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Metabolomics and wood development

catching a metabolome

Johansson, Annika I. (2013). Metabolomics and wood development. Diss. (sammanfattning/summary) Umeå : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2013:92
ISBN 978-91-576-7922-2
eISBN 978-91-576-7923-9
[Doctoral thesis]

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Abstract

The tree industry is one of Sweden's most important economic sectors, producing pulp, paper, wooden goods and wood as a bioenergy source. Understanding the biology behind the processes of tree growth and wood development is a key to maximizing the use of wood as raw material. The term "metabolome" refers to the complete set of small-molecule metabolites to be found within a biological sample. Since metabolites can be viewed as down-stream products of gene transcription, protein expression and enzymatic activity the metabolites are believed to reflect activity in cells more accurately than the transcript and protein complements. Metabolomics aims to identify and quantify all metabolites in a biological sample and thereby link biochemical information to a phenotype. In the course of the work underlying this thesis we have developed analytical tools for metabolomics and applied these tools to reveal metabolite patterns, with a focus on various aspects of wood development.

Firstly we development of a rapid and reliable method for processing GC-TOFMS data, that enables us to move from GC-MS chromatograms via metabolite identification to biological interpretation. To address the low identification ratios characteristic of GC-MS metabolomics studies, a database containing the predicted retention indices of ~13 000 metabolite structures was developed. Since metabolomic studies only gives a snapshot of the metabolic status of a cell and it is the metabolic fluxes within the cell that are the key determinant of cell activity, an LC-MS based method for the measurement of nitrogen fluxes was evaluated using plants fed with ¹⁵N.

As winter approaches trees in temperate zones halt the growth of the vascular cambium and put the meristems into a dormant state. In order to gain a better understanding of the environmental and hormonal regulation of the process of activity-dormancy transitions in aspen trees we performed metabolite profiling of the cambial tissue at different stages over the year.

Finally a metabolic roadmap of wood development in Populus was created by combining targeted analysis of plant hormones and amino acids in parallel with high sensitivity untargeted LC-MS and GC-MS analyses. We were able, for the first time in a plant metabolomics study, to describe changes in metabolite profiles following the route of differentiation from cell division to cell death.

Authors/Creators:Johansson, Annika I.
Title:Metabolomics and wood development
Subtitle:catching a metabolome
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :2013
Volume:2013:92
Number of Pages:80
Papers/manuscripts:
NumberReferences
I.Jonsson, P., Johansson, A. I., Gullberg, J., Trygg, J., A, J., Grung, B., Marklund, S., Sjostrom, M., Antti, H. & Moritz, T. (2005). High-throughput data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses. Analytical Chemistry, 77, 5635-5642.
II.II Druart, N.*, Johansson, A.*, Baba, K., Schrader, J., Sjodin, A., Bhalerao, R. R., Resman, L., Trygg, J., Moritz, T. & Bhalerao, R. P. 2007. Environmental and hormonal regulation of the activity-dormancy cycle in the cambial meristem involves stage-specific modulation of transcriptional and metabolic networks. Plant Journal, 50, 557-573.
III.Johansson, A. I., Gullberg, J., Trygg, J., Linusson, A. & Moritz, T. A retention index prediction database to increase the rate of identification of non-annotated GC-MS mass spectra. (manuscript)
IV.Johansson, A.I., Aguetoni Cambui, C., Campbell, C., Hurry, V., Näsholm, T. & Moritz, T. A liquid chromatography – mass spectrometry method for determine ¹⁵N- incorporation into amino acids and amines in plants. (manuscript)
V.Johansson, A.I., Sundberg, B. & Moritz, T. A metabolite roadmap of the wood forming tissue in Populus. (manuscript)
Place of Publication:Umeå
Publisher:Institutionen för skoglig genetik och växtfysiologi, Sveriges lantbruksuniversitet
ISBN for printed version:978-91-576-7922-2
ISBN for electronic version:978-91-576-7923-9
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:F Plant production > F62 Plant physiology - Growth and development
K Forestry > K01 Forestry - General aspects
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 104 Chemical Sciences > Analytical Chemistry
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Biochemistry and Molecular Biology
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Developmental Biology
Agrovoc terms:wood, metabolites, biological production, nitrogen, dormancy, biological development, mass spectrometry
Keywords:metabolomics, wood development, mass spectrometry, retention index, QSRR, nitrogen flux
URN:NBN:urn:nbn:se:slu:epsilon-e-1723
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-1723
ID Code:10926
Department:(S) > Dept. of Forest Genetics and Plant Physiology
Deposited By: Annika I. Johansson
Deposited On:13 Dec 2013 07:51
Metadata Last Modified:14 Dec 2014 20:04

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