Epigenetics is an important layer of transcriptional control necessary for cell-type specific gene regulation. We developed computational methods to analyze the combinatorial effect and large-scale organizations of genome-wide distributions of epigenetic marks. Throughout this dissertation, we show that regions containing multiple genes with similar epigenetic patterns are found throughout the genome, suggesting the presence of several chromatin domains. In Chapter 1, we develop a hidden Markov model (HMM) for detecting the types and locations of epigenetic domains from multiple histone modifications. We use this method to analyze a published ChIP-seq dataset of five histone modification marks in mouse embryonic stem cells. We successfully detect domains of consistent epigenetic patterns from ChIP-seq data, providing new insights into the role of epigenetics in longrange gene regulation. In Chapter 2, we expand our model to investigate the genome-wide patterns of histone modifications in multiple human cell lines. We find that chromatin states can be used to accurately classify cell differentiation stage, and that three cancer cell lines can be classified as differentiated cells. We also found that genes whose chromatin states change dynamically in accordance with differentiation stage are not randomly distributed across the genome, but tend to be embedded in multi-gene chromatin domains. Moreover, many specialized gene clusters are associated with stably occupied domains. In the last chapter, we develop a more sophisticated, tiered HMM to include a domain structure in our chromatin annotation. We find that a model with three domains and five sub-states per domain best fits our data. Each state has a unique epigenetic pattern, while still staying true to its domain’s specific functional aspects and expression profiles. The majority of the genome (including most introns and intergenic regions) has low epigenetic signals and is assigned to the same domain. Our model outperforms current chromatin state models due to its increased domain coherency and interpretation.

There are many tools available for the study of post-translational modifications. The majority of these tools is specific towards the individual modification and involves separation of modified proteins from non-modified ones. The drawback of using a modification specific method is that there is a lack of flexibility in its usage for other modifications. The goal of these studies was to investigate the possibility of obtaining a similar separation effect by fractionating post-translationally modified proteins based on the physical properties of proteins. The post-translational modification chosen to be the basis of this study was the O-GlcNAc modification. Using the C2C12 mouse myoblast cell line, it was determined that the optimal conditions for producing lysates containing increased yields of O-GlcNAc modified proteins was to treat differentiated C2C12 cells with 10nM insulin, 12g/L glucose and 2mM of the O-GlcNAcase inhibitor Streptozotocin for 24 hours. Using the optimized lysis buffer, it was shown that protein separation by surface charge using standard anion exchange separation did not provide enough resolution or material to obtain any identifications of modified proteins. However, when a chromatofocusing method which separates proteins on the basis of their isoelectric points was used, a separation scheme with larger capacity and higher resolution was possible. Using this separation method followed by gel electrophoresis of individual fractions, proteins which are potentially O-GlcNAc modified were identified by mass spectrometry. It was evident from the number of protein bands observed per fraction on the Coomassie stained gels and the number of proteins identified per protein band by mass spectrometry that further reduction in sample complexity was required to assist in the positive identification of O-GlcNAc modified proteins. Among the identified proteins, 32 percent were metabolic proteins, 21 percent were protein processing proteins, 16 percent were structural proteins and the remainder a mix of other proteins. Unfortunately, it was not possible to validate the presence or absence of the O-GlcNAc modification on these proteins using available methodologies such as immunoprecipitation. As such, further work is required to optimize the separation strategy and to verify the usefulness of this separation strategy in identifying O-GlcNAc/post-translationally modified proteins.

Multiple computational algorithms were developed for analyzing ChIP-seq datasets of histone modifications. For basic ChIP-seq data processing, the problems of ambiguous short sequence read mapping and broad peak calling of diffuse ChIP-seq signals were solved by novel statistical methods. Their performance was systematically evaluated compared with existing approaches. The potential utility of finding meaningful biological information was demonstrated by the applications on real datasets. For biological question driven data mining, several important topics were selected for algorithm developments, including hypothesis-driven insulator prediction, unbiased chromatin boundary element discovery and combinatorial histone modification signature inference. The integrative computational pipeline for insulator prediction not only produced a list of putative insulators but also recovered specific associated chromatin and functional features. Selected predictions have been experimentally validated. The unbiased chromatin boundary element prediction algorithm was feature-free and had the capability to discover novel types of boundary elements. The predictions found a set of chromatin features and provided the first report of tRNA-derived boundary elements in the human genome. The combinatorial chromatin signature algorithm employed chromatin profile alignments for unsupervised inferences of histone modification patterns. The signatures were associated with various regulatory elements and functional activities. Both the computational advantages and the biological discoveries were discussed.

Erectile dysfunction and cardiovascular disease share etiologies, and commonly coexist. One unifying concept is that the arterial insufficiency in hypertension is also the primary basis for blunted sexual responses. The objective of these studies was to characterize the age-related changes in the structure and function of the pudendal artery (the main resistance vessel) in young and old normotensive and hypertensive animals in relation to erectile function. In addition, we assessed the impact of antihypertensive treatments and lifestyle modifications, such as exercise and/or caloric restriction, on erectile responses and the structure and function of the pudendal artery. In 30 week old hypertensive rats or following re-challenges at 50 and 70 weeks, antihypertensive treatment (enalapril or hydralazine) did not prevent the age-related decline in erectile function. Experiments involving cross-over kidney transplantations between treated and untreated young hypertensive rats revealed that changes in penile vasculature and not the level of arterial pressure were important for normalizing erectile responses. In addition, intervention with exercise and caloric restriction showed that these treatments substantially improved erectile responses in normotensive and hypertensive rats. The pudendal artery in young normotensive rats was found to have a thick medial layer but a relatively small lumen. With age, the pudendal lumen didn’t change, but all components of the medial layer were markedly increased. Of interest, the smooth muscle cells within the pudendal medial layer became more disorganized with aging, although iii contractions were similar. In contrast, endothelium-dependent relaxation decreased with age. Young hypertensive rats also had an increased wall thickness, but not lumen diameter or extracellular matrix. Antihypertensive therapy significantly decreased the pudendal wall thickness. In aging hypertensive rats, the pudendal artery walls were even thicker, lumen decreased and extracellular matrix greatly enhanced compared to younger rats. In addition, there were numerous regions of intimal thickening associated with marked disruptions of the internal elastic lamina. Moreover, pudendal smooth muscle cells bordering the intima and in the neointima were round in shape, and electron microscopy confirmed their synthetic state. Taken together, these findings provide key evidence of the importance of the structure and function of the pudendal artery in facilitating erectile responses. / Thesis (Ph.D, Pharmacology & Toxicology) -- Queen's University, 2009-05-19 12:55:30.469

El presente estudio examina cómo se traducen algunos gerundios de la novela El paraíso en la otra esquina de Mario Vargas Llosa del español al sueco por el traductor Peter Landelius. El análisis muestra que en la mayor parte de los casos se recurre a varias estrategias para expresar el gerundio español en sueco, como el imperfecto, la construcción “y” + imperfecto, preposiciones, omisión del verbo o subordinadas de relativo. En muy pocos casos, el 6 %, se mantiene la forma del gerundio en la traducción. Además, el análisis confirma la hipótesis de que si el gerundio español se sustituye por otras formas verbales o construcciones gramaticales en sueco, algunos matices semánticos y estilísticos que se configuran en la novela de Vargas Llosa se pierden o se modifican en la traducción al sueco. / The present study investigates how some gerunds in the novel The Way to Paradise by Mario Vargas Llosa is translated to Swedish by the translator Peter Landelius. The analysis shows that different strategies are used, such as the past tense, the construction “and” + the past tense, prepositions, omission of the verb or subordinate relative clauses. In very few cases, 6 %, the gerund is kept in the translation. The analysis confirms the hypothesis, when the gerund in the Spanish text is replaced by other grammatical constructions in Swedish, some semantic and stylistic nuances configured in Vargas Llosa’s novel are lost or modified in the Swedish translation.

Le diabète mellitus de type I est une maladie de plus en plus abondante. Cette dernière est caractérisée par la destruction auto-immunitaire des îlots de Langerhans incluant les cellules de type [bêta] qui produisent de l'insuline dans le pancréas endocrinien. Une option de traitement pour les patients atteints de cette maladie est notamment une greffe des îlots de Langerhans. Ce traitement est limité dû au nombre restreint de donneurs d'organes et aussi à la perte de fonctionnalité des îlots suite à la greffe. Les études effectuées tout au long de cette thèse ont pour optique d'adresser ces contraintes par le biais de la science des biomatériaux. La thèse débute avec un survol détaillé des concepts de base et des complexités associés aux interactions de type cellules et surfaces trouvées dans la littérature. II s'agit spécifiquement des interactions physiques et chimiques, des systèmes expérimentaux ainsi que des caractérisations et modifications associés aux interactions entre cellules et surfaces. La première étude de nature expérimentale examine la morphogenèse des cellules progénitrices ductales (PANC-1 cell line) vers des îlots qui produisent des agrégats semblables à des îlots (ILA). Le tout est fait sur des surfaces de carboxyméthyl dextrane (CMD) sur lesquelles le RGD est greffé via un lien covalent. L'expression des marqueurs d'lLAs (cytokeratin-19, Ki67, et E-cadherin) qui peuvent être associés à un changement de phénotype de ces cellules a été évaluée ainsi que la sécrétion et l'expression de l'insuline. La seconde étude de nature expérimentale a pour optique l'immobilisation de la fibronectine (FN) sur les mêmes surfaces de CMD mentionnées auparavant sur lesquelles des cellules ayant un phénotype [bêta] (INS-1 cell line) ont proliféré. Lors du processus d'immobilisation, plusieurs solutions ont été étudiées. L'immobilisation de la fibronectine sur des surfaces de CMD a été validée par la spectrométrie de photoélectrons induits par rayons X. Le mécanisme d'immobilisation a été déterminé par imagerie et mesures de force par microscopie à force atomique, la spectroscopie de dichroïsme circulaire ainsi que par la diffusion dynamique de la lumière. De plus, la croissance des cellules de type INS-1 et la sécrétion d'insuline ont été évaluées. La dernière étude de nature expérimentale visait l'étude de la coculture des cellules endothéliales et des îlots de porc dans un gel de fibrine. L'effet de la présence des cellules endothéliales sur la production d'insuline des îlots a été évalué. De plus, l'apoptose cellulaire en coculture a été évaluée et comparée aux cultures simples.

Andelen äldre i samhället har ökat och därmed har även förekomsten av demenssjukdomar tilltagit. Aktivitet är av stor betydelse för personer med demenssjukdom, dock påverkar sjukdomen ofta individens aktivitetsförmåga och det kan bli svårt att utföra dagliga aktiviteter. Syftet med studien var därför att kartlägga och beskriva arbetsterapeutiska åtgärder som främjar delaktighet i dagliga aktiviteter hos personer med demenssjukdom. En litteraturstudie genomfördes, och datainsamlingen skedde både genom en systematisk sökning i databaser och genom sekundär sökning. Sammanlagt inkluderades 14 vetenskapliga artiklar i studien. En latent innehållsanalys genomfördes, och meningsbärande enheter i samtliga artiklar identifierades. Mönster i den insamlade datan kunde därmed urskiljas och analyseras. Resultatet presenterar förbättrande och kompenserade arbetsterapeutiska interventioner genom anpassning av aktivitet och miljö, samt kognitiv träning. Individanpassning av aktivitet efter intresse och funktion, anpassning av den fysiska miljön, samt handledning av vårdpersonal och anhöriga, ledde till ökad självständighet och delaktighet i dagliga aktiviteter. Resultatet har påvisat att arbetsterapeutiska åtgärder har goda möjligheter att öka upplevelsen av delaktighet i dagliga aktiviteters hos personer med en demenssjukdom. / The number of older people in society is increasing, and along with it so is the prevalence of dementia. Activity is of great importance for people with dementia, but the disease has negative effects on the ability to perform everyday occupations. The purpose of this study was therefore to describe occupational therapy interventions that promote participation in daily activities in persons with dementia. Data was collected through a systematic search using five databases, and through a manual search. Altogether, 14 articles were included in the study. The data were analyzed using a qualitative content analysis. Patterns were identified and later analyzed. The study proposes compensatory and remedial interventions, such as modifying the physical environment to accommodate the disability, simplifying activities and improving cognitive functioning to facilitate performance in daily activities. By making individualized modifications of the physical environment, coaching caregivers, and adapting activities to personal requirements and interests, people with dementia are given a greater opportunity to be independent and to experience participation in daily activities. This study shows that occupational therapy interventions can have positive effects on persons with dementia and on their possibilities to participate in daily activities.

La maladie cardiovasculaire (MCV) représente encore aujourd’hui l’une des principales causes de décès et d’hospitalisation au Canada. Parmi les facteurs de risque de la MCV, la dyslipidémie est l’un des plus importants. En effet, des concentrations plasmatiques élevées de cholestérol transporté par les lipoprotéines de faibles densités (c-LDL), de triglycérides, ainsi que des concentrations faibles de cholestérol transporté par les lipoprotéines de hautes densités (c-HDL) ont été à maintes reprises identifiées comme des facteurs de risque indépendants de la MCV. Plusieurs facteurs héréditaires et environnementaux ont été associés aux concentrations de lipides plasmatiques. Toutefois, les facteurs héréditaires permettraient d’expliquer la plus grande proportion de la variabilité interindividuelle du bilan lipidique, particulièrement pour le c-HDL. Malgré l’étude de plusieurs millions de modifications génétiques, les principales causes moléculaires responsables de la forte héritabilité des concentrations de c-HDL demeurent pour l’instant encore inconnues. Afin d’expliquer l’héritabilité manquante des concentrations de lipides plasmatiques, plusieurs hypothèses ont été avancées. La présente thèse de doctorat se concentre sur celle suggérant que l’étude de la méthylation de l’ADN, une modification épigénétique considérée comme un facteur héréditaire non traditionnel, permettrait d’identifier de nouveaux fondements moléculaires associés aux dyslipidémies. Dans un premier temps, nous avons analysé la méthylation de l’ADN de plusieurs gènes du métabolisme lipoprotéique chez des sujets atteints d’hypercholestérolémie familiale (HF), un modèle humain de la MCV. Grâce à cette approche, nous avons pu démontrer que la méthylation de l’ADN de plusieurs gènes candidats (ABCA1, ABCG1, CETP, LIPC, LPL et PLTP) était associée à la variabilité du bilan lipidique, ainsi qu’avec les antécédents de maladies coronariennes athérosclérotiques. Dans un deuxième temps, une étude de la méthylation à l’échelle du génome d’un sous-groupe de patients HF nous a permis d’identifier de nouveaux loci associés à la concentration de c-HDL. Nous avons notamment observé que la méthylation de l’ADN du promoteur des gènes TNNT1 et ADRB3 était non seulement associée aux concentrations de c-HDL, mais également avec d’autres facteurs de risque de la MCV. L’ensemble des résultats présentés dans cette thèse démontre que la méthylation de l’ADN contribue à la variabilité du bilan lipidique à jeun de patients atteints d’HF et que l’étude des modifications épigénétiques pourrait aider à expliquer l’héritabilité manquante des concentrations de c-LDL, de c-HDL et de triglycérides plasmatiques.

This thesis is a phenomenological study that has been carried out via two semi-structured interviews with an -  in conventional ways of categorising - 22 years old white, heterosexual, and middleclass Swedish woman, referred to as “Andrea”. The thesis aims to explore the becomings of Andrea in connection with cosmetic body modifications and her experiences in relation to this of fitting and misfitting, which are related to the dis/ability system. The aim of this thesis has also been to situate her as an embodied female subject in an intersectional context, in addition to her own experiences, as multiple social categorizations intra-act in the creation of dis/ability. The thesis takes its point of departure in Rosi Braidotti’s theorization of nomadic subjectivity and employs her notion of subjectivity as a negotiation between desire and power, with the goal of analysing the affirmative potential of cosmetic body modifications, as well as being critical towards them and their effects. Rosemarie Garland-Thomson’s concepts of fitting/misfitting are used in order to analyse the intra-actions between body and environment as well as how cosmetic body modifications affect the fit and/or misfit of Andrea.  Sara Ahmed’s notion of orientation has been employed in relation to this, with the aim of showing how beauty, whiteness, femininity, and economic wealth are produced and sustained. In the thesis it is analysed how Andrea, in complex ways desires molarity at the same time as she actively resists “fixed” positionings of her. Andrea contributes to a deconstruction of the fixity of molar identity as her resistance disrupts the flow of expected behaviors - something which creates moments of imperceptibility. The thesis furthermore argues that Andrea uses cosmetic body modifications as an affirmative deconstruction of power in addition to it being a force that drives her towards the desired molarity.

With an increasingly aging population, a significant challenge in implantology is the creation of biomaterials that actively promote and accelerate tissue integration while offering excellent mechanical properties. Engineered surfaces with superimposed micro and nanoscale topographies showed great potential to control and direct biomaterial-host tissue interactions. However, these modified surfaces require a careful assessment to prevent potential adverse effects on the fatigue resistance, a factor which may ultimately cause premature failure of biomedical implants. In this context, the surfaces of two widely used biocompatible metals, namely CP Ti and Ti-6Al-4V, were engineered through simple yet efficient chemical treatments which demonstrated the ability to confer exciting new bioactive capacities. The qualitative and quantitative assessments of the fatigue resistance of polished and treated metals were carried out. Results from this study highlight the importance of mechanical considerations in the development and evaluation of nanoscale surface treatments for metallic biomedical implants.