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Publications - Stress and Develop Biology

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Books and chapters

Hummel, J.; Strehmel, N.; Bölling, C.; Schmidt, S.; Walther D.; Kopka, J. Mass spectral search and analysis using the Golm metabolome. (Weckwerth, W.; Kahl, G.). 321-343, (2013) ISBN: 978-3-527-32777-5 DOI: 10.1002/9783527669882.ch18

The novel “omics” technologies of the postgenomic era generate large multiplexed phenotyping datasets, which can only inadequately be published in the traditional journal and supplemental formats. For this reason, public databases have been developed that utilize the efficient communication of knowledge through the World Wide Web. This trend also applies to the metabolomics field, which is, after genomics, transcriptomics, and proteomics, the fourth major systems-level phenotyping platform. Each different analytical technology used in metabolomics studies requires specific reference data for metabolite identification and optimal data formats for reporting the complex metabolite profiling data features. Therefore, we envision that every technology platform or even each high-throughput metabolomic laboratory will establish dedicated databases, which will communicate between each other and will be integrated by meta-databases and web services. The Golm Metabolome Database (GMD) (http://gmd.mpimp-golm.mpg.de/) is a metabolomic database, maintained by the Max Planck Institute of Molecular Plant Physiology, that was initiated around a nucleus of reference data from gas chromatography–mass spectrometry metabolite profiling data and is now developing toward a general mass spectrometry-based repository of reference metabolite profiles for essential plant tissues and typical variations of growth conditions. This chapter describes the mass spectral searches and analyses currently supported by the GMD. We specifically address the searches for the different chemical entities within GMD, namely the metabolites, reference substances, and the chemically derivatized analytes. We report the diverse options for mass spectral analyses and highlight the decision tree-supported prediction of chemical substructures, a feature of GMD that currently appears to be a unique among the many tools for the analysis of gas chromatography–electron ionization mass spectra.
Books and chapters

Scheel, D.; Wasternack, C. Signal transduction in plants: Cross-talk with the environment (Scheel, D., Wasternack, C.). University Press, Oxford, UK 1-5, (2002)

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Books and chapters

Eschen-Lippold, L.; Bauer, N.; Löhr, J.; Palm-Forster, M.A.; Lee, J. Rapid mutagenesis-based analysis of phosphorylation sites in mitogen-activated protein kinase substrates.  (Komis, G.; Šamaj, J.). Methods Mol Biol 1171, 183-192, (2014) ISBN: 978-1-4939-0922-3 DOI: 10.1007/978-1-4939-0922-3_15

Mitogen-activated protein kinases (MAPKs) are versatile phosphorylating enzymes which regulate multiple proteins involved in gene expression, cell architecture, plant development and reaction to diverse abiotic and biotic factors. The main aim of Plant MAP Kinases: Methods and Protocols is to provide established and new MAPK protocols adapted to the challenges posed by working with plants. The book contains 19 chapters which encompass a wide array of methods progressively scaling from the single gene, protein or cell level to large-scale arrays of proteomic, phosphoproteomic and interactomic data in order to uncover previously unidentified plant MAPK signaling pathways and to tackle with the challenging task of substrate identification. Techniques for MAPK sequence analysis and subcellular localization helping to identify their substrates and subcellular compartmentalization are also provided. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.
Books and chapters

Scheel, D.; Nürnberger, T. Signal transduction in plant defense responses (Punja, Z.K.). The Haworth Press, Inc., Binghamton, USA 1-30, (2004)

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Books and chapters

Scheel, D.; Blume, B.; Brunner, F.; Fellbrich, G.; Dalbøge, H.; Hirt, H.; Kauppinen, S.; Kroj, T.; Ligterink, W.; Nürnberger, T.; Tschöpe, M.; Zinecker, H.; zur Nieden, U. Receptor-mediated signal transduction in plant defense (de Wit, P.J.G.M., Bisseling, T., Stiekema, W.J.). International Society for Molecular Plant-Microbe Interactions, St. Paul, U.S.A. 2, 131-135, (2000)

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Books and chapters

Hirt, H.; Scheel, D. Receptor-mediated MAP kinase activation in plant defense (Hirt, H.). Springer-Verlag, Heidelberg 27, 85-93, (2000)

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Books and chapters

Rosahl, S.; Feussner, I. Oxylipins (Murphy, D.). Blackwell Publishing, Oxford 329-354, (2004)

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Books and chapters

Scheel, D. Oxidative burst and the role of reactive oxygen species in plant-pathogen interactions (Inzé, D., van Montagu, M.). Taylor & Francis, London, UK 137-153, (2002)

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Books and chapters

Clemens, S.; Thomine, S.; Schroeder, J.I. Molecular mechanisms that control plant tolerance to heavy metals and possible roles towards manipulating metal accumulation (Oksman-Caldentey, K.-M., Barz, W.). Plant Biotechnology and Transgenic Plants 665-691, (2003)

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