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Publications - Stress and Develop Biology

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Books and chapters

Doell, S.; Arens, N.; Mock, H. Liquid Chromatography and Liquid Chromatography–Mass Spectrometry of Plants: Techniques and Applications (Meyers, R. A., ed.). (2019) ISBN: 9780470027318 DOI: 10.1002/9780470027318.a9912.pub2

Mass spectrometry coupled with LC (liquid chromatography) separation has developed into a technique routinely applied for targeted as well as for nontargeted analysis of complex biological samples, not only in plant biochemistry. Earlier on, LC‐MS (liquid chromatography–mass spectrometry) was mostly part of the efforts for identification of one or few unknown metabolites of interest as part of a phytochemical study. As a major strategy, unknown compounds had to be purified in sufficient quantities. The purified fractions were then subjected to LC‐MS/MS as part of the structural elucidation, mostly complemented by NMR (nuclear magnetic resonance) analysis. With the advance of mass spectrometry instrumentation, LC‐MS is now widely applied for analysis of crude plant extracts and large numbers (100s to 1000s) of samples. It has become an essential part of metabolomic studies (see Metabolomics), aiming at the comprehensive coverage of the metabolite profiles of cells, tissues, or organs. Owing to the huge chemical diversity of small molecules, conditions for the extraction will restrict the subfraction of the metabolome, which can be actually analyzed. The conditions for LC have to be adjusted to allow good separation of the particular metabolites from the respective extract. Major consideration will be the selection of an appropriate column and suitable eluents, the establishment of gradient profiles, temperature conditions, and so on.
Books and chapters

Böttcher, C.; von Roepenack-Lahaye, E.; Scheel, D. Resources for metabolomics (Schmidt, R. & Bancroft, I., eds.). Plant Genetics and Genomics: Crops and Models 9, 469-503, (2011) ISBN: 978-1-4419-7118-0 DOI: 10.1007/978-1-4419-7118-0_17

Metabolomics is developing toward an integral component of functional genomics approaches. The large structural diversity of plant metabolites requires different analytical techniques for broad metabolite analysis. In addition, new bioinformatics tools and databases are necessary for data analysis and storage. This chapter describes the resources available for comprehensive analysis of plant secondary metabolites focusing on Arabidopsis thaliana and Brassica species. In particular, a platform for non-targeted profiling of semi-polar plant metabolites based on liquid chromatography coupled to mass spectrometry is described.
Books and chapters

Knogge, W. Diseases affecting barley: scald (Ed. Oliver R). Burleigh Dodds Series in Agricultural Science 183-215, (2018) ISBN: 9781786762160 DOI: 10.19103/as.2018.0039.10

Scald (leaf blotch), caused by the hemibiotrophic pathogen Rhynchosporium commune, is one of the major diseases of barley worldwide. Typical disease symptoms consist of necrotic areas on the leaf blades. Yield losses are manifested as reduced kernel quality, size and number per ear. This chapter reviews the origins, epidemiology and other characteristic features of scald, and considers the agricultural consequences of the pathogen’s biology. It then considers resistance breeding programmes in which more than a dozen major resistance genes as well as quantitative trait loci have been identified, and discusses strategies to minimize the damage caused by the disease comprising agricultural practices and different fungicides.
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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