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Detta examensarbete granskar analysverktyg ur ett tvärvetenskapligt perspektiv. Det finns en hel del olika analysverktyg idag som analyserar specifika typer av omik data och därför undersöker vi hur många det finns samt vad de kan göra. Genom att definiera ett antal specifika krav såsom hur många typer av omik data den kan hantera, noggrannhet av verktygets analys så kan man se vilka som är mest lämpliga analysverktygen när det gäller kartläggning av omik data. Resultaten visar att det idag inte finns analysverktyg som uppfyller de specifikt angivna kraven eller huvudsyftet genom testning av programvaran. Ingenuity analysverktyget är det närmaste vi kan komma för de krav som vi söker. På begäran av slutanvändaren testades två analysverktyg för att se om en kombination av dessa kan uppfylla slut användarens krav. Analysverktyget Uniprot batch converter testas med FEvER men resultat är inte framgångsrikt, då kombinationen av dessa verktyg inte är bättre än Ingenuity analysverktyget. Fokus vänds mot en alternativ kombination som är en hemsida och heter NCBI. Hemsidan har en sökmotor kopplad till flera olika analysverktyg som är gratis att använda. Genom sökmotorn kan ”omik” data kombineras och mer än ett inmatat värde kan hanteras i taget. Eftersom tekniken snabbt går framåt innebär det däremot att nya analysverktyg behövs för data hantering och inom en snar framtid så har vi kanske ett analysverktyg som uppfyller kraven av slutanvändarna. / This thesis examines PATs from a multidisciplinary view. There are a lot of PAT's existing today analyzing specific type of omics data, therefore we investigate them and what they can do. By defining some specific requirements such as how many omics data types it can handle, the accuracy of the PAT can be obtained to get the most suitable PAT when it comes to mapping omics data to pathways. Results show that no PATs found today fulfills the specific set of requirements or the main goal though software testing. The Ingenuity PAT is the closest to fulfill the requirements. Requested by the end user, two PATs are tested in combination to see if these can fulfill the requirements of the end user. Uniprot batch converter was tested with FEvER and results did not turn out successfully since the combination of the two PATs is no better than the Ingenuity PAT. Focus then turned to an alternative combination, a homepage called NCBI that have search engines connected to several free PATs available thus fulfilling the requirements. Through the search engine “omics” data can be combined and more than one input can be taken at a time. Since technology is rapidly moving forward, the need for new tools for data interpretation also grows. It means that in a near future we may be able to find a PAT that fulfills the requirements of the end users.

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Innovative methods to control the viscosity and turbulence in the flow of liquid suspension can be engineered by way of incorporating the concepts of electric and magnetic field into the rheology of complex fluids. Rheology of liquid Chocolate is a very crucial factor in determining the cost of manufacturing process as well as formulating varieties of end consumer products, for example, containing less fat. We have invented a method to lower the viscosity of liquid chocolate flow with the application of electric field. In the lab, we have found that viscosity of chocolate samples is reduced by 40~50% with our method. Thus, fat content in those samples can be reduced by 10% or more. Therefore, we expect to see much healthier and tastier chocolate product in the market once this technology gets implemented in commercial manufacturing. High viscosity and turbulence in blood flow greatly increase the risk of cardiac diseases. Hence, discovering new method to address turbulence suppression and viscosity reduction is critically important. In our study, we have found that in the in-vitro experiment, if blood is subjected to flow through a channel placed inside a strong magnetic field, its viscosity reduces by 10~20%. Based on these findings, a Megneto-Rheology (MR) therapeutic device has been developed to examine the effect on the blood pressure in human subjects. Preliminary clinical trials show that application of this MR therapy reduces blood pressure by 10% or more. In this thesis, above mentioned inventions for the flow of Blood and liquid Chocolate will be thoroughly discussed. / Physics / Accompanied by two .mpeg4 files.

Cardiovascular disease (CVD) is the leading cause of death worldwide, and is projected to remain so for at least the next decade. Ever since its discovery in the urine and blood of children with inborn errors of metabolism, homocysteine (Hcy) at elevated plasma concentrations has been associated with CVD clinically and epidemiologically. Observational studies and meta-analyses have noted that changes in plasma Hcy by 5μM increase the odds ratio of developing coronary artery disease by 1.6-1.8 among other CVD. Clinical trials aimed at reducing plasma Hcy for benefit against development of subsequent cardiovascular events have had unconvincing results, but have moreover failed to address the mechanisms by which Hcy contributes to CVD. Recommendations from national agencies like the American Heart Association and the United States Preventive Services Task Force emphasize primordial prevention as a way to combat CVD. Reducing plasma Hcy as secondary and primary interventions does not fulfill this recommendation. In order to best understand the role of Hcy in CVD, an investigation into its mechanisms of action must be undertaken before measures of primordial prevention can be devised. Numerous experimental studies in the literature identify vascular endothelium as a target for the pathological effects of Hcy. Endothelial injury and impairment are contributory processes to atherosclerosis, and Hcy has been demonstrated to inhibit endothelial cell (EC) growth and proliferation through mechanisms involving cell cycle arrest, oxidative stress, and programmed cell death in vitro. Animal models have also confirmed that high levels of Hcy accelerate atherosclerotic plaque development and lead to impairment of vascular reendothelialization following injury. Hcy has been shown to have the opposite effect in vascular smooth muscle cells (SMC), causing their proliferation and again contributing to atherosclerosis. The cell-type specificity of Hcy remains to be understood, and among the aims of this research was to further characterize the effects of Hcy in EC. The overarching goal was discovery in order to direct future investigations of Hcy-mediated pathology. To begin, the first investigation considered the transcriptional and regulatory milieu in EC following exposure to Hcy. High-throughput screening using microarrays determined the effect of Hcy on 26,890 mRNA and 1,801 miRNA. Two different in vitro models of hyperhomocysteinemia (HHcy) were considered in this analysis. The first used a high dose of 500µ Hcy to mimic plasma concentrations of patients wherein the transsulfuration pathway of Hcy metabolism is impaired as in inborn cystathionine-ß-synthase deficiency. The other set of conditions used 50µ Hcy in the presence of adenosine to approximate impairment of the remethylation pathway of Hcy metabolism wherein s-adenosylhomocysteine accumulates, thus inhibiting s-adenosylmethionine formation and methylation reactions. These distinctions are important because most clinical trials do not distinguish between causes of HHcy, thereby ignoring the specific derangements underlying HHcy. mRNA and miRNA expression changes for both sets of treatment conditions identified CVD as a common network of Hcy-mediated pathology in EC. Moreover, methylation-specific conditions identified cell cycle modulation as a major contributory mechanism for this pathology, which agrees with recent findings in the literature. Analysis of significant mRNA changes and significant miRNA changes independently identified roles for Hcy in CVD and cell cycle regulation, thereby suggesting that miRNA may mediate the effects of Hcy in addition to gene expression changes alone. To investigate the role of Hcy in the cell cycle further, the next set of investigations considered the effect of Hcy under conditions approximating impaired remethylation in early cell cycle events. Previous studies have demonstrated that Hcy inhibits cyclin A transcription in EC via demethylation of its promoter. Conversely, Hcy induces cyclin A expression in SMC, again making the case for a cell type-specific mechanism in EC. Preceding cyclin A transcription and activation, canonical events in the early cell cycle include D-type cyclin activation, retinoblastoma protein (pRB) phosphorylation, and transcription factor E2F1 activation. In a series of in vitro experiments on EC, it was seen that Hcy inhibits expression of cyclin D2 and cyclin D3, but not cyclin D1. Next, pRB phosphorylation was seen to be decreased following treatment with Hcy. This also led to decreased E2F1 expression. However, this series of events could be reversed with E2F1 supplementation, allowing the cell cycle to proceed. As Hcy exerts a number of its effects via regulation of gene transcription, a final series of investigations aimed to predict potential targets of Hcy by examining patterns of transcription factor binding among known targets of Hcy regulation. Gene promoters of Hcy-modulated genes were analyzed in order to determine common transcription factors that potentially control their regulation. The locations of CpG-rich regions in promoters were identified to determine which regions would be most susceptible to regulation by DNA methylation. Next, high-throughput next-generation sequencing (NGS) and bisulfite NGS was performed for DNA from EC treated with Hcy in order to determine methylation changes after Hcy treatment. A number of potential transcription factors and their binding sites were identified as potential mediators of Hcy-mediated gene regulation. Taken together, these investigations represent an exploration of Hcy-mediated pathology in CVD, by focusing upon novel regulatory mechanisms in EC. Objective high-throughput arrays identified roles for Hcy in CVD and cell cycle pathways regulated by miRNA and gene expression, which were confirmed experimentally in vitro. These observations led to an investigation and identification of common transcription factors that potentially regulate Hcy-altered gene expression. This framework may be used to guide future investigations into the complex pathological network mediating the effects of Hcy in CVD. First, identification of a role for miRNA in mediating the effects of Hcy represents a novel regulatory mechanism, heretofore largely unexplored. Next, expanding the role of Hcy in EC cell cycle regulation to identify upstream mediators greatly adds to the published literature. Finally, noting that these changes center upon transcriptional and post-transcriptional regulation gives import to developing methods to characterize promoter and transcription factor regulation. The investigations presented herein and their results provide evidence that the future of Hcy research is vibrant, relevant, and not nearly surfeit. / Pharmacology

Cardiovascular disease remains the leading cause of morbidity and mortality worldwide and Myocardial Infarction (MI) and subsequent heart failure remains the leading cause for death. Despite the improvement in prognosis and treatment of acute MI patients, the underlying causes including loss of cardiomyocytes and microvasculature remain potential risk and lack proper and efficient solutions. Stem cell-based therapies for repair and regeneration have evolved and have been applied in clinical trials. Different types of stem cells, including Endothelial progenitor cell (EPC), Mesenchymal Stem Cell (MSC), induced Pluripotent Stem Cell (iPSC) and cardiac progenitor cells etc. have been used for potential long term recovery and cardiac regeneration. However, results from the clinical trials have been largely disappointing and improvement in cardiac functions have been modest likely due to the limitations of cell therapy including low integration in myocardium, poor survival, cellular dysfunction and limited differentiation ability. It is therefore necessary and urgent to develop cell free alternatives as next generation regenerative therapies. There is a consensus that the beneficial effect of stem cell therapy is largely due to paracrine effects. Exosomes have recently emerged as important functional units mediating stem cell paracrine effects. Exosomes are the family of extracellular vesicles (EV) which are 30-150nm in size, secreted by almost all types of cells and responsible for cell-cell communication via delivering their cargo including RNAs and proteins to host cells. Studies from our and other labs have shown that exosomes mimic parental stem cell in improving post-MI functions. The essential feature of exosome is decided by their cargo including RNA and protein, which are subject to dynamic changes depending on the environment of parental cells. Our studies were focused on Endothelial Progenitor Cell (EPC)-derived exosomes. EPCs are generated in bone marrow, and home to the site of tissue injury and orchestrate neovascularization and tissue repair. Patients with ischemic heart disease, are usually accompanied with comorbidities such as systemic inflammation, aging, diabetes, etc. which are known to compromise EPC functions. We hypothesized that EPCs under inflammatory stress produce dysfunctional exosomes with altered RNA and protein content, leading to impaired cardiac reparative properties. We chose interleukin-10 knockout (IL-10KO) mice as a model of systemic inflammation. EPCs were isolated from IL-10KO and wild-type (WT) mice, and their exosomes (Exo) were compared for their reparative properties both in vitro and in vivo. Our in vitro studies showed WT-EPC-Exo treatment attenuated recipient cell apoptosis, enhanced cell mobilization and tube formation, whereas IL-10KO-EPC-Exo were functionally deficient or even had detrimental effects. We used MI mouse model to compare the in vivo function of two groups of exosomes and found WT-EPC-Exo treatment significantly improved left ventricular (LV) cardiac function, inhibited cell death, promoted angiogenesis and attenuated cardiac remodeling; while these cardioprotective effects were lost in IL-10KO-EPC-Exo treated group. Both in vitro and in vivo studies proved that even the same progenitor cell type (EPCs), under inflammatory stimulus (IL-10KO), secretes exosomes with different reparative properties. Next, we explored whether the observed difference in exosome function is caused by altered exosome content. Using Next Generation RNA Sequencing (NGS RNAseq) and mass spectrometry we found RNA and protein expression patterns were drastically different in wild type and IL-10 knockout EPC derived exosomes. This evidence leads to the conclusion that alteration in exosome content is fundamental for exosome function. We picked two candidates that are highly enriched in IL-10KO-EPC-Exo for further study, miR-375 and Integrin-Linked Kinase (ILK). We treated IL-10KO-EPC with anti-miR against miR-375 and siRNA against ILK separately, and successfully decreased the expression of miR-375 and ILK in both EPCs and EPC derived exosomes. Then we explored the function of those miR and protein ‘modified exosomes’ with similar in vitro and in vivo experiments as previously described. Compared to IL-10KO-EPC-Exo, miR-375 knockdown exosomes showed enhanced angiogenesis and inhibited cell apoptosis, while ILK knockdown in exosomes rescued functions in both in vitro and in vivo experiments. These results suggested the possibility that exosome manipulation of identified factors may partially rescue their reparative functionality. In summary, our studies revealed that stem cell derived exosomes are capable for independent cardiac repair in ischemic heart disease, however, parental stem cells under pathological stimulus secrete dysfunctional exosomes with altered RNA and protein content. Exosome function can be rescued or enhanced through RNA and protein content modification. / Biomedical Sciences

<p> Hypertension and reduced arterial distensibility are independent risk factors for cardiovascular disease. Previous research has found that isometric training reduces resting blood pressure (RBP) (Wiley et al. 1992; Taylor et al. 2003) yet the mechanisms responsible remain elusive. Improved arterial distensibility may contribute to this reduction in RBP. The purpose of the present study was threefold: 1) to replicate the RBP lowering effect of isometric handgrip (IHG) exercise; 2) to compare IHG and isometric leg press (ILP) based in their RBP lowering effects; and 3) to determine if central or peripheral arterial distensibility improved with IHG or ILP. The population examined was people whom were medicated for hypertension.</p> <p> RBP, as assessed by brachial oscillometry, and arterial distensibility, as assessed by Doppler ultrasound and applanation tonometry in the carotid, brachial and femoral arteries, were measured pre training, after 4 weeks of training, and post training. Participants performed unilateral IHG exercise (n=10) or ILP exercise (n=9) 3 times/week for 8 weeks at 30% MVC or acted as a non-exercising control group (n=5).</p> <p> Results indicated that the present study was unable to reproduce the RBP reductions noted in previous studies using IHG exercise. Also, the ILP exercise group did not experience reductions in RBP. Finally, neither central nor peripheral arterial distensibility improved in the IHG or ILP group when compared to the control group.</p> <p> Although these findings are contrary to our hypotheses one must consider that the control group examined contained very few subjects. This may have limited our ability to detect statistically significant changes in RBP and arterial distensibility.</p> / Thesis / Master of Science (MSc)

Cerebral palsy (CP) is no longer just a childhood disability. Children with CP grow up and become adolescents and eventually adults. However their risk of cardiovascular disease (CVD) and multimorbidity, defined as the presence of at least two chronic conditions, is poorly understood. This thesis sought to investigate CVD risk in individuals with CP and identify important health variables to understand and prevent multimorbidity development in this population. First, we discovered that adults with CP have an increased prevalence of CVD and an increased risk of death due to CVD compared to the general population, which raises concerns about CVD in people with CP and warrants further study. We investigated differences in cardiovascular health and moderate-to-vigorous physical activity (MVPA) in ambulatory adolescents and adults with CP between Gross Motor Function Classification System (GMFCS) levels I and II. Our findings suggest individuals who are GMFCS level II may be at increased risk for CVD in comparison to individuals who are GMFCS level I. We then evaluated longitudinal changes in risk factors of CVD in a cohort of individuals with CP. After a time interval of 4.0 ± 1.2 years, we found decreased absolute and relative brachial artery flow mediated dilation as measures of endothelial function, while carotid artery intima media thickness increased. We also discovered that 75% of participants with CP reported poor sleep quality, 80% engaged in less than the recommended 150 minutes of MVPA per week and 14% had poor eating behaviours. Taken together, this research suggests that individuals with CP experience accelerated aging for disease progression, specifically CVD, and that physical activity, sleep, and nutrition, together, could provide a framework for a lifestyle intervention to reduce and prevent multimorbidity risk in individuals with CP. / Thesis / Doctor of Philosophy (PhD) / Cerebral palsy is the most common child-onset physical disability. The disability can result in low levels of physical activity, obesity, and risk for morbid conditions that get worse over the lifecourse. The studies in this thesis furthered our understanding of cardiovascular disease and cardiovascular disease risk, investigated the relationship between physical activity and cardiovascular health, and evaluated changes in cardiovascular disease risk over time in individuals with cerebral palsy. We investigated three modifiable behaviours in individuals with cerebral palsy, which told us that they have poor sleep quality, do not engage in the recommended amount of physical activity, and could be at risk for poor nutrition. This work suggests that individuals with CP may be at an accelerated risk for cardiovascular disease, and that physical activity, sleep, and nutrition are important and modifiable factors that should be assessed and managed in this population.