Investigations into the effect of nucleoside modifications on the physicochemical properties and biological function of DNA and RNA

This thesis explores the effect of chemical nucleoside modification on the physicochemical and biological properties of nucleic acids. Positional alteration on the Watson-Crick edge of purines and pyrimidines, the “C-H” edge of pyrimidines, as well as both the Hoogsteen and sugar edges of purines were attempted by means of copper catalyzed azide-alkyne cycloaddition. For this purpose, nucleic acid building blocks carrying terminal alkynes were synthesized and introduced into oligonucleotides by solid-phase oligonucleotide chemistry. rnOf particular interest was the effect of nucleoside modification on hydrogen bond formation with complementary nucleosides. The attachment of propargyl functionalities onto the N2 of guanosine and the N4 of 5-methylcytosine, respectively, followed by incorporation of the modified analogs into oligonucleotides, was successfully achieved. Temperature dependent UV-absorption melting measurements with duplexes formed between modified oligonucleotides and a variety of complementary strands resulted in melting temperatures for the respective duplexes. As a result, the effect that both the nature and the site of nucleoside modification have on base pairing properties could thus be assisted. rnTo further explore the enzymatic recognition of chemically modified nucleosides, the oligonucleotide containing the N2-modified guanosine derivative on the 5’-end, which was clicked to a fluorescent dye, was subjected to knockdown analyses of the eGFP reporter gene in the presence of increasing concentrations of siRNA duplexes. From these dose-dependent experiments, a clear effect of 5’-labeling on the knockdown efficiency could be seen. In contrast, 3’-labeling was found to be relatively insignificant.rn

A model for radiofrequency electromagnetic field predictions at outdoor and indoor locations in the context of epidemiological research

We present a geospatial model to predict the radiofrequency electromagnetic field from fixed site transmitters for use in epidemiological exposure assessment. The proposed model extends an existing model toward the prediction of indoor exposure, that is, at the homes of potential study participants. The model is based on accurate operation parameters of all stationary transmitters of mobile communication base stations, and radio broadcast and television transmitters for an extended urban and suburban region in the Basel area (Switzerland). The model was evaluated by calculating Spearman rank correlations and weighted Cohen's kappa (kappa) statistics between the model predictions and measurements obtained at street level, in the homes of volunteers, and in front of the windows of these homes. The correlation coefficients of the numerical predictions with street level measurements were 0.64, with indoor measurements 0.66, and with window measurements 0.67. The kappa coefficients were 0.48 (95%-confidence interval: 0.35-0.61) for street level measurements, 0.44 (95%-CI: 0.32-0.57) for indoor measurements, and 0.53 (95%-CI: 0.42-0.65) for window measurements. Although the modeling of shielding effects by walls and roofs requires considerable simplifications of a complex environment, we found a comparable accuracy of the model for indoor and outdoor points.

ABCA4 and ROM1: Implications for modification of the PRPH2-associated macular dystrophy phenotype

To identify the causative mutation leading to autosomal dominant macular dystrophy, cone dystrophy, and cone-rod dystrophy in a five-generation family and to explain the high intrafamilial phenotypic variation by identifying possible modifier genes.

Comparison of two scoring systems for evaluation of treatment outcome in patients with complete bilateral cleft lip and palate

Objective : To compare two scoring systems: the Huddart/Bodenham system (HB system) and the Bauru-BCLP yardstick (BCLP yardstick), which classify treatment outcome in terms of dental arch relationships in patients with complete bilateral cleft lip and palate (CBCLP). The predictive value of these scoring systems for treatment outcome was also evaluated. Design : Retrospective longitudinal study. Patients : Dental arch relationships of 43 CBCLP patients were evaluated at 6, 9, and 12 years. Setting : Treatment outcome in BCLP patients using two scoring systems. Main Outcome Measures : For each age group, the HB scores were correlated with the BCLP yardstick scores using Spearman's correlation coefficient. The predictive value of the two scoring systems was evaluated by backward regression analysis. Results : Intraobserver Kappa values for the BCLP yardstick scoring for the two observers were .506 and .627, respectively, and the interobserver reliability ranged from .427 and .581. The intraobserver reliability for the HB system ranged from .92 to .97 and the interobserver reliability from .88 to .96. The BCLP yardstick scores of 6 and 9 years together were predictors for the outcome at 12 years (explained variance 41.3%). Adding the incisor and lateral HB scores in the regression model increased the explained variance to 67%. Conclusions : The BCLP yardstick and the HB system are reliable scoring systems for evaluation of dental arch relationships of CBCLP patients. The HB system categorizes treatment outcome into similar categories as the BCLP yardstick. In case a more sensitive measure of treatment outcome is needed, selectively both scoring systems should be used.

Uptake of regular chlamydia testing by U.S. women: a longitudinal study

Background Routine chlamydia screening is a recommended preventive intervention for sexually active women aged ≤25 years in the U.S. but rates of regular uptake are not known. Purpose This study aimed to examine rates of annual chlamydia testing and factors associated with repeat testing in a population of U.S. women. Methods Women aged 15–25 years at any time from January 1, 2002, to December 31, 2006 who were enrolled in 130 commercial health plans were included. Data relating to chlamydia tests were analyzed in 2009. Chlamydia testing rates (per 100 woman-years) by age and rates of repeated annual testing were estimated. Poisson regression was used to examine the effects of age and previous testing on further chlamydia testing within the observation period. Results In total, 2,632,365 women were included. The chlamydia testing rate over the whole study period was 13.6 per 100 woman years after adjusting for age-specific sexual activity; 8.5 (95% CI=6.0, 12.3) per 100 woman-years in those aged 15 years; and 17.7 (95% CI=17.1, 18.9) in those aged 25 years. Among women enrolled for the entire 5-year study period, 25.9% had at least one test but only 0.1% had a chlamydia test every year. Women tested more than once and older women were more likely to be tested again in the observation period. Conclusions The low rates of regular annual chlamydia testing do not comply with national recommendations and would not be expected to have a major impact on the control of chlamydia infection at the population level.

Long-Term outcome in patients with mild traumatic brain injury: A prospective observational study

Mild traumatic brain injury (MTBI) is common; up to 37% of adult men have a history of MTBI. Complaints after MTBI are persistent headaches, memory impairment, depressive mood disorders, and disability. The reported short- and long-term outcomes of patients with MTBI have been inconsistent. We have now investigated long-term clinical and neurocognitive outcomes in patients with MTBI (at admission, and after 1 and 10 years).

Delayed diagnosis of acute ischemic stroke in children - a registry-based study in Switzerland

QUESTIONS UNDER STUDY/PRINCIPLES: After arterial ischemic stroke (AIS) an early diagnosis helps preserve treatment options that are no longer available later. Paediatric AIS is difficult to diagnose and often the time to diagnosis exceeds the time window of 6 hours defined for thrombolysis in adults. We investigated the delay from the onset of symptoms to AIS diagnosis in children and potential contributing factors.

Frequency-dependent social dominance in a color polymorphic cichlid fish

A mechanism commonly suggested to explain the persistence of color polymorphisms in animals is negative frequency-dependent selection. It could result from a social dominance advantage to rare morphs. We tested for this in males of red and blue color morphs of the Lake Victoria cichlid, Pundamilia. Earlier work has shown that males preferentially attack the males of their own morph, while red males are more likely to win dyadic contests with blue males. In order to study the potential contribution of both factors to the morph co-existence, we manipulated the proportion of red and blue males in experimental assemblages and studied its effect on social dominance. We then tried to disentangle the effects of the own-morph attack bias and social dominance of red using simulations. In the experiment, we found that red males were indeed socially dominant to the blue ones, but only when rare. However, blue males were not socially dominant when rare. The simulation results suggest that an own-morph attack bias reduces the social dominance of red males when they are more abundant. Thus, there is no evidence of symmetric negative frequency-dependent selection acting on social dominance, suggesting that additional fitness costs to the red morph must explain their co-existence.

Response and long-term control of bone metastases after peptide receptor radionuclide therapy with (177)Lu-octreotate

Peptide receptor radionuclide therapy (PRRT) is an efficient treatment for gastroenteropancreatic neuroendocrine tumors (GEP NETs), with outstanding overall response rates and survival. However, little is known about the particular efficacy regarding bone metastasis (BM).

All-cause mortality in treated HIV-infected adults with CD4 >=500/mm3 compared with the general population: evidence from a large European observational cohort collaboration{dagger}

Using data from a large European collaborative study, we aimed to identify the circumstances in which treated HIV-infected individuals will experience similar mortality rates to those of the general population.

Exposure to environmental microorganisms and childhood asthma

Children who grow up in environments that afford them a wide range of microbial exposures, such as traditional farms, are protected from childhood asthma and atopy. In previous studies, markers of microbial exposure have been inversely related to these conditions.

Gene-environment interaction for childhood asthma and exposure to farming in Central Europe

Asthma is a disease in which both genetic and environmental factors play important roles. The farming environment has consistently been associated with protection from childhood asthma and atopy, and interactions have been reported with polymorphisms in innate immunity genes.

The GABRIEL Advanced Surveys: study design, participation and evaluation of bias

Exposure to farming environments has been shown to protect substantially against asthma and atopic disease across Europe and in other parts of the world. The GABRIEL Advanced Surveys (GABRIELA) were conducted to determine factors in farming environments which are fundamental to protecting against asthma and atopic disease. The GABRIEL Advanced Surveys have a multi-phase stratified design. In a first-screening phase, a comprehensive population-based survey was conducted to assess the prevalence of exposure to farming environments and of asthma and atopic diseases (n = 103,219). The second phase was designed to ascertain detailed exposure to farming environments and to collect biomaterial and environmental samples in a stratified random sample of phase 1 participants (n = 15,255). A third phase was carried out in a further stratified sample only in Bavaria, southern Germany, aiming at in-depth respiratory disease and exposure assessment including extensive environmental sampling (n = 895). Participation rates in phase 1 were around 60% but only about half of the participating study population consented to further study modules in phase 2. We found that consenting behaviour was related to familial allergies, high parental education, wheeze, doctor diagnosed asthma and rhinoconjunctivitis, and to a lesser extent to exposure to farming environments. The association of exposure to farm environments with asthma or rhinoconjunctivitis was not biased by participation or consenting behaviour. The GABRIEL Advanced Surveys are one of the largest studies to shed light on the protective 'farm effect' on asthma and atopic disease. Bias with regard to the main study question was able to be ruled out by representativeness and high participation rates in phases 2 and 3. The GABRIEL Advanced Surveys have created extensive collections of questionnaire data, biomaterial and environmental samples promising new insights into this area of research.

Lipid profiles and outcome in patients treated by intravenous thrombolysis for cerebral ischemia

OBJECTIVE:To determine whether low low-density lipoprotein cholesterol (LDL-C) but not high-density lipoprotein cholesterol (HDL-C) and triglyceride concentrations are associated with worse outcome in a large cohort of ischemic stroke patients treated with IV thrombolysis. METHODS:Observational multicenter post hoc analysis of prospectively collected data in stroke thrombolysis registries. Because of collinearity between total cholesterol (TC) and LDL-C, we used 2 different models with TC (model 1) and with LDL-C (model 2). RESULTS:Of the 2,485 consecutive patients, 1,847 (74%) had detailed lipid profiles available. Independent predictors of 3-month mortality were lower serum HDL-C (adjusted odds ratio [(adj)OR] 0.531, 95% confidence interval [CI] 0.321-0.877 in model 1; (adj)OR 0.570, 95% CI 0.348-0.933 in model 2), lower serum triglyceride levels ((adj)OR 0.549, 95% CI 0.341-0.883 in model 1; (adj)OR 0.560, 95% CI 0.353-0.888 in model 2), symptomatic ICH, and increasing NIH Stroke Scale score, age, C-reactive protein, and serum creatinine. TC, LDL-C, HDL-C, and triglycerides were not independently associated with symptomatic ICH. Increased HDL-C was associated with an excellent outcome (modified Rankin Scale score 0-1) in model 1 ((adj)OR 1.390, 95% CI 1.040-1.860). CONCLUSION:Lower HDL-C and triglycerides were independently associated with mortality. These findings were not due to an association of lipid concentrations with symptomatic ICH and may reflect differences in baseline comorbidities, nutritional state, or a protective effect of triglycerides and HDL-C on mortality following acute ischemic stroke.