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<p>Autism Spectrum Disorder (ASD) is a heterogeneous disorder with a high burden of suffering and economic cost to society. The current Thesis represents a systematic attempt to investigate ASD heterogeneity, as it relates to the measurement and classification of the clinical phenotype. The Thesis integrates information from multiple constructs (symptoms, traits, behaviours), methods (factor analysis, cluster analysis, and factor mixture modeling), populations (clinical and high-risk samples) and time points (at diagnosis and at age 6) for the investigation of the underlying structure of the ASD phenotype in young children. The Thesis consists of four interrelated empirical studies and one Editorial. Results can be organized into three overarching themes: 1) in preschool children with ASD core diagnostic symptoms (social communication deficits and repetitive behaviours) appear to overlap with other emotional/behavioural problems (attention, withdrawal, anxiety, aggression, emotional reactivity); 2) along the heterogeneous autism spectrum there appear to be distinct, relatively homogeneous subgroups of children; on average, children across these subgroups differ in their levels of symptom severity, adaptive skills, and emotional/behavioural problems; 3) the underlying structure of the ASD symptom phenotype changes as children grow and develop. Thesis findings lend support to a much-needed shift in our conceptual and methodological approach to the study of measurement and classification of autism pathology: that is, instead of a set of categorical symptoms that present early in childhood and remain static over the life span, ASD might be better understood as a complex and dynamic disorder, structured on both categorical and dimensional constructs that vary not only across individuals at any given point, but also within individuals across time.</p> / Doctor of Philosophy (PhD)

The purported chemopreventive and chemotherapeutic properties of the dietary phytochemical resveratrol continue to undergo active investigations. Systemic pharmacokinetics of this compound revealed that it was rapidly and extensively metabolized into its sulfate and glucuronide conjugates. This extensive metabolism leads to high plasma levels of resveratrol sulfates and glucuronides and very low levels of the parent compound (low bioavailability). These observations raised many questions, some of which this body of work examined and has helped to explain. Chapter 1 presents a detailed introduction to resveratrol and its role in colorectal cancer chemoprevention. It also lays the foundation for the hypotheses generated and the studies presented in succeeding chapters. In chapter 2, we explored the possibility that resveratrol metabolites possess intrinsic activity and thus contribute to the observed effects of the parent. The mono-sulfated and glucuronidated conjugates of trans-resveratrol were synthesized and tested for antiproliferative activity in a panel of mammalian cell lines. Their activity was then compared with the parent compound. Resveratrol was shown to be antiproliferative in all cell lines studied while no discernible antiproliferative activity was observed for the metabolites. Chapter 3 details the results of the glucuronidation kinetics of cis and trans-resveratrol isomers across a wide concentration range chosen to mimic blood levels following high dose consumption. Human tissue microsomes and recombinant supersomes over-expressing the enzymes (UGTs) of interest were used for these studies. Our results show the presence of atypical kinetics for the formation of resveratrol glucuronides across most of the protein sources used. Prior to this study, the full glucuronidation kinetics of total resveratrol had not been conducted. In chapter 4, we examined the association between genetic polymorphisms in the major enzymes (UGT1A1 and UGT1A6) and rates of glucuronidation of trans and cis-resveratrol. We set out to correlate functional genetic variations in these UGTs with their catalytic rates and a positive association was made for cis-resveratrol and UGT1A6 where the UGT1A6 variants mediated higher glucuronidation rates compared to the reference genotype. Chapter 5 explored the inherent ability of resveratrol to induce its own glucuronidation upon chronic dosing. Enzyme induction has been proposed as a mechanism that may contribute to the low bioavailability of resveratrol. Since dietary polyphenols like resveratrol are not consumed in isolation, we also studied the effects of combining resveratrol with two dietary polyphenols (curcumin and chrysin) on two chemoprevention endpoints - i) antiproliferation and ii) UGT enzyme induction. Our results indicate that resveratrol is capable of inducing UGT1A1 expression and activity in a non-concentration dependent manner and this induction as well as its antiproliferative effects are enhanced by both curcumin and chrysin. In summary, en route to probing the activity of resveratrol metabolites, we optimized two synthetic routes and generated measurable quantities of these compounds for future use. While the in vitro kinetics of resveratrol did not allow for any in vivo predictions, we were able to show alterations in resveratrol metabolism with respect to genotypic differences and enzyme induction that may contribute to the observed low bioavailability profile. / Pharmaceutical Sciences

No / Traditional Chinese medicine (TCM) investigates the clinical diagnosis and treatment regularities in a typical schema of personalized medicine, which means that individualized patients with same diseases would obtain distinct diagnosis and optimal treatment from different TCM physicians. This principle has been recognized and adhered by TCM clinical practitioners for thousands of years. However, the underlying mechanisms of TCM personalized medicine are not fully investigated so far and remained unknown. This paper discusses framework of TCM personalized medicine in classic literatures and in real-world clinical settings, and investigates the underlying mechanisms of TCM personalized medicine from the perspectives of network medicine. Based on 246 well-designed outpatient records on insomnia, by evaluating the personal biases of manifestation observation and preferences of herb prescriptions, we noted significant similarities between each herb prescriptions and symptom similarities between each encounters. To investigate the underlying mechanisms of TCM personalized medicine, we constructed a clinical phenotype network (CPN), in which the clinical phenotype entities like symptoms and diagnoses are presented as nodes and the correlation between these entities as links. This CPN is used to investigate the promiscuous boundary of syndromes and the co-occurrence of symptoms. The small-world topological characteristics are noted in the CPN with high clustering structures, which provide insight on the rationality of TCM personalized diagnosis and treatment. The investigation on this network would help us to gain understanding on the underlying mechanism of TCM personalized medicine and would propose a new perspective for the refinement of the TCM individualized clinical skills.

The genus Gluconobacter consists of acetic acid bacteria which have the ability to generate acidic products from their substrates, particularly acetic acid from ethanol. For this reason, the gluconobacters live in acidic, sugary environments such as flowers, honey bees, fruits, cider, vinegar, wine and beer. The gluconobacters carry out a strictly respiratory type of metabolism using only oxygen as a terminal electron acceptor. They do not completely oxidize a substrate to carbon dioxide. Instead, they partially oxidize the substrate using membrane-bound dehydrogenases and excrete the product into the surrounding growth medium. It is these limited oxidations that make the gtuconobacters industrially useful. Although much is known about the physiology of the limited oxidations in the gluconobacters, little is known of their genetics, particularly, their plasmids. The overall purpose of this dissertation was to determine if Gluconobacter plasmids correlate with oxidative capability and/or antibiotic resistance. To achieve this goal, I first needed a way to screen strains of Gluconobacter for their ability to oxidize many different substrates. 'developed an assay that used an unusual artificial electron acceptor, tetranitroblue tetrazolium (TNBT) and then tested the ability of six strains to oxidize 13 chemical compounds. Although most strains were able to oxidize the 13 compounds tested, they accomplished this with varying extents of oxidation. These differences were noted even with strains representing the same species. / Ph. D.

The broad autism phenotype (BAP) has been defined both behaviorally and biologically. There has been little research on the association of the BAP, behaviorally defined, with neural or cognitive biomarkers typically associated with Autism Spectrum Disorder (ASD). People diagnosed with ASD tend to show reduced gaze fixation toward the eye region, but much less eye-tracking research has been done related to the BAP (Boraston & Blakemore, 2007). In this study, we sought to assess eye gaze patterns in people with the behaviorally defined BAP, as defined by a score of 30 or above on the Autism Spectrum Quotient (AQ; Baron-Cohen et al., 2001). It was hypothesized that the BAP group participants would exhibit longer average fixation duration to the eye region during an emotion recognition condition, relative to a free-viewing condition, whereas the comparison group participants (defined as an AQ score of 24 and below) would not show a difference in fixation duration to the eye region between conditions. Nine hundred and thirty-nine undergraduates completed an online survey, and 45 of these students (15 BAP group and 30 comparison group) participated in the eye-tracking session, where they viewed a series of human faces, each presented twice within a condition. Results revealed a significant negative relationship between social anxiety and eye region fixation duration in the free-viewing condition, for both presentations of faces. Contrary to expectation, BAP predicted longer eye region fixation duration in the free-viewing condition, for the second presentation of faces. Possible explanations for these surprising findings are discussed. / Master of Science

Cancer is arguably one of the most dangerous diseases and the major causes of death in the modern day. It becomes increasingly harder to treat and cure the disease as it makes progress. Detecting cancer at an early stage can help in preventing it from affecting an organism. However, it is very hard to detect at an early stage. The best possible way to tackle this disease is to first study it at a cellular level. This study aims at identifying various phenotypic traits of these cells in the Dielectrophoresis (DEP) based microfluidic device experimental setup and subsequently classifying the cells from the rest. A general framework for automatic labeling, identifying and classifying the malignant from the dead cells is developed in this work. The framework shows a top-down approach starting from static background subtraction, tracking, automatic labeling, feature extraction and finally classification. The data used in this work are videos of live and dead human prostate cancer (PC-3) cells flowing through the microfluidic device. Previous studies have shown that there are significant differences in morphological attributes between cancerous and non-cancerous cells. We focus mainly on shape, texture and geometry as the prominent attribute in our work and subsequently use them for classification. In this work we obtain good tracking results through optical flow as compared to previous work. For classification, linear classifiers such as logistic regression and linear Support Vector Machine (SVM) showed decent results. The machine learning algorithms use Histogram of Oriented Gradient (HOG) features plus the elliptical features as a combined feature vector. The elliptic features branch out this study to another direction that is useful in calculation of physical properties such as the cell elasticity through video processing and we propose a model for the same for the given setup. Currently, the elasticity of a single cell is calculated using expensive and time consuming procedures such as the atomic force microscopy (AFM). Using our framework, we can potentially obtain elasticity for a batch of cells in much less time. Also, our cell classification algorithm procedure is suitable for real time applications and can be a proposed futuristic concept for selective killing of cells. / Master of Science

The penicillin-binding proteins (PBPs) synthesize and modify peptidoglycan (PG), the main structural element of the bacterial cell wall. PBPs and PG synthesis are highly conserved in all bacteria and both have been important targets for antibiotic and antibacterial development. In the Gram positive bacterium Bacillus subtilis, PBP1 is composed of the four domains S, N, P, and C in order from the N- to C-terminus. It plays important roles in vegetative PG synthesis. Compared to the wild type B. subtilis, the PBP1 null mutant has decreased growth rate, cell diameter, and PG crosslinking; the cell population has more long cells; and the colonies have raised and smooth edges. In this work, we constructed six mutant forms of PBP1 that were tagged with a C-terminal FLAG epitope, to complement the wild type gene. We examined the colony and cell morphologies, and PBP1 localization in the mutant strains. The removal of the cytoplasmic region of the PBP1 S domain and the replacement of PBP1 S domain by PBP4 S domain did not change the colony morphologies, and each of these two mutations had minor effects on growth rate, cell diameter, PG crosslinking and generation of long cells in the cell population. The single point mutation in the active site of the N or P domain presumably removed the enzymatic activity, and each mutation caused slower growth rate, decreased cell diameter and PG crosslinking. The point mutation in the P domain had a minor effect on the colony morphology and formation of long cells; while the mutation in the N domain altered the colony morphology, and resulted in high percentage of long cells that is comparable to the PBP1 null mutant. The C domain of PBP1 has no apparent enzymatic activity, but the loss of it altered the colony morphology, and caused slower growth rate, decreased cell diameter, and PG crosslinking. In the wild type B. subtilis, PBP1 localizes to the septum. This septum localization specificity was lost in strains expressing PBP1 without the C domain, with PBP4 S domain, or with a point mutation in the active site of the N domain. PBP1 with a point mutation in the active site of the P domain, or without the cytoplasmic region of the S domain, had decreased septum localization specificity. These findings were used to develop a model of how PBP1 domain functioning in B. subtilis. / Master of Science