. The second part of this thesis describes biophysical interactions of detergents with either peptides or other detergent molecules. Firstly, the effects induced by a single polar substitution on the structure and topology of model α-helical transmembrane segments were investigated. Upon substitution of a central isoleucine for an asparagine, diffusion NMR measurements revealed that the asparagine-containing peptide bound ~ 20% less detergent. Secondly, NMR was used to investigate the micellization process. A rapid method to determine thermodynamic and volumetric parameters, which relies on a single subtle change in the 1H chemical shift, was developed. The thermodynamic quantities were then related to spectroscopic studies of topology and micelle structure.

Keywords: HMQC
molecular imaging
MRI
PEG
poly(ethylene glycol)
quantitative
Advisor: Prosser, Robert S
Macdonald, Peter M