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Combined profiling in aspen

a systems biology approach

Obudulu, Ogonna (2015). Combined profiling in aspen. Diss. (sammanfattning/summary) Umeå : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2015:91
ISBN 978-91-576-8380-9
eISBN 978-91-576-8381-6
[Doctoral thesis]

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Abstract

This thesis presents efficient systems biology modelling strategies for integrating complex multi-platform datasets in order to increase our understanding of stress biology, wood formation and secondary cell wall formation in Populus trees and connected responses to perturbations in organisms, particularly aspen. It is based on studies reported in four appended papers, designated Papers I-IV.

Paper I describes an enhanced framework for investigating and understanding multi-level oxidative stress responses and their influence on phenotypic variation in transgenic hipI-superoxide dismutase Populus plants. Paper II presents a modelling strategy based on a combination of Principal Component Analysis (PCA), Orthogonal Projections to Latent Structures (OPLS), and an enhanced stepwise linear modelling approach. This strategy revealed major transitions in the proteomes along the wood developmental series in Populus tremula (aspen) pinpointing, for example, the location of the cambial cell divisions leading to phloem and xylem cells, and the location of the secondary cell wall formation zone.

A pairwise multivariate OPLS approach was applied in the study described in Paper III to analyse proteome dynamics during tension wood formation of Populus trees. Pairwise comparisons of four corresponding phases/tissue types in normal and tension wood formation allowed identification of several processes that were strongly enhanced and/or unique during tension wood formation.

These multidisciplinary approaches together with a recently developed formulation of the OnPLS method was used in Paper IV to analyse a set of transgenic Populus trees carrying an RNAi construct for the Populus secretory carrier-associated membrane protein3 (PttSCAMP3) gene. Multilevel analysis of datasets from nine platforms (RNA sequencing, proteomic, metabolomic and wood chemical analyses) revealed a critical function for PttSCAMP proteins in wood formation and elucidated the underlying molecular mechanism. The systems biology approach presented in this thesis provides novel types of tools for elucidating stress responses and wood formation in Populus trees. Exploitation of very recent advances in multivariate methods such as OnPLS allowed the simultaneous combination of transcriptomic, proteomic and metabolomic data, as well as identification of differences and connections between the data sets, which would not have been possible using standard statistical methods.

Authors/Creators:Obudulu, Ogonna
Title:Combined profiling in aspen
Subtitle:a systems biology approach
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :3 September 2015
Depositing date:4 September 2015
Volume:2015:91
Number of Pages:61
Papers/manuscripts:
NumberReferences
ISrivastava V*, Obudulu O*, Bygdell J, Löfstedt T, Rydén P, Nilsson R, Ahnlund M, Johansson A, Jonsson P, Freyhult E, Qvarnström J, Karlsson J, Melzer M, Moritz T, Trygg J, Hvidsten TR, Wingsle G. (2013). OnPLS integration of transcriptomic, proteomic and metabolomic data shows multilevel oxidative stress responses in the cambium of transgenic hipIsuperoxide dismutase Populus plants. BMC Genomics, 14:893. * Joint first authors and equal contributors
IIObudulu O, Bygdell J, Sundberg B, Moritz T, Hvidsten TR, Trygg J, Wingsle G. Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development (submitted).
IIIBygdell J, Obudulu O, Nilsson R, Srivastava MK, Srivastava V, Sundberg B, Trygg J, Wingsle G. Protein expression in tension wood formation in Populus, monitored at high tissue resolution (manuscript).
IVObudulu O, Mähler N, Skotare T, Bygdell J, Abreu IN, Ahnlund M, Gandla ML, Petterle A, Gerber L, Moritz T, Hvidsten TR, Jönsson LJ, Wingsle G, Trygg J, Tuominen H. A systems approach reveals functions of secretory carrier-associated membrane proteins in wood formation of Populus trees (manuscript).
Place of Publication:Umeå
Publisher:Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-8380-9
ISBN for electronic version:978-91-576-8381-6
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:F Plant production > F60 Plant physiology and biochemistry
K Forestry > K01 Forestry - General aspects
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Forest Science
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Wood Science
Agrovoc terms:populus, wood, lignification, cell walls, stress, gene expression, transcription, molecular biology, multivariate analysis, models
Keywords:Systems biology, transcriptomics, proteomics, metabolomics, Populus, multivariate statistics, omics, wood development, aspen
URN:NBN:urn:nbn:se:slu:epsilon-e-2907
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-2907
ID Code:12583
Faculty:S - Faculty of Forest Sciences
Department:(S) > Dept. of Forest Genetics and Plant Physiology
External funders:Swedish Research Council
Deposited By: Ogonna Obudulu
Deposited On:07 Sep 2015 06:57
Metadata Last Modified:07 Sep 2015 06:57

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