The studies in this thesis describe the development of a microarray based minisequencing system and its application to highly parallel genotyping of single nucleotide polymorphisms. The technical developments included identification of a three-dimensional microarray surface coating with high binding capacity for oligonucleotides modified with amino groups as the most optimal one for the system. The system was also established for multiplexed, reproducible quantitative analysis of SNP alleles both on the level of DNA and RNA. The sensitivity of the system to distinguish SNP alleles present as a minority in a mixed sample was found to be 1-6%. The microarray based minisequencing system was applied in a pharmacogenetic study on antihypertensive drug response. A panel of 74 SNPs located in candidate genes related to blood pressure regulation were genotyped in DNA samples from hypertensive patients that had been treated with the antihypertensive drugs irbesartan or atenolol. Multiple regression analysis of the genotype data against the reduction in blood pressure identified genotype combinations of four to five SNPs that explain 44-56% of the reduction in blood pressure in the two treatment groups. The genotypes of two individual SNPs in the angiotensinogen (AGT) gene and a SNP in the low density lipoprotein receptor (LDLR) gene appeared to be associated to reduced blood pressure after treatment with atenolol, while a SNP in the apolipoprotein B (APOB) gene was associated to blood pressure reduction after irbesartan treatment. The genotype of one SNP in the adrenergic alpha-2A-receptor gene (ADRA2A) was related to the reduction in left ventricular mass following atenolol treatment while the genotypes of two SNPs, one in the APOB gene and one in the AGT gene were related to the reduction in left ventricular mass in the patients treated with irbesartan.

<p>Insects encounter many microorganisms in nature and to survive they have developed counter measures against the invading pathogens. In <i>Drosophila melanogaster</i> research on insect immunity has mainly been focused on infections by bacteria and fungi. We have explored the immune response against natural infections of the parasite <i>Octosporea muscaedomesticae</i> and the <i>Drosophila</i> C virus as compared to natural infections of bacteria and fungi. By using Affymetrix <i>Drosophila</i> GeneChips, we were able to obtain 48 genes uniquely induced after parasitic infection. It was also clearly shown that natural infections led to different results than when injecting the pathogens. </p><p>In order to search for the ultimate role of the lepidopteran protein hemolin, we used RNA interference (RNAi). We could show that injection of double stranded RNA (dsRNA) of <i>Hemolin</i> in pupae of <i>Hyalophora cecropia</i> led to embryonic malformation and lethality and that there was a sex specific difference. We continued the RNAi investigation of hemolin in another lepidopteran species, <i>Antheraea pernyi</i>, and discovered that hemolin was induced by dsRNA<i> per se</i>. A similar induction of hemolin was seen after infection with baculovirus and we therefore performed <i>in vivo</i> experiments on baculovirus infected pupae. We could show that a low dose of ds<i>Hemolin</i> prolonged the period before the <i>A. pernyi</i> pupae showed any symptoms of infection, while a high dose led to a more rapid onset of symptoms. By performing <i>in silico</i> analysis of the hemolin sequence from <i>A. pernyi</i> in comparison with other<i> Hemolin</i> sequences, it was possible to select a number of sites that either by being strongly conserved or variable could be important targets for future studies of hemolin function.</p>

This thesis presents genetic studies aiming at enlarging our knowledge regarding the genetic factors underlying two immune-mediated diseases, hypothyroidism and autoimmune Addison’s disease (AAD), in dogs and humans, respectively. Genetic and environmental factors are indicated to contribute to canine hypothyroidism, which can be considered a model for human Hashimoto’s thyroiditis (HT). In Paper I we performed the first genome-wide association (GWA) study of this disease in three high-risk dog breeds (Gordon Setter, Hovawart and Rhodesian Ridgeback). Using an integrated GWA and meta-analysis strategy, we identified a novel hypothyroidism risk haplotype located on chromosome 12 being shared by the three breeds. The identified haplotype, harboring three genes previously not associated with hypothyroidism, is independent of the dog leukocyte antigen region and significantly enriched across the affected dogs. In Paper II we performed a GWA study in another high-risk breed (Giant Schnauzer) and detected an associated locus located on chromosome 11 and conferring protection to hypothyroidism. After whole genome resequencing of a subset of samples with key haplotypes, we fine mapped the region of association that was subsequently screened for the presence of structural variants. We detected a putative copy number variant overlapping with the upstream region of the IFNA7 gene, which is located in a region of high genomic complexity. Remarkably, perturbed activities of type I Interferons have been extensively associated with HT and general autoimmunity. In Paper III we performed the first large-scale genetic study of human AAD, a rare autoimmune disorder characterized by dysfunction and ultimately destruction of the adrenal cortex. We resequenced 1853 immune-related genes comprising of their coding sequences, untranslated regions, as well as conserved intronic and intergenic regions in extensively characterized AAD patients and control samples, all collected in Sweden. We identified BACH2 gene as a novel risk locus associated with AAD, and we showed its independent association with isolated AAD. In addition, we confirmed the previously established AAD association with the human leukocyte antigen complex. The results of these studies will hopefully help increasing the understanding of such diseases in dogs and humans, eventually promoting their well-being.

början av 2000-talet sekvenserades det första hela mänskliga genomet och sedan dess har teknikerna förfinats, effektiviserats och förbättrats, så att utvecklingen på många områden, däribland forskningen om människans evolution, går fortare än någonsin tidigare. Från att ha sekvenserat en molekyl i taget är det idag möjligt att sekvensera miljontals molekyler parallellt och dessutom till ett så lågt pris att fler nu har möjlighet att använda sig av teknikerna. Bara under de senaste fem åren har det hänt mycket på området människans evolution och det är detta som vi kommer redogöra för i den här studien. Vi redovisar nya upptäckter –såsom att Homo naledi artbestämdes 2015 –, stärker gamla hypoteser –såsom att Homo sapiens utvandrade ur Afrika –samt stryker andra hypoteser –såsom att Australopithecus afarensis skulle vara den saknade länken mellan släktet Australopithecus och släktet Homo. Mycket har skett inom forskningen på människans evolution. Tillgång till nya biologiska tekniker har tillsammans med paleontologiska upptäckter bidragit till att skapa en större samstämmighet inom båda områden. Genom att teknikerna utvecklas och kompletterar varandra kan en större konsensus i resultaten skapas. Att utvecklingen av forskningen går fort fram har konsekvenser även för kurslitteraturen i gymnasieskolan. Vi analyserar därför om gymnasielitteraturen hinner med samt om förenklingarna som görs i den är rimlig. Det är svårt att avgöra om kurslitteraturen uppdateras i tillräcklig takt då förenklingarna är så pass stora. Vi anser att flera av de jämförda böckerna är tvetydiga i sina beskrivningar och framställer fakta som säkerställd, vilket inte alltid stämmer överens med hur området ser ut i verkligheten.

<p><b>Purpose.</b> The main aim of the present study was to evaluate the effect of a low fat, low lactose diet on acute and late gastrointestinal side effects of pelvic radiotherapy. We also wanted to evaluate if such a treatment would influence the patients health related quality of life (HRQOL) in any way.</p><p><b>Background</b>. Cancer therapies and their side effects may cause nutritional problems and malnutrition. Pelvic radiotherapy, a common treatment modality for patients with carcinoma of the endometrium or cervix, is associated with both acute and late side effects that may affect nutritional status. Acute injury may lead to impaired absorption of nutrients and fluid. The patients experience diarrhoea, weight loss, nausea and vomiting. Bile salt malabsorption may be a factor in the pathogenesis of the diarrhoea. In cases of bile salt malabsorption a low fat diet will cause decreased bile salt excretion and thereby relief of symptoms. This assumption was evaluated in a small, non-randomised study in 1985. The results indicated that a low fat diet may reduce the frequency of diarrhoea and use of anti-diarrhoeal agents during radiotherapy. These findings were regarded as promising and since nutrition management guidelines for radiation enteritis were lacking in the literature, a clinical trial was planned.</p><p><b>Methods</b>. The study was designed as an open randomised clinical trial and conducted at the Norwegian Radium Hospital (NRH). The intervention diet (low fat, low lactose) was to be followed during and six weeks after radiotherapy. Measurements were performed at basement, the 3rd and last week of radiotherapy, six week after and then every 8th week. The entire period was one year. In November 1993 the surviving patients were approached again and asked to complete a questionnaire package similar to the one completed during the clinical trial. The study population was recruited from the department of gynaecology at NRH. The main selection criteria were pelvic radiotherapy (dose above 40 Gy) age = 75 years and a WHO functional status = 2. Patients were consecutive included from May 1988 through May 1990 and 143 women were included. Seventy-one were assigned to the intervention diet and 72 to the control group. In November 1993, 94 women were alive without any known relapse and 79 (84%) accepted participation. The women registered use of Loperamid and the daily number and consistency of bowel movements. The data on bowel movements was categorised and used to evaluate if diarrhoea was present or not. Nutritional status was evaluated by the means of weight development, arm muscle circumference (AMC), serum transferring (STF) and serum albumin (s-Alb). Dietary intake was assessed by 48-hour recall prior to radiotherapy, 4-days unweighed dietary record during radiotherapy and 7-days weighed dietary records during follow-up. 24-hour urinary nitrogen was used to validate the food records. HRQOL was defined as the patients' self-reported subjective physical and psychosocial situation as a consequence of disease and treatment. It was measured with the EORTC Core Quality of Life Questionnaire 36-item version (EORTC QLQ-C36).</p><p><b>Results</b>. During the last week of radiotherapy 14 patients (23%) in the intervention group and 32 (48%) in the control group reported diarrhoea (p< 0.01). The intervention group also used less anti-diarrhoea medication than the control group, 0.6 tablets per day versus 1.1 (p<0.01). Six weeks after end of radiotherapy, no group differences were found with regard to bowel movements or medication. The intervention group had a lower energy intake than the control group during radiotherapy, 5.7 MJ versus 6.5 MJ (p<0.05). The mean daily fat intake was respectively 34.3 g and 60.1 g (p<0.001). The intervention group received a significant lower part of the energy from milk products, meats, fats and sugar than the control group, and consumed more energy from vegetables and fruits, cereals and fish. Weight loss was more pronounced in the intervention group (mean reduction of 2.6 kg versus 1.7 kg) than in the control group (ns) during treatment. Mean values of AMC, s-Alb and STF were within the reference range in both groups during the entire observation period. During the last week of radiotherapy six patients (9%) in the intervention group and 4 (6%) in the control group were mildly depleted (ns). At 12 weeks and after one year none of the patients could be categorised as malnourished. No major differences in HRQOL were found between the two groups during radiotherapy and one-year follow up. Within the control group an association between diarrhoea and deteriorated role functioning, physical functioning and fatigue was found during the last week of radiotherapy that was not found in the intervention group. Regarding late effects of radiotherapy (3-4 years after radiotherapy) both groups had more diarrhoea than in the general population, 23.8 versus 9.5 (p<0.01). There was however a tendency to more pronounced diarrhoea in the control group (29.6 (SD=27.3)) than in the intervention group (19.4 (SD=25.4)) though not statistical significant. Substantial diarrhoea was associated deteriorated SF and fatigue. </p><p><b>Conclusions</b>. The intervention group had less diarrhoea and used less Loperamide during radiotherapy than the control group. This finding did not affect nutritional status since no differences in nutritional status were found between the two groups. Both groups had a reduced energy intake and weight loss during radiotherapy. In the control group diarrhoea increased fatigue and had negative effects on physical functioning and role functioning. The intervention did not lead to differences in late radiation injury and chronic diarrhoea 3-4 years after treatment but diarrhoea was most prominent in the control group. Diarrhoea as a late effect increased fatigue and had a negative influence on social well being.</p>

<p>The onset of cigarette smoking begins primarily in adolescence, and prevalence of smoking among adolescents has been increased during the last ten years. The prevalence of adolescent smoking increases with age and is more common or at least as common in girls as in boys in most western countries.</p><p>Until recently the intensive investigation on health effects of smoking has been mostly conducted among adults. In adolescence the long-term health consequences have been reviewed, but current health problems are probably more important to adolescents and may be more motivating for smoking prevention and cessation. Increased morbidity among adolescent smokers has been reported, but specific current health problems and medication use have received little attention. More</p><p>Control of smoking is a primary health goal. An underlying premise for promotion of physical activity in adolescence is that it may mead to a healthy lifestyle persisting through adulthood. Encouraging participation in sports has been recommended as smoking prevention and as part of smoking cessation programs. Smoking habits within different types of sports has received less attention, and whether physical activity has an impact on lung function is debated.</p><p>Adolescent smokers are often unsuccessful in quitting and difficult to recruit and retain in smoking cessation programs. Occasional smoking may be the strongest risk factor for daily smoking, but occasional smokers could be an important target group for smoking cessation who could be discouraged from moving into daily smoking status. </p><p>The first aim of this thesis was to study associations between smoking and current health status by examining associations between daily smoking and subjective health problems (Paper 1), and gender specific effects on respiratory symptoms and lung function (Paper II). The associations between physical activity and lung function in never smokers and daily smokers were also assessed (Paper III). The second aim was to study factors that might be useful in smoking</p>

<p>Preeclampsia is a complex and variable maternal disturbance that ranges from a dramatic onset at early gestation to slowly developing symptoms towards term. Hypertension and renal involvement with proteinuria are cardinal signs, which are often accompanied by fluid retention, blood-clotting dysfunction, and reduced organ perfusion. HELLP (haemolysis, elevated liver enzymes, and low platelet count) syndrome is regarded as a variant of preeclampsia, and the fulminante disease, eclampsia, includes convulsions. Preeclampsia is the main cause of maternal and fetal morbidity and mortality in western countries (1, 2), and in Nordic countries, 17 percent of maternal deaths have been ascribed to preeclampsia (2). Antenatal care in Norway includes on average 12 doctor/midwife consultations per pregnancy (3), and since blood pressure monitoring and urinary testing are main aims of the consultations, preeclampsia is a pregnancy complication that also generates substantial societal costs.</p> / Paper II, III, IV and V reproduced with permission of Elsevier, sciencedirect.com

<p>Stroke is the third leading cause of death and the major course of long-term disabilities in industrialized countries. Most surviving stroke patients show some degree of spontaneous recovery, but persistent symptoms in sensorimotor and cognitive functions are common. The symptoms can be reproduced in experimental stroke models in rats by occlusion of the middle cerebral artery. Housing rats in an enriched environment (EE), i.e. group housing in a large cage with toys that are changed daily, increases neuronal plasticity in healthy rats and can also improve functional recovery after experimental stroke. </p><p> The present thesis investigates the effect of EE on the recovery of sensorimotor and cognitive functions one month after focal cerebral ischemia in rats, with emphasis on the underlying molecular mechanisms. Furthermore, EE-induced effect on gene expression in healthy rats was investigated after different periods of EE-housing and at different time points of the day. </p><p> We show an improved recovery of both sensorimotor and cognitive functions in rats housed in EE for one month after focal cerebral ischemia. The recovery of sensorimotor function correlated significantly to mRNA expression of the plasticity associated transcription factors NGFI-A and NGFI-B in hippocampus and cortical regions outside the infarct. Social interaction seems to be an important component for the beneficial effects of EE after focal cerebral ischemia. Microarray analysis of hippocampal gene expression after one month of postischemic environmental enrichment revealed no confirmable EE-induced changes that could explain the improved recovery in spatial memory. Interestingly, healthy rats housed in EE showed increased mRNA expression of NGFI-A and Krox-20 exclusively during the dark period of the day compared to rats housed in isolation. In addition, EE housed rats had a substantial diurnal variation in NGFI-A, Krox-20 and NGFI-B mRNA expression; this was absent in single-housed rats. EE-induced changes in gene expression are more evident during the dark period of the day, when rats are more active and can benefit from the stimulating environment. This is important to consider in future investigation of putative mediators of the EE-induced neuronal plasticity. </p><p> In summary, these findings may contribute to an increased understanding of the underlying molecular mechanisms behind improved functional recovery in rats housed in enriched environment after focal cerebral ischemia.</p>

<p>A novel technology for protein detection, proximity ligation, has been developed along with improved methods for <i>in situ</i> synthesis of DNA microarrays. Proximity ligation enables a specific and quantitative transformation of proteins present in a sample into nucleic acid sequences. As pairs of so-called proximity probes bind the individual target protein molecules at distinct sites, these reagents are brought in close proximity. The probes consist of a protein specific binding part coupled to an oligonucleotide with either a free 3’- or 5’-end capable of hybridizing to a common connector oligonucleotide. When the probes are in proximity, promoted by target binding, then the DNA strands can be joined by enzymatic ligation. The nucleic acid sequence that is formed can then be amplified and quantitatively detected in a real-time monitored polymerase chain reaction. This convenient assay is simple to perform and allows highly sensitive protein detection. Parallel analysis of multiple proteins by DNA microarray technology is anticipated for proximity ligation and enabled by the information carrying ability of nucleic acids to define the individual proteins. Assays detecting cytokines using SELEX aptamers or antibodies, monoclonal and polyclonal, are presented in the thesis.</p><p>Microarrays synthesized <i>in situ</i> using photolithographic methods generate impure products due to damaged molecules and interrupted synthesis. Through a molecular inversion mechanism presented here, these impurities may be removed. At the end of synthesis, full-length oligonucleotides receive a functional group that can then be made to react with the solid support forming an arched structure. The 3’-ends of the oligonucleotides are then cleaved, removing the impurities from the support and allowing the liberated 3’-hydroxyl to prime polymerase extension reactions from the inverted oligonucleotides. The effect of having pure oligonucleotides probes compared to ones contaminated with shorter variants was investigated in allele specific hybridization reactions. Pure probes were shown to have greater ability to discriminate between matched and singly mismatched targets at optimal hybridization temperatures.</p>

<p>The mature vascular system is composed of a network of blood vessels organized into arteries, capillaries, and veins. The vessels are composed of endothelial cells surrounded by smooth muscle cells and embedded in a specialized basement membrane. The demand for oxygen during embryonal development regulates vessel formation through a process denoted vasculogenesis. These primitive vessels are further remodeled through proliferation, sprouting and migration of endothelial cells in a process denoted angiogenesis. Vasculogenesis and angiogenes are regulated by growth factors, such as vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF).</p><p>To study vasculogenesis and angiogenesis, we employed differentiating embryonal stem cells (embryoid bodies). Vascularization of embryoid bodies follows a vascular pattern highly reminiscent of the in vivo pattern, leading to expression of a set of endothelial cell markers. Treatment of the embryoid bodies with different angiogenic growth factors led to distinct vascular morphologies. Expression of VEGF receptor-2 was an absolute demand for proper vascular development. PDGF-BB was shown to be potent in regulating vascular plexus formation in embryoid bodies. PDGF-BB induced capillary formation by promoting endothelial cell migration and differentiation. Hypoxia is a powerful inducer of angiogenic growth factors, such as VEGF-A, leading to angiogenesis. Hypoxia treatment induced an extensive vascular network that covered the entire embryoid body. Hypoxia-induced vascularization still occurred when VEGF receptor function was blocked, indicating that other pathway than VEGF/VEGF receptors may be critical for hypoxia-driven vessel formation. </p><p>Heparan sulfated proteoglycans (HSPGs) are present in the vascular basement membrane and are known to modulate angiogenic growth factor effects on endothelial cells in normal and pathological conditions such as tumor growth and formation of metastases. We employed heparin as an HSPG equivalent to show that PDGF-BB stimulation of PDGF a-receptor phosphorylation was augmented by heparin, resulting in increased mitogen activated protein kinase (MAPK) and protein kinase B PKB/Akt activation, and enhanced cellular migration towards PDGF-BB.</p>