Hybridisierungskinetiken von Oligo- und Polynukleotiden an Glas-Oberflächen

Cytosolische Sulfotransferasen katalysieren den Transfer der Sulfonatgruppe auf endogene Verbindungen wie z.B. Steroide oder Katecholamine sowie auf Xenobiotika. Die Sulfonierung bestimmter Substanzen führt abhängig von deren Struktur jedoch zur Bildung reaktiver, mutagener and carcinogener Metaboliten. Im SULT1A1-Gen wurden Punktmutationen ('Single-Nucleotide-Polymorphisms', SNPs) identifiziert, die zu Aminosäureaustausch führen. Der am häufigsten vorkommende Austausch G638A führt zu den beiden Alloenzymen SULT1A1*Arg213 und *His213. Um mögliche Assoziationen zwischen Krankheitsbildern und bestimmten SULT1A1 Genotypen feststellen zu können, ist eine Untersuchungsmethode notwendig, bei der in kurzer Zeit der Genotyp möglichst vieler Probanden ermittelt werden kann. Daher soll anhand des Modells der humanen Sulfotransferase SULT1A1 der Einfluß von Punktmutationen auf das Hybridisierungsverhalten von Oligo- und Polynukleotiden untersucht werden. Diese Untersuchungen dienen als Vorversuche für die Etablierung und Automatisierung der SNP-Analyse auf DNA-Chips, die den gewünschten Probendurchsatz ermöglichen soll. Die SNP-Analyse erfolgt mittels Glasfaser-Optik. Auf einer streptavidinbeschichteten Glasfaser-Oberfläche ist ein 13 Bp langes Oligonukleotid - der SNP und 12 flankierende Nukleotide - über Biotin immobilisiert. Nach Zugabe eines mit Fluorescein gelabelten Proben-Amplifikats findet die Hybridisierung am 13mer statt. Anschließend wird durch Spülen mit Puffer die Dissoziation des Polynukleotids ausgelöst. Anhand des emittierten Fluoreszenz-Signals kann die Reaktionsgeschwindigkeitskonstante der Dissoziation bestimmt werden. Es konnte gezeigt werden, daß sich die Dissoziationsgeschwindigkeit eines mis-match (Bsp. Mutante - Wildtyp) wesentlich von der eines full-match (Bsp. Mutante - Mutante) unterscheidet. Es ist somit möglich, anhand der Dissoziationskinetik Mutante und Wildtyp eines SNP-haltigen DNA-Abschnitts zu identifizieren

The relation between inflammation and neurodegeneration in multiple sclerosis brains

Some recent studies suggest that in progressive multiple sclerosis, neurodegeneration may occur independently from inflammation. The aim of our study was to analyse the interdependence of inflammation, neurodegeneration and disease progression in various multiple sclerosis stages in relation to lesional activity and clinical course, with a particular focus on progressive multiple sclerosis. The study is based on detailed quantification of different inflammatory cells in relation to axonal injury in 67 multiple sclerosis autopsies from different disease stages and 28 controls without neurological disease or brain lesions. We found that pronounced inflammation in the brain is not only present in acute and relapsing multiple sclerosis but also in the secondary and primary progressive disease. T- and B-cell infiltrates correlated with the activity of demyelinating lesions, while plasma cell infiltrates were most pronounced in patients with secondary progressive multiple sclerosis (SPMS) and primary progressive multiple sclerosis (PPMS) and even persisted, when T- and B-cell infiltrates declined to levels seen in age matched controls. A highly significant association between inflammation and axonal injury was seen in the global multiple sclerosis population as well as in progressive multiple sclerosis alone. In older patients (median 76 years) with long-disease duration (median 372 months), inflammatory infiltrates declined to levels similar to those found in age-matched controls and the extent of axonal injury, too, was comparable with that in age-matched controls. Ongoing neurodegeneration in these patients, which exceeded the extent found in normal controls, could be attributed to confounding pathologies such as Alzheimer's or vascular disease. Our study suggests a close association between inflammation and neurodegeneration in all lesions and disease stages of multiple sclerosis. It further indicates that the disease processes of multiple sclerosis may die out in aged patients with long-standing disease

KNIME-CDK: Workflow-driven cheminformatics

BACKGROUND: Cheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of molecular structures, and downstream analysis. For this purpose, scientific workflow platforms such as the Konstanz Information Miner can be used if provided with the right plug-in. A workflow-based cheminformatics tool provides the advantage of ease-of-use and interoperability between complementary cheminformatics packages within the same framework, hence facilitating the analysis process. RESULTS: KNIME-CDK comprises functions for molecule conversion to/from common formats, generation of signatures, fingerprints, and molecular properties. It is based on the Chemistry Development Toolkit and uses the Chemical Markup Language for persistence. A comparison with the cheminformatics plug-in RDKit shows that KNIME-CDK supports a similar range of chemical classes and adds new functionality to the framework. We describe the design and integration of the plug-in, and demonstrate the usage of the nodes on ChEBI, a library of small molecules of biological interest. CONCLUSIONS: KNIME-CDK is an open-source plug-in for the Konstanz Information Miner, a free workflow platform. KNIME-CDK is build on top of the open-source Chemistry Development Toolkit and allows for efficient cross-vendor structural cheminformatics. Its ease-of-use and modularity enables researchers to automate routine tasks and data analysis, bringing complimentary cheminformatics functionality to the workflow environment

IgG Antibodies against Measles, Rubella, and Varicella Zoster Virus Predict Conversion to Multiple Sclerosis in Clinically Isolated Syndrome

BACKGROUND:Multiple sclerosis (MS) is characterized by a polyspecific B-cell response to neurotropic viruses such as measles, rubella and varicella zoster, with the corresponding antibodies measurable in CSF as the so-called "MRZ reaction" (MRZR). We aimed to evaluate the relevance of MRZR to predict conversion of patients with clinically isolated syndrome (CIS) to MS, and to compare it to oligoclonal bands (OCB) and MRI. METHODOLOGY/PRINCIPAL FINDINGS:MRZR was determined in a prospective study over 2 years including 40 patients that remained CIS over follow-up (CIS-CIS) and 49 patients that developed MS (CIS-RRMS) using ELISA. Using logistic regression, a score (MRZS) balancing the predictive value of the antibody indices included in MRZR was defined (9 points measles, 8 points rubella, 1 point varicella zoster, cutpoint: sum of scores greater 10). MRZR and MRZS were significantly more frequent in CIS-RRMS as compared to CIS-CIS (p=0.04 and p=0.02). MRZS showed the best positive predictive value (PPV) of all parameters investigated (79%, 95%-CI: 54-94%), which could be further increased by combination with MRI (91%, 95%-CI: 59-99%). CONCLUSIONS/SIGNIFICANCE:Our data indicate the relevance of MRZR to predict conversion to MS. It furthermore shows the importance of weighting the different antibody indices included in MRZR and suggest that patients with positive MRZR are candidates for an early begin of immunomodulatory therapy

Contactin-1 and Neurofascin-155/-186 Are Not Targets of Auto-Antibodies in Multifocal Motor Neuropathy

Multifocal motor neuropathy is an immune mediated disease presenting with multifocal muscle weakness and conduction block. IgM auto-antibodies against the ganglioside GM1 are detectable in about 50% of the patients. Auto-antibodies against the paranodal proteins contactin-1 and neurofascin-155 and the nodal protein neurofascin-186 have been detected in subgroups of patients with chronic inflammatory demyelinating polyneuropathy. Recently, auto-antibodies against neurofascin-186 and gliomedin were described in more than 60% of patients with multifocal motor neuropathy. In the current study, we aimed to validate this finding, using a combination of different assays for auto-antibody detection. In addition we intended to detect further auto-antibodies against paranodal proteins, specifically contactin-1 and neurofascin-155 in multifocal motor neuropathy patients’ sera. We analyzed sera of 33 patients with well-characterized multifocal motor neuropathy for IgM or IgG anti-contactin-1, anti-neurofascin-155 or -186 antibodies using enzyme-linked immunosorbent assay, binding assays with transfected human embryonic kidney 293 cells and murine teased fibers. We did not detect any IgM or IgG auto-antibodies against contactin-1, neurofascin-155 or -186 in any of our multifocal motor neuropathy patients. We conclude that auto-antibodies against contactin-1, neurofascin-155 and -186 do not play a relevant role in the pathogenesis in this cohort with multifocal motor neuropathy

Case–control study and meta-analysis of SULT1A1 Arg213His polymorphism for gene, ethnicity and environment interaction for cancer risk

Cytosolic sulphotransferase SULT1A1 plays a dual role in the activation of some carcinogens and inactivation of others. A functional polymorphism leading to Arg213His substitution (SULT1A1*2) affects its catalytic activity and thermostability. To study the association of SULT1A1*2 polymorphism with tobacco-related cancers (TRCs), a case–control study comprising 132 patients with multiple primary neoplasm (MPN) involving TRC and 198 cancer-free controls was carried out. One hundred and thirteen MPN patients had at least one cancer in upper aerodigestive tract including lung (UADT-MPN). SULT1A1*2 showed significant risk association with UADT-MPN (odds ratio (OR)=5.50, 95% confidence interval (CI): 1.09, 27.7). Meta-analysis was conducted combining the data with 34 published studies that included 11 962 cancer cases and 14 673 controls in diverse cancers. The SULT1A1*2 revealed contrasting risk association for UADT cancers (OR=1.62, 95% CI: 1.12, 2.34) and genitourinary cancers (OR=0.73, 95% CI: 0.58, 0.92). Furthermore, although SULT1A1*2 conferred significant increased risk of breast cancer to Asian women (OR=1.91, 95% CI: 1.08, 3.40), it did not confer increased risk to Caucasian women (OR=0.92, 95% CI: 0.71, 1.18). Thus risk for different cancers in distinct ethnic groups could be modulated by interaction between genetic variants and different endogenous and exogenous carcinogens

Biomarkers of Multiple Sclerosis

The search for an ideal multiple sclerosis biomarker with good diagnostic value, prognostic reference and an impact on clinical outcome has yet to be realized and is still ongoing. The aim of this review is to establish an overview of the frequent biomarkers for multiple sclerosis that exist to date. The review summarizes the results obtained from electronic databases, as well as thorough manual searches. In this review the sources and methods of biomarkers extraction are described; in addition to the description of each biomarker, determination of the prognostic, diagnostic, disease monitoring and treatment response values besides clinical impact they might possess. We divided the biomarkers into three categories according to the achievement method: laboratory markers, genetic-immunogenetic markers and imaging markers. We have found two biomarkers at the time being considered the gold standard for MS diagnostics. Unfortunately, there does not exist a single solitary marker being able to present reliable diagnostic value, prognostic value, high sensitivity and specificity as well as clinical impact. We need more studies to find the best biomarker for MS.publishersversionPeer reviewe