When the human genome project was completed, it revealed a surprising result. 98% of the genome did not code for protein of which more than 50% are repeats— later known as ”Junk DNA”. However, comparative genomics unveiled that many noncoding elements are evolutionarily constrained; thus luckily to have a role in genome stability and regulation. Though, their exact functions remained largely unknown. Several large international consortia such as the Functional Annotation of Mammalian Genomes (FANTOM) and the Encyclopedia of DNA Elements (ENCODE) were set to understand the structure and the regulation of the genome. Specifically, these endeavors aim to measure and reveal the transcribed components and functional elements of the genome. One of the most the striking findings of these efforts is that most of the genome is transcribed, including non-conserved noncoding elements and repeat elements. Specifically, we investigated the evolution and epigenetic properties of noncoding elements. 1. We compared genomes of evolutionarily distant species and showed the ubiquity of constrained noncoding elements in metazoa. 2. By integrating multi-omic data (such as transcriptome, nucleosome profiling, histone modifications), I conducted a comprehensive analysis of epigenetic properties (chromatin states) of conserved noncoding elements in insects. We showed that those elements have distinct and protective sequence features, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. 3. I focused on the relationship between enhancers and repetitive elements. Using Cap Analysis of Gene Expression (CAGE) and RNASeq, I compiled a full catalog of active enhancers (a class of noncoding elements) during myogenesis of human primary cells of healthy donors and donors affected by Duchenne muscular dystrophy (DMD). Comparing the two time-courses, a significant change in the epigenetic landscape in DMD was observed that lead to global dysregulation of enhancers and associated repetitive elements.

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Thesis--University of Florida. / Description based on print version record. Typescript. Vita. Bibliography: leaves 185-202.

The accumulation of metal contaminants in the human environment has received a great deal of attention during the last several years as it has become apparent that their presence, in excess, represents a threat to human health. Biochemical assays to determine concentrations of metals in the human body have used such tissues as blood, bone, hair, nails and, more recently, teeth. The present study attempts to provide further evidence for the use of deciduous teeth as indicators of human exposure to concentrations of lead, copper and zinc as a result of ore smelting operations in Kamloops and Trail, British Columbia. Kamloops represents an area of minimum exposure to smelter operations in contrast to Trail where a lead/zinc smelter has been operating for many years. Concentrations of lead, copper and zinc in deciduous teeth from geographically-stable Kamloops children, aged 5 years to 12 years, were compared to concentrations found in a similar population of geographically-stable Trail children. Whole teeth were digested in nitric and perchloric acids and trace element concentrations were determined using inductively coupled plasma emission spectroscopy. Mean lead and zinc concentrations for Kamloops and Trail teeth, respectively, were: 31.6 ± 7.33 ppm and 48.2. ± 11.5 ppm for lead (p < 0.05) and 103.4 ± 23.6 ppm and 111.9 ± 15.4 ppm for zinc. Copper was undetectable at < 1 ppm in all teeth. Locally-grown foods from each area and foods grown elsewhere were also analyzed for lead, copper and zinc in an effort to establish the possible contribution of these elements from local food resources in Kamloops and Trail. Twenty-four hour diet composites were collected and analyzed for copper and zinc by atomic absorption spectroscopy. Mean copper and zinc concentrations for foods grown in Kamloops and Trail, respectively, were: 1.5 ± 0.4 ppm and 1.6 ± 0.9 ppm for copper and 3. 2 ± 1.3 ppm and 3.1 ± 0.9 ppm for zinc. Mean copper and zinc concentrations for non-locally grown foods collected from Kamloops and Trail, respectively, were: 1.1 ± 0.2 ppm and 1.6 ± 0.8 ppm for copper and 5.8 ± 1.9 ppm and 6.5 ± 0.3 ppm for zinc. Lead was determined by plasma emission spectroscopy, and was found to be undetectable at < 1 ppm in all food samples. To assess the extent of maximal consumption of locally-grown foods, selected home gardeners in the Brocklehurst district of Kamloops and the Genelle district of Trail were interviewed. Seasonal consumption and home food preservation practices were determined. In addition, 24-hour diet recalls were obtained from 177 Brocklehurst district children in September and April, 1977-78 to determine "typical" eating patterns of these children. . The amount of locally-grown foods consumed was dependent mainly on season of the year; however, choice of food by the children on the whole did not differ from fall to spring. The recalls also indicated that males consumed more food than females, particularly protein. Meals, especially breakfast, were frequently missed, and non-nutritious snacks were common to the diets of many of the children. Results from this study indicated that, although deciduous tooth lead concentrations were significantly (p<0.05) higher in Trail than in Kamloops, samples of locally-grown foods obtained in 1978 from these two communities were not excessively high in lead, zinc or copper. In fact, these elements in foods compared well to concentrations reported in other areas of North America. It would appear, then, that the higher concentrations of lead in Trail teeth are a result of increased intake from other environmental sources. Analyses of food consumption patterns of gardening families revealed that local foods comprised an important part of the diet. Measures should be taken to ensure the continued safety of foods in areas where mineral mining and smelting occur. / Land and Food Systems, Faculty of / Graduate

published_or_final_version / Mathematics / Master / Master of Philosophy

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