Topologically correct intersection curves of tori and natural quadrics

This thesis provides efficient and robust algorithms for the computation of the intersection curve between a torus and a simple surface (e.g. a plane, a natural quadric or another torus), based on algebraic and numeric methods. The algebraic part includes the classification of the topological type of the intersection curve and the detection of degenerate situations like embedded conic sections and singularities. Moreover, reference points for each connected intersection curve component are determined. The required computations are realised efficiently by solving quartic polynomials at most and exactly by using exact arithmetic. The numeric part includes algorithms for the tracing of each intersection curve component, starting from the previously computed reference points. Using interval arithmetic, accidental incorrectness like jumping between branches or the skipping of parts are prevented. Furthermore, the environments of singularities are correctly treated. Our algorithms are complete in the sense that any kind of input can be handled including degenerate and singular configurations. They are verified, since the results are topologically correct and approximate the real intersection curve up to any arbitrary given error bound. The algorithms are robust, since no human intervention is required and they are efficient in the way that the treatment of algebraic equations of high degree is avoided.

Transcriptional dynamics of the human DMD locus

The human DMD locus encodes dystrophin protein. Absence or reduced levels of dystrophin (DMD or BMD phenotype, respectively) lead to progressive muscle wasting. Little is known about the complex coordination of dystrophin expression and its transcriptional regulation is a field of intense interest. In this work we found that DMD locus harbours multiple long non coding RNAs which orchestrate and control transcription of muscle dystrophin mRNA isoforms. These lncRNAs are tissue-specific and highly expressed during myogenesis, suggesting a possible role in tissue-specific expression of DMD gene isoforms. Their forced ectopic expression in human muscle and neuronal cells leads to a specific and negative regulation of endogenous dystrophin full lenght isoforms. An intriguing aspect regarding the transcription of the DMD locus is the gene size (2.4Mb). The mechanism that ensures the complete synthesis of the primary transcript and the coordinated splicing of 79 exons is still completely unknown. By ChIP-on-chip analyses, we discovered novel regions never been involved before in the transcription regulation of the DMD locus. Specifically, we observed enrichments for Pol II, P-Ser2, P-Ser5, Ac-H3 and 2Me-H3K4 in an intronic region of 3Kb (approximately 21Kb) downstream of the end of DMD exon 52 and in a region of 4Kb spanning the DMD exon 62. Interestingly, this latter region and the TSS of Dp71 are strongly marked by 3Me-H3K36, an histone modification associated with the regulation of splicing process. Furthermore, we also observed strong presence of open chromatin marks (Ac-H3 and 2Me-H3K4) around intron 34 and the exon 45 without presence of RNA pol II. We speculate that these two regions may exert an enhancer-like function on Dp427m promoter, although further investigations are necessary. Finally, we investigated the nuclear-cytoplasmic compartmentalization of the muscular dystrophin mRNA and, specifically, we verified whether the exon skipping therapy could influence its cellular distribution.

Charakterisierung und funktionelle Analyse verschiedener Isoformen von Clusterin (Apolipoprotein J)

Clusterin (CLU), auch bekannt unter dem Namen Apolipoprotein J (ApoJ), wird von Zellen als hetreodimeres Glykoprotein exprimiert und in den extrazellulären Raum sezerniert. Es wird daher auch als sezerniertes CLU (sCLU) bezeichnet. Neben sCLU sind auch nicht-sezernierte Isoformen von CLU bekannt, die in der vorliegenden Arbeit erforscht wurden. Ziel dabei war es, die Expression, die Biogenese, sowie die Funktion dieser Proteine zu ergründen. Nicht-sezernierte CLU-Formen werden ausschließlich von Zellen exprimiert, die zuvor einer Stresssituation ausgesetzt wurden. Dies konnte insbesondere durch Kultur verschiedener Zelllinien bei erhöhter Temperatur oder durch Behandlung mit dem Proteasominhibitor MG 132 demonstriert werden, worauf neben sCLU auch 50 kDa bzw. 45 kDa große, nicht-sezernierte CLU-Proteine in geringen Mengen exprimiert wurden. Bezüglich der Biogenese dieser Proteine wurden mehrere Hypothesen bzw. Mechanismen diskutiert und in dieser Arbeit untersucht: alternative Translationsstartpunkte auf verschiedenen mRNAs, alternatives Splicing einzelner mRNAs sowie Retrotranslokation oder Mistranslokation von sCLU-Vorläuferproteinen. Um die Hypothesen eruieren zu können, musste zuerst eine Expressionsanalyse der bekannten CLU-mRNAs durchgeführt werden. Über 5’-RACE, semi-quantitative und quantitative PCRs wurde die Expression von vier CLU-mRNAs sowie deren Induktion auf Zellstress hin festgestellt. Variante 1 (BP211675) ist die dominante CLU-mRNA und macht über 99,5 % an CLU-mRNA in unbehandelten sowie in gestressten Zellen aus. Des Weiteren sind geringste Mengen der mRNA-Varianten 2 und 3 (NR_038335.1 und NR_045494.1) detektiert worden, deren Sequenzen sich lediglich in ihrem alternativen Exon 1 von Variante 1 unterscheiden. Schließlich konnte die Expression von Variante 1 [Δex2] festgestellt werden, welcher durch alternatives Splicing, i.e. Exon-skipping, das Exon 2 mit der ER-Signalsequenz-codierenden Region (SSCR) fehlt. HEK 293-Zellen, die transient mit je einer der rekombinanten CLU-mRNAs in Form rekombinanter cDNA transfiziert wurden, exprimierten neben großen Mengen sCLU auch geringe Mengen an den nicht-sezernierten CLU-Isoformen. Die anschließend durchgeführten in vitro Mutagenesen belegen, dass alle Isoformen ausgehend von distinkten Translationsstartpunkten aus synthetisiert werden. CLU1-449 (50 kDa) wird als prä-Proprotein von sCLU ausgehend von einem Startcodon auf Exon 2 unmittelbar vor der SSCR translatiert. Unter Zellstress-Bedingungen kann es zu einer Mistranslokation während der co-translationalen Translokation kommen, sodass Teile von CLU1-449 im Cytosol akkumulieren. CLU21-449 (50 kDa) wird ausgehend von einem CUG-Startcodon downstream der SSCR über interne Translationsinitiation gebildet. Analoges gilt für CLU34-449 (45 kDa), welches von einem AUG-Startcodon auf Exon 3 translatiert wird. CLU34-449 ist außerdem die einzige CLU-Form die von Variante 1 [Δex2] codiert wird. Somit konnten drei der in der Literatur postulierten Mechanismen zur Ent-stehung nicht-sezernierter CLU-Isoformen in gestressten Zellen verifiziert werden. Die Mistranslokation von sCLU-Vorläuferproteinen, welche entscheidend zum Auftreten der nicht-sezernierten CLU-Formen beiträgt, die Alternative Translationsinitiation an distinkten Startcodons sowie das alternative Splicing von CLU-mRNA-Variante 1. Weiterführende Experimente bestätigten, dass alle nicht-sezernierten CLU-Isoformen im Cytosol der Zellen lokalisiert sind und keine Glykosylierungen tragen. Somit konnte ein weiterer, in der Literatur kontrovers diskutierter Punkt bezüglich dieser Proteine geklärt werden. Abschließend wurde die physiologische Funktion der einzelnen CLU-Isoformen analysiert. Dabei zeigte sich, dass ausschließlich sCLU eine Chaperonaktivität zukommt, die es ermöglicht, durch Hitze denaturierte Zielproteine in Lösung zu halten. Diese Funktion konnte nicht für die cytosolischen Iso¬formen bestätigt werden. Weiterhin konnte keine Auswirkung einzelner CLU-Formen auf die intrinsische Apoptose oder auf den NF κB-vermittelten Signaltransduktionsweg festgestellt werden, obgleich entsprechende Einflüsse von anderen Arbeitsgruppen postuliert wurden. Die hier gemachten Beobachtungen werfen daher die Frage auf, ob den nicht-sezernierten, cytosolischen CLU-Isoformen überhaupt eine physiologische Funktion zukommt und stellen aktuelle Hypothesen bezüglich der Rolle von CLU bei pathophysiologischen Prozessen infrage.

The CFTR frameshift mutation 3905insT and its effect at transcript and protein level

Cystic fibrosis (CF) is one of the most common genetic diseases in the Caucasian population and is characterized by chronic obstructive pulmonary disease, exocrine pancreatic insufficiency, and elevation of sodium and chloride concentrations in the sweat and infertility in men. The disease is caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, which encodes a protein that functions as chloride channel at the apical membrane of different epithelia. Owing to the high genotypic and phenotypic disease heterogeneity, effects and consequences of the majority of the CFTR mutations have not yet been studied. Recently, the frameshift mutation 3905insT was identified as the second most frequent mutation in the Swiss population and found to be associated with a severe phenotype. The frameshift mutation produces a premature termination codon (PTC) in exon 20, and transcripts bearing this PTC are potential targets for degradation through nonsense-mediated mRNA decay (NMD) and/or for exon skipping through nonsense-associated alternative splicing (NAS). Using RT-PCR analysis in lymphocytes and different tissue types from patients carrying the mutation, we showed that the PTC introduced by the mutation does neither elicit a degradation of the mRNA through NMD nor an alternative splicing through NAS. Moreover, immunocytochemical analysis in nasal epithelial cells revealed a significantly reduced amount of CFTR at the apical membrane providing a possible molecular explanation for the more severe phenotype observed in F508del/3905insT compound heterozygotes compared with F508del homozygotes. However, further experiments are needed to elucidate the fate of the 3905insT CFTR in the cell after its biosynthesis.

Isolated growth hormone deficiency type 2: from gene to therapy

Isolated growth hormone deficiency type-2 (IGHD-2), the autosomal-dominant form of GH deficiency, is mainly caused by specific splicing mutations in the human growth hormone (hGH) gene (GH-1). These mutations, occurring in and around exon 3, cause complete exon 3 skipping and produce a dominant-negative 17.5 kD GH isoform that reduces the accumulation and secretion of wild type-GH (wt-GH). At present, patients suffering from IGHD-2 are treated with daily injections of recombinant human GH (rhGH) in order to reach normal height. However, this type of replacement therapy, although effective in terms of growth, does not prevent toxic effects of the 17.5-kD mutant on the pituitary gland, which can eventually lead to other hormonal deficiencies. Considering a well-known correlation between the clinical severity observed in IGHD-2 patients and the increased expression of the 17.5-kD isoform, therapies that specifically target this isoform may be useful in patients with GH-1 splicing defects. This chapter focuses on molecular strategies that could represent future directions for IGHD-2 treatment.

The cytochrome P450 aromatase lacking exon 5 is associated with a phenotype of nonclassic aromatase deficiency and is also present in normal human steroidogenic tissues

OBJECTIVE: The previously described c655G>A mutation of the human cytochrome P450 aromatase gene (P450aro, CYP19) results in aberrant splicing due to disruption of a donor splice site. To explain the phenotype of partial aromatase deficiency observed in a female patient described with this mutation, molecular consequences of the c655G>A mutation were investigated. DESIGN: To investigate whether the c655G>A mutation causes an aberrant spliced mRNA lacking exon 5 (-Ex5), P450aro RNA was analysed from the patient's lymphocytes by reverse transcription polymerase chain reaction (RT-PCR) and by splicing assays performed in Y1 cells transfected with a P450aro -Ex5 expression vector. Aromatase activity of the c655G>A mutant was predicted by three dimensional (3D) protein modelling studies and analysed in transiently transfected Y1 cells. Exon 5 might be predicted as a poorly defined exon suggesting a susceptibility to both splicing mutations and physiological alternative splicing events. Therefore, expression of the -Ex5 mRNA was also assessed as a possibly naturally occurring alternative splicing transcript in normal human steroidogenic tissues. PATIENTS: An aromatase deficient girl was born with ambiguous genitalia. Elevated serum LH, FSH and androgens, as well as cystic ovaries, were found during prepuberty. At the age of 8.4 years, spontaneous breast development and a 194.6 pmol/l serum oestradiol level was observed. RESULTS: The -Ex5 mRNA was found in lymphocytes of the P450aro deficient girl and her father, who was a carrier of the mutation. Mutant minigene expression resulted in complete exon 5 skipping. As expected from 3D protein modelling, -Ex5 cDNA expression in Y1 cells resulted in loss of P450aro activity. In addition, the -Ex5 mRNA was present in placenta, prepubertal testis and adrenal tissues. CONCLUSIONS: Alternative splicing of exon 5 of the CYP19 gene occurs in the wild type (WT) as well as in the c655G>A mutant. We speculate that for the WT it might function as a regulatory mechanism for aromatization, whereas for the mutant a relative prevalence of the shorter over the full-length protein might explain the phenotype of partial aromatase deficiency.

The pharmacokinetic profile of fesoterodine: similarities and differences to tolterodine

BACKGROUND: Fesoterodine is a new antimuscarinic agent developed for the treatment of overactive bladder. Fesoterodine itself is inactive and is rapidly and extensively converted by ubiquitous esterases to its principal active moiety, 5-hydroxymethyl tolterodine (5-HMT). 5-HMT is formed via biotransformation of both fesoterodine and tolterodine, albeit by different metabolising enzymes, viz. esterases and CYP2D6 respectively. Tolterodine is a potent muscarinic receptor antagonist and has been used for the treatment of overactive bladder for over ten years. The objective of this study was to establish the pharmacokinetic profile of fesoterodine and to highlight ist potential pharmacokinetic advantages over tolterodine. DESIGN: Single-centre, open-label, randomised, 4-way crossover study in a total of 24 healthy male volunteers. Single oral doses of 4, 8, or 12 mg fesoterodine were administered after an overnight fast. In addition, the 8 mg dose was also administered after a standard high-fat and high-calorie breakfast. Blood and urine samples for the analysis of 5-HMT were collected before and multiple times after drug administration for pharmacokinetic analysis. RESULTS: The mean peak plasma concentration (Cmax) of 5-HMT and the mean area under the time versus concentration curve (AUC) increased proportionally with the fesoterodine dose. These two parameters were some 2-fold higher in CYP2D6 poor metabolisers, whereas the time to peak plasma concentration (tmax) and half life (t1/2) were not influenced by the dose or the CYP2D6 metaboliser status. If fesoterodine was taken following a high-fat breakfast, we observed small increases in Cmax and AUC. In spite of these modest genetic influences and food effects on the pharmacokinetics of fesoterodine, the overall interindividual variability in Cmax levels was relatively little compared to previously published reports using tolterodine. CONCLUSIONS: Due to the esterase-mediated cytochrome P450-independent formation of 5-HMT and involvement of multiple metabolic and renal excretion pathways in the elimination of 5-HMT, the effects of patient-intrinsic and -extrinsic factors on the pharmacokinetics of fesoterodine are only modest, with some 2-fold higher 5-HMT exposure. Therefore, in contrast to tolterodine, no reduction of fesoterodine dosage is required under conditions of reduced elimination. In most cases of drug interaction or renal/hepatic impairment, the fesoterodine dose may be increased to 8 mg/day based on individual patients' response, or patients may be required to remain at the initial recommended dose of 4 mg/day.

Liraglutide once a day versus exenatide twice a day for type 2 diabetes: a 26-week randomised, parallel-group, multinational, open-label trial (LEAD-6)

BACKGROUND: Unlike most antihyperglycaemic drugs, glucagon-like peptide-1 (GLP-1) receptor agonists have a glucose-dependent action and promote weight loss. We compared the efficacy and safety of liraglutide, a human GLP-1 analogue, with exenatide, an exendin-based GLP-1 receptor agonist. METHODS: Adults with inadequately controlled type 2 diabetes on maximally tolerated doses of metformin, sulphonylurea, or both, were stratified by previous oral antidiabetic therapy and randomly assigned to receive additional liraglutide 1.8 mg once a day (n=233) or exenatide 10 microg twice a day (n=231) in a 26-week open-label, parallel-group, multinational (15 countries) study. The primary outcome was change in glycosylated haemoglobin (HbA(1c)). Efficacy analyses were by intention to treat. The trial is registered with ClinicalTrials.gov, number NCT00518882. FINDINGS: Mean baseline HbA(1c) for the study population was 8.2%. Liraglutide reduced mean HbA(1c) significantly more than did exenatide (-1.12% [SE 0.08] vs -0.79% [0.08]; estimated treatment difference -0.33; 95% CI -0.47 to -0.18; p<0.0001) and more patients achieved a HbA(1c) value of less than 7% (54%vs 43%, respectively; odds ratio 2.02; 95% CI 1.31 to 3.11; p=0.0015). Liraglutide reduced mean fasting plasma glucose more than did exenatide (-1.61 mmol/L [SE 0.20] vs -0.60 mmol/L [0.20]; estimated treatment difference -1.01 mmol/L; 95% CI -1.37 to -0.65; p<0.0001) but postprandial glucose control was less effective after breakfast and dinner. Both drugs promoted similar weight losses (liraglutide -3.24 kg vs exenatide -2.87 kg). Both drugs were well tolerated, but nausea was less persistent (estimated treatment rate ratio 0.448, p<0.0001) and minor hypoglycaemia less frequent with liraglutide than with exenatide (1.93 vs 2.60 events per patient per year; rate ratio 0.55; 95% CI 0.34 to 0.88; p=0.0131; 25.5%vs 33.6% had minor hypoglycaemia). Two patients taking both exenatide and a sulphonylurea had a major hypoglycaemic episode. INTERPRETATION: Liraglutide once a day provided significantly greater improvements in glycaemic control than did exenatide twice a day, and was generally better tolerated. The results suggest that liraglutide might be a treatment option for type 2 diabetes, especially when weight loss and risk of hypoglycaemia are major considerations.

Doxycycline-controlled splicing modulation by regulated antisense U7 snRNA expression cassettes

Many diseases affect pre-mRNA splicing, and alternative splicing is a major source of proteome diversity and an important mechanism for modulating gene expression. The ability to regulate a specific splicing event is therefore desirable; for example, to understand splicing-associated pathologies. We have developed methods based on modified U7 snRNAs, which allow us to induce efficient skipping or inclusion of selected exons. Here, we have adapted these U7 tools to a regulatable system that relies on a doxycycline-sensitive version of the Kruppel-associated box (KRAB)/KAP1 transcriptional silencing. Co-transduction of target cells with two lentiviral vectors, one carrying the KRAB protein and the other the regulatable U7 cassette, allows a tight regulation of the modified U7 snRNA. No leakage is observed in the repressed state, whereas full induction can be obtained with doxycycline in ng ml(-1) concentrations. Only a few days are necessary for a full switch, and the induction/repression can be repeated over several cycles without noticeable loss of control. Importantly, the U7 expression correlates with splicing correction, as shown for the skipping of an aberrant beta-globin exon created by a thalassaemic mutation and the promotion of exon 7 inclusion in the human SMN2 gene, an important therapeutic target for spinal muscular atrophy.

Effect of oral calcium loading on intact PTH and calcitriol in idiopathic renal calcium stone formers and healthy controls

The calciuric response after an oral calcium load (1000 mg elemental calcium together with a standard breakfast) was studied in 13 healthy male controls and 21 recurrent idiopathic renal calcium stone formers, 12 with hypercalciuria (UCa x V > 7.50 mmol/24 h) and nine with normocalciuria. In controls, serum 1,25(OH)2 vitamin D3 (calcitriol) remained unchanged 6 h after oral calcium load (50.6 +/- 5.1 versus 50.9 +/- 5.0 pg/ml), whereas it tended to increase in hypercalciuric (from 53.6 +/- 3.2 to 60.6 +/- 5.4 pg/ml, P = 0.182) and fell in normocalciuric stone formers (from 45.9 +/- 2.6 to 38.1 +/- 3.3 pg/ml, P = 0.011). The total amount of urinary calcium excreted after OCL was 2.50 +/- 0.20 mmol in controls, 2.27 +/- 0.27 mmol in normocalciuric and 3.62 +/- 0.32 mmol in hypercalciuric stone formers (P = 0.005 versus controls and normocalciuric stone formers respectively); it positively correlated with serum calcitriol 6 h after calcium load (r = 0.392, P = 0.024). Maximum increase in urinary calcium excretion rate, delta Ca-Emax, was inversely related to intact PTH levels in the first 4 h after calcium load, i.e. more pronounced PTH suppression predicted a steeper increase in urinary calcium excretion rate. Twenty-four-hour urine calcium excretion rate was inversely related to the ratio of delta calcitriol/deltaPTHmax after calcium load (r = -0.653, P = 0.0001), indicating that an abnormally up-regulated synthesis of calcitriol and consecutive relative PTH suppression induce hypercalciuria.(ABSTRACT TRUNCATED AT 250 WORDS)

Prevalence of tooth wear on buccal and lingual surfaces and possible risk factors in young European adults

To assess the prevalence of tooth wear on buccal/facial and lingual/palatal tooth surfaces and identify related risk factors in a sample of young European adults, aged 18-35 years. Calibrated and trained examiners measured tooth wear, using the basic erosive wear examination (BEWE) on in 3187 patients in seven European countries and assessed the impact of risk factors with a previously validated questionnaire. Each individual was characterized by the highest BEWE score recorded for any scoreable surface. Bivariate analyses examined the proportion of participants who scored 2 or 3 in relation to a range of demographic, dietary and oral care variables. The highest tooth wear BEWE score was 0 for 1368 patients (42.9%), 1 for 883 (27.7%), 2 for 831 (26.1%) and 3 for 105 (3.3%). There were large differences between different countries with the highest levels of tooth wear observed in the UK. Important risk factors for tooth wear included heartburn or acid reflux, repeated vomiting, residence in rural areas, electric tooth brushing and snoring. We found no evidence that waiting after breakfast before tooth brushing has any effect on the degree of tooth wear (p=0.088). Fresh fruit and juice intake was positively associated with tooth wear. In this adult sample 29% had signs of tooth wear making it a common presenting feature in European adults.

Dietary Intakes of Children From Food Insecure Households

The objective of this cross-sectional study is to compare the dietary behaviors of children from low food secure (LFS) households with children from very low food secure (VLFS) households over an entire day, and during meals specifically consumed at home —breakfast, snack, and dinner. Parents of the recruited children completed a demographic questionnaire, along with USDA's 6-item short form food security questionnaire. Children completed 24-hour dietary recalls in person. Complete data from 102 children 9 to 12 years old were used. Using ANOVA to assess the differences among groups in intakes over an entire day and during meals consumed at home, no significant differences were found, except for vitamin C intake during breakfast. Based on the definitions of LFS and VLFS, it was hypothesized that children from VLFS group would have lower dietary intakes compared to children from the LFS group. However, this study found little difference. Speculations have been made for these findings and implications for research have been presented.

Nuclear antisense effects in cyclophilin A pre-mRNA splicing by oligonucleotides: A comparison of tricyclo-DNA with LNA

The nuclear antisense properties of a series of tricyclo(tc)-DNA oligonucleotide 9-15mers, targeted against the 3' and 5' splice sites of exon 4 of cyclophilin A (CyPA) pre-mRNA, were evaluated in HeLa cells and compared with those of corresponding LNA-oligonucleotides. While the 9mers showed no significant antisense effect, the 11-15mers induced exon 4 skipping and exon 3+4 double skipping to about an equal extent upon lipofectamine mediated transfection in a sequence and dose dependent manner, as revealed by a RT-PCR assay. The antisense efficacy of the tc-oligonucleotides was found to be superior to that of the LNA-oligonucleotides in all cases by a factor of at least 4-5. A tc-oligonucleotide 15mer completely abolished CyPA mRNA production at 0.2‘M concentration. The antisense effect was confirmed by western blot analysis which revealed a reduction of CyPA protein to 13% of its normal level. Fluorescence microscopic investigations with a fluorescein labeled tc-15mer revealed a strong propensity for homogeneous nuclear localization of this backbone type after lipofectamine mediated transfection, while the corresponding lna 15mer showed a less clear cellular distribution pattern. Transfection without lipid carrier showed no significant internalization of both tc- and LNA-oligonucleotides. The obtained results confirm the power of tricyclo-DNA for nuclear antisense applications. Morover, CyPA may become an interesting therapeutic target due to its important role in the early steps of the viral replication of HIV-1.