Improved De Novo Peptide Sequencing using LC Retention Time Information

Liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) is an important tool in proteomics for identifying the peptides in a sample. Liquid chromatography temporally separates the peptides and tandem mass spectrometry analyzes the peptides, that elute one after another, by measuring their mass-to-charge ratios and the mass-to-charge ratios of their prefix and suffix fragments. De novo peptide sequencing is the problem of reconstructing the amino acid sequences of the analyzed peptide from this measurement data. While previous approaches solely consider the mass spectrum of the fragments for reconstructing a sequence, we propose to also exploit the information obtained from liquid chromatography. We study the problem of computing a sequence that is not only in accordance with the experimental mass spectrum, but also with the retention time of the separation by liquid chromatography. We consider three models for predicting the retention time of a peptide and develop algorithms for de novo sequencing for each model. An evaluation on experimental data from synthesized peptides for two of these models shows an improved performance compared to not using the chromatographic information.ISSN:1868-896

GS-8374, a novel HIV protease inhibitor, does not alter glucose homeostasis in cultured adipocytes or in a healthy-rodent model system

Adverse effects induced by HIV protease inhibitors (PIs) are a significant factor in limiting their clinical success. PIs directly contribute to peripheral insulin resistance and alterations in lipid metabolism. GS-8374 is a novel PI with potent antiretroviral activity and a favorable resistance profile. Here we report on the potential of GS-8374 to adversely affect glucose and lipid homeostasis. Acute effects of GS-8374 and control PIs on glucose uptake and lipid accumulation were assessed in vitro in mouse OP9 and primary human adipocytes, respectively. GS-8374 and atazanavir showed no effect on insulin-stimulated deoxyglucose uptake, whereas ritonavir and lopinavir caused significant reductions. Similarly, in vitro lipid accumulation was not significantly affected in adipocytes treated with either GS-8374 or atazanavir. In euglycemic-hyperinsulinemic clamp experiments performed in rats during acute infusion of therapeutic levels of PIs, sustained serum GS-8374 levels of 8 μM had no effect on peripheral glucose disposal (similar to the findings for atazanavir). Comparable serum levels of lopinavir and ritonavir produced acute 19% and 53% reductions in in vivo glucose disposal, respectively. In conclusion, similar to atazanavir, but unlike ritonavir and lopinavir, GS-8374 neither affects insulin-stimulated glucose uptake in adipocytes in culture nor acutely alters peripheral glucose disposal in a rodent model system. These results dissociate the antiretroviral activity of GS-8374 from adverse effects on insulin sensitivity observed with some of the first-generation PIs and provide further support for the use of these experimental systems in the preclinical evaluation of novel PIs

Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes

The Web-based software tool Genevestigator provides powerful tools for biologists to explore gene expression across a wide variety of biological contexts. Its first releases, however, were limited by the scaling ability of the system architecture, multiorganism data storage and analysis capability, and availability of computationally intensive analysis methods. Genevestigator V3 is a novel meta-analysis system resulting from new algorithmic and software development using a client/server architecture, large-scale manual curation and quality control of microarray data for several organisms, and curation of pathway data for mouse and Arabidopsis. In addition to improved querying features, Genevestigator V3 provides new tools to analyze the expression of genes in many different contexts, to identify biomarker genes, to cluster genes into expression modules, and to model expression responses in the context of metabolic and regulatory networks. Being a reference expression database with user-friendly tools, Genevestigator V3 facilitates discovery research and hypothesis validation

RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization

Background RT-qPCR is a sensitive and increasingly used method for gene expression quantification. To normalize RT-qPCR measurements between samples, most laboratories use endogenous reference genes as internal controls. There is increasing evidence, however, that the expression of commonly used reference genes can vary significantly in certain contexts. Results Using the Genevestigator database of normalized and well-annotated microarray experiments, we describe the expression stability characteristics of the transciptomes of several organisms. The results show that a) no genes are universally stable, b) most commonly used reference genes yield very high transcript abundances as compared to the entire transcriptome, and c) for each biological context a subset of stable genes exists that has smaller variance than commonly used reference genes or genes that were selected for their stability across all conditions. Conclusion We therefore propose the normalization of RT-qPCR data using reference genes that are specifically chosen for the conditions under study. RefGenes is a community tool developed for that purpose. Validation RT-qPCR experiments across several organisms showed that the candidates proposed by RefGenes generally outperformed commonly used reference genes. RefGenes is available within Genevestigator at http://www.genevestigator.com

Distribution hierarchies in directed networks

Recently, Ahnert and Fink [AF08] showed that some classes of directed networks are cleanly separated in the space of the clustering signature. In this work we will study the relation hierarchy among subgraph distributions in directed networks and derive how the clustering signature ts into this hierarchy. Thereby we gather a fundamental understanding of the network dynamics and build a framework for the analysis of stochastic processes

Micropayment : IT-Security & IT-Risk

Auch für Geschäftsmodelle rund um das Internet gilt: Nutzen, Aufwand und Risiken implementierter Dienste müssen für alle Beteiligten in einem ausgewogenen Verhältnis zueinander stehen. Dies gilt umso mehr, wenn der Dienst aus der Transaktion kleinster Geldbeträge besteht. Unternehmen, die im Internet finanzielle Transaktionen auf Micropayment-Ebene gewinnbringend realisieren wollen, brauchen somit effiziente IT-Lösungen und sollten diese bewerten können. Letzteres ist dann die Aufgabe des IT-Risk-Assessments. Dabei betreten sie oft Neuland und suchen Unterstützung bei der angewandten Forschung- und Entwicklung (aF&E) der Fachhochschulen. Hierfür bietet die Kommission für Technologie und Innovation KTI, eine Förderagentur des Bundes, eine Plattform. Im KTI-geförderten Projekt MICROPAYMENT entwickelt das Institut für angewandte Informationstechnologie InIT der ZHAW School of Engineering zusammen mit der milliPay Systems AG, Zürich, einen solchen Bezahldienst weiter