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Metabolomics : a tool for studying plant biology

Gullberg, Jonas (2005). Metabolomics : a tool for studying plant biology. Diss. (sammanfattning/summary) Umeå : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2005: 88
ISBN 91-576-6987-2
[Doctoral thesis]

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Abstract

In recent years new technologies have allowed gene expression, protein and metabolite profiles in different tissues and developmental stages to be monitored. This is an emerging field in plant science and is applied to diverse plant systems in order to elucidate the regulation of growth and development. The goal in plant metabolomics is to analyze, identify and quantify all low molecular weight molecules of plant organisms. The plant metabolites are extracted and analyzed using various sensitive analytical techniques, usually mass spectrometry (MS) in combination with chromatography. In order to compare the metabolome of different plants in a high through-put manner, a number of biological, analytical and data processing steps have to be performed. In the work underlying this thesis we developed a fast and robust method for routine analysis of plant metabolite patterns using Gas Chromatography-Mass Spectrometry (GC/MS). The method was performed according to Design of Experiment (DOE) to investigate factors affecting the extraction and derivatization of the metabolites from leaves of the plant Arabidopsis thaliana. The outcome of metabolic analysis by GC/MS is a complex mixture of approximately 400 overlapping peaks. Resolving (deconvoluting) overlapping peaks is time-consuming, difficult to automate and additional processing is needed in order to compare samples. To avoid deconvolution being a major bottleneck in high through-put analyses we developed a new semi-automated strategy using hierarchical methods for processing GC/MS data that can be applied to all samples simultaneously. The two methods include base-line correction of the non-processed MS-data files, alignment, time-window determinations, Alternating Regression and multivariate analysis in order to detect metabolites that differ in relative concentrations between samples. The developed methodology was applied to study the effects of the plant hormone GA on the metabolome, with specific emphasis on auxin levels in Arabidopsis thaliana mutants defective in GA biosynthesis and signalling. A large series of plant samples was analysed and the resulting data were processed in less than one week with minimal labour; similar to the time required for the GC/MS analyses of the samples.

Authors/Creators:Gullberg, Jonas
Title:Metabolomics : a tool for studying plant biology
Year of publishing :September 2005
Volume:2005: 88
Number of Pages:61
Papers/manuscripts:
NumberReferences
ALLGullberg, J., Jonsson, P., Nordström, A., Sjöström, M. & Moritz, T. 2004. Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Analytical Biochemistry 331, 283-295. Jonsson, P.*, Gullberg, J.*, Nordström, A., Kusano, M., Kowalczyk, M., Sjöström, M. & Moritz, T. 2004. A strategy for identifying differences in large series of metabolomic samples analyzed by GC/MS. Analytical Chemistry 76, 1738-1745. Jonsson, P., Johansson, AI., Gullberg, J., Trygg, J., A, J., Grung, B., Marklund, S., Sjöström, M., Antti, H. & Moritz, T. 2005. High through-put data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyzes. Analytical Chemistry, In Press. Gullberg, J., Wiklund, S., Trygg, J., Sjöström, M., Harberd, NP. & Moritz, T. Effect of gibberellin signalling on IAA levels and metabolite profiles in Arabidopsis. (Manuscript)
Place of Publication:Umeå
ISBN for printed version:91-576-6987-2
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:U Auxiliary disciplines > U30 Research methods
F Plant production > F62 Plant physiology - Growth and development
Subjects:Not in use, please see Agris categories
Agrovoc terms:arabidopsis thaliana, chromatography, mass spectrometry, metabolites, methods, gibberellic acid
Keywords:Plant metabolomics Arabidopsis thaliana, Chromatography mass-spectrometry, Design of experiment, Deconvolution, Chemometric analysis, Gibberellin
URN:NBN:urn:nbn:se:slu:epsilon-720
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-720
ID Code:916
Department:(S) > Dept. of Forest Genetics and Plant Physiology
Deposited By: Jonas Gullberg
Deposited On:02 Sep 2005 00:00
Metadata Last Modified:02 Dec 2014 10:08

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