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Metabolomics

Nowadays, gene discovery has been made very efficient with the combination of deep sequencing and the exploitation of natural variation. Just in Arabidopsis, hundreds of genetic loci have been identified as influencing a wide variety of processes, and we aim to go from gene-of-interest to characterized protein product using approaches to “take a picture” of the comprehensive metabolome of the plant.

The IPB is currently operating a wide range of NMR and mass spectrometry instruments for metabolomics across all four departments, which are integrated into our Metabolomics Platform.

The experimental work is complemented by extensive Cheminformatics and Bioinformatics research to process and interpret the huge amounts of data. The IPB is operating the first European MassBank server, and hosts several online tools for metabolite identification.

Contact partner for all interests concerning the metabolomics platform is Dr. Steffen Neumann.

Publications by Tag: Metabolomics

Displaying results 1 to 2 of 2.

Publications

Altenburger, R.; Ait-Aissa, S.; Antczak, P.; Backhaus, T.; Barceló, D.; Seiler, T.-B.; Brion, F.; Busch, W.; Chipman, K.; López de Alda, M.; de Aragão Umbuzeiro, G.; Escher, B. I.; Falciani, F.; Faust, M.; Focks, A.; Hilscherova, K.; Hollender, J.; Hollert, H.; Jäger, F.; Jahnke, A.; Kortenkamp, A.; Krauss, M.; Lemkine, G. F.; Munthe, J.; Neumann, S.; Schymanski, E. L.; Scrimshaw, M.; Segner, H.; Slobodnik, J.; Smedes, F.; Kughathas, S.; Teodorovic, I.; Tindall, A. J.; Tollefsen, K. E.; Walz, K.-H.; Williams, T. D.; Van den Brink, P. J.; van Gils, J.; Vrana, B.; Zhang, X.; Brack, W. Future water quality monitoring — Adapting tools to deal with mixtures of pollutants in water resource management Sci Total Environ 512–513, 540–551, (2015) DOI: 10.1016/j.scitotenv.2014.12.057

Environmental quality monitoringofwaterresourcesis challenged with providing the basisfor safe guarding the environment against adverse biological effects of anthropogenic chemical contamination from diffuse and point sources. While current regulatory efforts focus on monitoring and assessing a few legacy chemicals, many more anthropogenic chemicals can be detected simultaneously in our aquatic resources. However, exposure to chemical mixtures does not necessarily translate into adverse biological effects nor clearly shows whether mitigationmeasures are needed. Thus, the question which mixtures are present and which have associated combined effects becomes central for defining adequate monitoring and assessment strategies. Here we describe the vision of the international, EU-funded project SOLUTIONS, where three routes are explored to link the occurrence of chemical mixtures at specific sites to the assessment of adverse biological combination effects. First of all, multi-residue target and non-target screening techniques covering a broader range of anticipated chemicalsco-occurring in the environment are being developed. By improving sensitivity and detection limits for known bioactive compounds of concern, new analytical chemistry data for multiple components can be obtained and used to characterise priority mixtures. This information on chemical occurrence will be used to predict mixture toxicity and toderive combined effecte stimatessuitable for advancing environmental quality standards. Secondly, bioanalytical tools will be explored to provide aggregate bioactivity measuresintegrating all components that produce common (adverse) outcomes even for mixtures of varying compositions. The ambition is to provide comprehensive arrays of effect-based tools and trait-based field observations that link multiple chemical exposures to various environmental protection goals more directly and to provide improved in situ observations for impact assessment of mixtures. Thirdly, effect-directed analysis (EDA) will be applied to identify major drivers of mixture toxicity. Refinements of EDA include the use of statistical approaches with monitoring information for guidance of experimental EDA studies. These three approaches will be explored using case studies at theDanube and Rhine river basins as well as rivers of the Iberian Peninsula. The synthesis offindings will be organised toprovide guidance for futuresolution-oriented environmenta lmonitoring and exploremore systematic ways to assess mixture exposures and combination effects in future water quality monitoring.
Publications

Moreno, P.; Beisken, S.; Harsha, B.; Muthukrishnan, V.; Tudose, I.; Dekker, A.; Dornfeldt, S.; Taruttis, F.; Grosse, I.; Hastings, J.; Neumann, S.; Steinbeck, C. BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology BMC Bioinformatics 16, 56, (2015) DOI: 10.1186/s12859-015-0486-3

Background: Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein setsannotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis.Results: We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology.Conclusions: BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

This page was last modified on 24.10.2018.

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