VictorJuiz/thesis huggingface dataset:
Search for DNA Methylation Biomarkers in the Circulating DNA of Prostate and Colorectal Cancer

Early diagnosis represents an effective way to improve patient prognosis in cancer. New opportunities for cancer diagnosis and screening may arise from identification of cancer-specific epigenetic alterations in the cell-free circulating DNA (cirDNA). This study investigated biomarkers at the level of DNA methylation in the plasma cirDNA of individuals affected with prostate cancer or colorectal cancer. A methylation-sensitive restriction enzyme-based method was used to enrich methylated DNA fractions, which were interrogated on CpG island and human genome tiling microarrays. A number of genes and non-coding loci exhibited differential methylation between prostate cancer patients and controls. The candidate loci identified from these microarray experiments underwent verification by bisulfite modification coupled with pyrosequencing. Our results suggest that microarray-based studies of DNA methylation in the cirDNA can be a promising avenue for the identification of epigenetic biomarkers in cancer.

Keywords: cancer
biomarkers
epigenetics
circulating DNA
early diagnosis
DNA methylation
Advisor: Petronis, Arturas
An in silico Characterization of Microbial Electrosynthesis for Metabolic Engineering of Biochemicals

A critical concern in metabolic engineering is the need to balance the demand and supply of redox intermediates. Bioelectrochemical techniques offer a promising method to alleviate redox imbalances during the synthesis of biochemicals. Broadly, these techniques reduce intracellular NAD+ to NADH and therefore manipulate the cell’s redox balance. The cellular response to such redox changes and the additional reducing can be harnessed to produce desired metabolites. In the context of microbial fermentation, these bioelectrochemical techniques can improve product yields and/or productivity. We have developed a method to characterize the role of bioelectrosynthesis in chemical production using the genome-scale metabolic model of E. coli. The results elucidate the role of bioelectrosynthesis and its impact on biomass growth, cellular ATP yields and biochemical production. The results also suggest that strain design strategies can change for fermentation processes that employ microbial electrosynthesis and suggest that dynamic operating strategies lead to maximizing productivity.

Keywords: in silico
bioelectrosynthesis
metabolic engineering
flux balance analysis
microbial electrosynthesis
SPEEQ
Advisor: Mahadevan, Radhakrishnan
Identifying Mechanisms Used by Adherent-invasive Escherichia coli Associated with Crohn Disease to Evade the Immune System

Background: Adherent-invasive Escherichia coli (AIEC) is a pathogen isolated from the ileum of patients with CD. IFNγ is a key mediator of immunity, which regulates inflammatory responses to microbial infections. Previously, we showed enterohemorrhagic E. coli prevents STAT1 activation. Aims: To determine; 1) whether activation of STAT1 by IFNγ was prevented following AIEC infection, and 2) define the mechanisms used. Methods: Human epithelial cells were infected with AIEC strains or other pathogenic and commensal E. coli strains. Following infection, cells were stimulated with IFNγ. Activation of STAT1, was monitored by immunoblotting. Results: AIEC strains prevented STAT1 phosphorylation in response to IFNγ. Effect required live bacteria with active protein synthesis. A bacterial product was responsible for blocking STAT1 signalling and interfered with downstream signalling cascades. Conclusion: Suppression of epithelial cell STAT1 signal transduction by AIEC strains represents a novel mechanism by which the pathogen evades host immune responses to the infection.

Keywords: Crohn Disease (CD)
Adherent-Invasive Escherichia coli (AIEC)
Interferon gamma (IFNγ)
Signal transducer and activator of transcription 1 (STAT1)
Advisor: Sherman, Philip M.
Differential Roles of Tryptophan Residues in the Functional Expression of Human Anion Exchanger 1

Anion exchanger 1 (AE1) is a 95 kDa glycoprotein that facilitates Cl-/HCO3- exchange across the erythrocyte plasma membrane. Seven conserved tryptophan (Trp) residues are in the AE1 membrane domain; at the membrane interface (Trp648, Trp662, and Trp723), in transmembrane segment (TM) 4 (Trp492 and Trp496), and in hydrophilic loops (Trp831, and Trp848). All 7 Trp residues were individually mutated into alanine (Ala) and phenylalanine (Phe) and transiently expressed in human embryonic kidney (HEK)-293 cells. The 7 Trp residues could be grouped into three classes according to the impact of the mutations on the functional expression of AE1: class 1, normal expression, class 2, expression decreased, and class 3, expression decreased by Ala substitution. These results indicate that Trp residues play differential roles in AE1 expression depending on their location in the protein and suggest that Trp mutants with a low expression are misfolded and retained in the ER.

Keywords: Anion exchanger 1
Membrane protein
Tryptophan
Protein expression
Protein function
Trafficking
Cell surface expression
N-glycosylation
Advisor: Reithmeier, Reinhart A. F.
The Effects of Immigrant Status and Ethnicity on the Propensity and Intensity of Informal Care Received in Canada

The literature on the effects of race and ethnicity on informal caregiving is sparse and incomplete. Furthermore, most caregiving studies do not control for immigrant status. In the few studies that have analyzed the impact of ethnicity on informal care, ethnicity was categorized as African American, Hispanic, or non-Hispanic White. In Canada, the relationship between informal care and immigrant status and ethnicity needs to be better understood as the country has a growing population of immigrants and individuals who will require informal care in the future. This thesis aims to understand how immigrant status and ethnicity affects the propensity and intensity of care received by using probit and ordinary least squares models. Throughout the thesis, immigrant status was measured as binary variable (0/1) and as year of immigration and region of origin.

Keywords: Informal Care
Immigrant Status
Advisor: Coyte, Peter C.
Resting Neural Activity Patterns in Auditory Brain Areas following Conductive Hearing Loss

Conductive hearing loss (otitis media) in young children can effect speech and language development. However, little is known about the effects of conductive loss on neural activity in the auditory system. Hypothesis: Conductive hearing loss will change resting activity levels at the inner hair cell synapse, and lead to auditory deprivation of central auditory pathways. A conductive loss was produced by blocking the ear canals in mice. Resting neural activity patterns were quantified in brainstem and midbrain using c-fos immuno-labelling. Experimental subjects were compared to normal hearing controls and subjects with cochlear ablation. Conductive loss subjects showed a trend in reduction in c-fos labelled cells in cochlear nucleus and the central nucleus of inferior colliculus compared to normal controls. Results seen in this study may indicate the influence of conductive hearing loss on the developing auditory brain during early postnatal years when the system is highly plastic.

Keywords: Conductive hearing loss
Auditory
c-fos
immunocytochemistry
spontaneous activity
otits media
inner hair cell
ribbon synapse
Advisor: Harrison, Robert
Cryoprecipitate Transfusion: Assessing Appropriateness and Dosing in Trauma

Cryoprecipitate is commonly used outside guidelines. In trauma, the appropriate cryoprecipitate dose and its impact on plasma fibrinogen levels are unclear. This retrospective study aims to evaluate: (1) the appropriateness of cryoprecipitate transfusion in trauma; and (2) the plasma fibrinogen response to cryoprecipitate transfusion during massive transfusion in trauma. Fibrinogen levels of < 1.0 g/L within 2 and 6 hours of cryoprecipitate transfusion were used for assessing appropriateness. Out of 394 events, 238 (60%) and 259 (66%) were considered appropriate using 2 and 6 hour criteria, respectively. A dose of 8.7 (±1.7) units caused a mean increase in fibrinogen levels of 0.55 (±0.24) g/L, or 0.06g/L per unit. In our hospital, where transfusion guidelines and policies for rapid blood product and laboratory turnaround times exist, it is possible to achieve high rates of appropriateness for cryoprecipitate transfusion in trauma. The current recommended dose causes a modest increase in fibrinogen levels.

Keywords: Cryoprecipitate transfusion
appropriateness
dosing
trauma
Advisor: Rizoli, Sandro Baleotti
Enzymes and Feedstocks for Sustainable Biomass Utilisation

Modern biorefineries provide a framework for the sustainable conversion of biomass to biofuels and biochemicals. In light of the recalcitrance of lignin in woody feedstocks, the native shrub eastern leatherwood is proposed as a model hypolignified species. Xylem tissue of this low-lignin plant contained syringyl-rich lignin that was more easily hydrolysed and did not appear to be localised in the middle lamellae. Also, leatherwood cellulose was less crystalline and the xylan was highly acetylated. While viable low-lignin plants will enable the sustainable utilisation of woody feedstocks, high-value bioproducts are needed to economise future biorefineries. The carbohydrate oxidoreductases galactose oxidase and glucooligosaccharide oxidase were studied for use in the oxidation and derivatisation of plant-derived polysaccharides for the production of such high-value bioproducts. The carbohydrate-binding module of galactose oxidase was necessary for recombinant protein production. Also, a mutant library of glucooligosaccharide oxidase variants was produced to generate enzymes with novel activity.

Keywords: biomass
biorefinery
feedstock
lignin
eastern leatherwood
carbohydrate oxidoreductase
galactose oxidase
glucooligosaccharide oxidase
Advisor: Master, Emma
The Role of Starch Physicochemical Properties in Determining the Glycaemic Index of Novel Potato Varieties

Potatoes are often thought of as high GI. It is known that cooking and cooling affect GI and that these effects may be mediated through the physicochemical properties of their starch. As part of a Canadian initiative to develop low GI potatoes, novel potato varieties which differed in starch composition were tested in 2 separate studies. In study 1, we determined the GI of 8 varieties and found that cooling produced a wide range of effects (0-50% reduction in GI). In study 2, four previously tested varieties were re-examined. A significant variety-x-treatment interaction (p<0.01) was observed with cooling reducing GI in some potatoes. Examination of the starch properties and their role in determining GI showed that RDS was positively associated with GI (r2= 0.85, p= 0.001) and SDS (r2=-0.60, p= 0.02) and amylose (r2=-0.99, p=0.007) negatively associated with GI. No relationship between RS and phosphorous content and GI was observed.

Keywords: Glycaemic Index
Potatoes
Advisor: Wolever, Thomas M. S.
Mutational Analysis of FERM Domain Proteins CG34347 and Cdep in Drosophila

Crumbs is a transmembrane protein and apical determinant in Drosophila epithelial cells. Its cytoplasmic tail contains a PDZ and a FERM domain-binding site through which Crumbs interacts with the FERM proteins Yurt, Moesin and Expanded. Recent evidence suggests that Crumbs can also interact with the uncharacterised FERM proteins CG34347 and Cdep. The main objective of my thesis was to generate mutations in CG34347 and Cdep to facilitate the functional analysis of these genes. I generated a mutation for Cdep that remains to be characterised and two mutant lines for CG34347; one lacking the first exon and one lacking the entire gene, using a FRT-based recombination strategy. Both CG34347 mutants cause severe ovarian defects. The most consistent defect is a multilayering of the interfollicular stalk. These defects are also observed when Notch, Hippo, Wingless and Hedgehog signalling pathways are overactive in ovaries suggesting that CG34347 participates in one of those pathways.

Keywords: Drosophila
Cell Signalling
Crumbs
Polarity
FERM
Cell Signalling
PatJ
Armadillo
Oogenesis
Interfollicular stalk
Notch
Wingless
Hedgehog
Hippo
Follicular epithelium
Cell division
Ovaries
Yurt
Advisor: Tepass, Ulrich
MAX-DOAS Measurements of Nitrogen Dioxide and Aerosol

Multi-axis differential optical absorption spectroscopy (MAX-DOAS) was applied to retrieve tropospheric NO2 and aerosol vertical profiles from downtown Toronto, and King City, Ontario during select periods in 2006 – 2010. Linear regression of MAX-DOAS NO2 vertical column density (VCD) versus OMI (satellite) VCD yielded a good correlation (R = 0.88) and MAX-DOAS negative bias of 20%, which was within the reported uncertainty of the MAX-DOAS and OMI VCD. The average regional Toronto VCD (remotely-sensed via MAX-DOAS and OMI) was half of the near-road VCD obtained in-situ (2.4 x 1016 ± 1.2 x 1016 molec/cm2). MAX-DOAS measurements of O4 were coupled with radiative transfer modeling to obtain vertical aerosol extinction profiles and aerosol optical depth (AOD). A strong linear agreement was observed between PM2.5 concentration and aerosol extinction coefficient (R = 0.92), and MAX-DOAS versus sun photometer AOD (slope = 0.94; R= 0.90).

Keywords: Differential Optical Absorption Spectroscopy
MAX-DOAS
tropospheric nitrogen dioxide and aerosol
vertical pollutant profiles
aerosol optical properties
Advisor: Evans, Greg J.
Characterization of Declohorinating Populations in the WBC-2 Consortium

The WBC-2 consortium was characterized using quantitative PCR and analytical techniques to associate growth of dechlorinating bacteria to each step of the 1,1,2,2-Tetrachloroethane (TeCA) degradation pathway. The consortium was found to degrade TeCA through dichloroelimination to trans-1,2-dichloroethene (tDCE), and reductive dehalogenation to Vinyl Chloride (VC) and ethene. Thus the pathway was hypothesized to provide three distinct niches for three genera of dechlorinating bacteria, Dehalobacter, Dehalogenimonas and Dehalococcoides. Using qPCR to track growth over two time course experiments at different inoculum dilutions, the Dehalobacter species showed significant growth on the first step of TeCA dihaloelimination to tDCE Dehalococcoides and Dehalogenimonas species grew on the dechlorination products. The Dehalogenimonas species, a novel non-Dehalococcoides, was found to grow only on tDCE. The Dehalococcoides species also grew on cDCE, less well on tDCE, and on VC.

Keywords: WBC-2
Dechlorination
Dehalococcoides
Dehalobacter
Dehalogenimonas
1,1,2,2-Tetrachloroethane
Advisor: Edwards, Elizabeth A.
The Effect of Molecular Weight on Polypropylene Foaming

The effect of molecular weight on polypropylene (PP) extrusion foaming was investigated and the process to make soft touch, largely expanded, high cell density non-crosslinked PP foam using environmental friendly CO2 is presented. In previous research, when the cell density was high, cell opening was dominant and large expansion could not be achieved even in HMS PP materials. The effects of processing and material parameters on the foam morphologies of PP materials with three different melt flow rate (MFR) were studied using single-screw tandem foam extrusion system. By selecting proper material and die, and by tailoring the processing conditions, large expansion (25 fold) and high cell density (>109 cells/cm3) was successfully achieved in the high MFR PP without any additives. The mechanism of locally induced crystallization was found to be significantly affecting the foaming behavior of PP and was successfully verified using SEM, DSC, HPDSC, shear viscosity and solubility measurements.

Keywords: Polypropylene Foaming
Extrusion
Crystallization
Non-crosslinked
Advisor: Park, Chul B.
Adsorption of Oligonucleotides on Quantum Dots Coated with Zwitterionic Ligands and other Water-soluble Ligands

A strategy to ameliorate non-specific adsorption of oligonucleotides onto Quantum Dots (QDs) is investigated where QDs are being used as a platform for the development of optical bioprobes for nucleic acid detection. Certain zwitterionic structures as coatings on QDs have recently been shown to reduce non-specific binding of proteins. In this thesis, a lysine side chain is attached to a dihydrolipoic acid (DHLA) derivative to create a zwitterionic bidentate ligand that has primary amine and carboxyl termini. Such coatings on CdSe/ZnS QDs were studied to assess adsorption of oligonucleotides across a range of pH to better understand the relationship between surface charge and adsorption. The change of pKa of charged terminal groups on QD surfaces for a variety of different water soluble ligands were evaluated using pseudo-titration curves, and indicated up to 3 orders of magnitude shift of pKa at a QD surface in comparison to pKa in bulk solution.

Keywords: Quantum dots
Zwitterionic
Advisor: Krull, Ulrich Jorg
Characterization of ZHX1 in Axillary Lymph Node-negative Breast Cancer

Women with breast cancer without local metastasis to the axillary lymph nodes (axillary lymph node-negative, ANN) have a good prognosis. However, 20 to 30% of patients with ANN breast cancer will still experience recurrence and distant metastases. Lymphatic invasion (LVI) is an important prognostic factor for ANN breast cancer. Zinc fingers and homeoboxes 1 (ZHX1) was identified as a candidate gene involved in LVI and associated with early recurrence of ANN breast cancer. I examined expression of ZHX1 in breast cancer cell lines and ANN breast tumour samples and discovered that it is expressed at variable levels. I also investigated ZHX1 copy number and determined that amplification does not appear to be a mechanism of its over-expression. From bioinformatic and proteomic analyses, ZHX1 was discovered to potentially be phosphorylated. Overall, these studies suggest that ZHX1 may be involved in ANN breast cancer.

Keywords: Breast Cancer
Gene Expression
Recurrence
Lymphatic Invasion
ZHX1
Advisor: Andrulis, Irene
The Haj in the Urbs Prima in Indis: The Regulation of Pilgrims and Pilgrim Traffic in Bombay, 1880 to 1914

In this thesis I argue that the management of Muslim pilgrims and the Haj traffic in Bombay was the result of the localization of an international regime of regulation aimed at controlling Hajis as mobile threats to public health and imperial security. International scientists, doctors, and politicians problematized Hajis as diseased, dangerous and disorderly through discourse produced in print material and at international conferences taking place across the globe. Local, elite concerns over their own power, Bombay’s urban spatial order, and the city’s international trade shaped the way these larger global and imperial projects were implemented in Bombay. These findings point to the importance of local, place-based social, political and economic structures in the day-to-day governance of empire.

Keywords: Bombay
Haj
Empire
Regulation
Advisor: Lewsis, Robert
The Effects of Distractions and Driver's Age on the Type of Crash and the Injury Severity Sustained by Occupants Involved in a Crash

This thesis investigates the associations between crash outcomes, the existence and type of driver distraction as well as driver’s age. The crash outcomes considered in this thesis consist of the type of crash as well as the injury severity sustained by occupants involved in the crash. An ordered logit model was built to predict the likelihood of severe injuries and a multinomial model was developed to predict the likelihood that a driver will be involved in one of three common crash types: singular, angular, and rearend. In these models, various factors (e.g., weather, driver’s gender, and speeding) have been statistically controlled for, but the main focus was on the interaction of driver’s age and distraction type. The findings of this thesis have implications for policy making and prioritizing capabilities of distraction-related safety systems.

Keywords: Driver Distraction
Human Factors
Injury Severity
Crash Type
Ordered Logit Model
Multinominal Model
Advisor: Birsen, Donmez
Lanthanide-encoded Poly(styrene-co-methacrylic Acid) Microspheres: Synthesis and Characterization

Lanthanide-encoded polystyrene-co-methacrylic acid (P(S-MAA)) microspheres with narrow size distributions were synthesized by two-stage dispersion polymerization. I examined how the amounts of methacrylic acid (MAA) and lanthanide (Ln) salts affect the composition of the particles formed in the reaction. Also, I performed a systematic study of Ln ion release into different aqueous solutions. In normal buffers, these particles were stable against ion leakage, even upon prolonged storage and stirring. When strong chelating agent ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DTPA) were present in buffer, the loss of Ln ions increased to 15 % after 8 weeks. A preliminary kinetic study of Ln ion incorporation was performed to help understand the particle formation mechanism.

Keywords: polystyrene
dispersion polymerization
lanthanide
mass cytometry
microspheres
ion release
Advisor: Winnik, Mitchell A.
Costimulation-mediated Rescue of Superantigen-activated T cells in an Animal Model of Kawasaki Disease

Lactobacillus casei cell wall extract (LCWE)- induced coronary arteritis in mice models Kawasaki disease (KD). LCWE injections consist of T-cell dependent factors that expand superantigen (SAg)-activated T-cell receptor (TCR) Vβ6+ cells, and T-cell independent factors (i.e. TLR2 activity) that localize and sustain the immune response. TLR2 can upregulate costimulatory molecules to rescue SAg-activated T-cells from apoptosis. Accordingly, SAg-activated costimulation-rescued TCRVβ6+ cells are predicted to express activation markers, produce cytokines and be able to induce coronary arteritis. MAM was identified as a SAg able to activate TCRVβ6+ cells in a manner similar to LCWE; however a combination of MAM and TLR2 agonist Pam3Cys could not induce coronary arteritis. As another marker of disease, leukocyte recruitment molecule expression in the hearts of MAM+Pam3Cys- injected mice was found to be lower than in LCWE- injected mice. Therefore, LCWE contains unique features beyond TCRVβ6 stimulation and TLR2 activity that are important for disease induction.

Keywords: kawasaki disease
superantigens
Advisor: Yeung, Rae S. M.
In Silico Metabolic Network Reconstruction of Scheffersomyces Stipitis

In this study, a genome-scale metabolic model was constructed using published genomic and biochemical data. By employing the flux balance analysis (FBA) framework, the model was able to accurately predict ethanol yields on various carbon substrates, secretion profiles, and key characteristics of central metabolism under various growth conditions. A by-product of the model development was the construction of a pathway genome data-base (PGDB) of the yeast, named PichCyc. The PGDB was constructed using Pathway Tools and the database contains 5,841 genes, 1,457 reactions, 994 gene-associated reactions, and 1,475 metabolites. Pathway Tools also facilitated the annotation of an additional 155 genes through the use of Pathway Hole Filler. Together with the constraint-based model, a platform for model-guided metabolic engineering, high-throughput data contextualization, and a public-access online genomic/biochemical database was created.

Keywords: metabolic model
S. stipitis
FBA
Advisor: Mahadevan, Radhakrishnan