Literature DB >> 16220342

Metabolomics and its role in understanding cellular responses in plants.

Ritu Bhalla1, Kothandaraman Narasimhan, Sanjay Swarup.   

Abstract

A natural shift is taking place in the approaches being adopted by plant scientists in response to the accessibility of systems-based technology platforms. Metabolomics is one such field, which involves a comprehensive non-biased analysis of metabolites in a given cell at a specific time. This review briefly introduces the emerging field and a range of analytical techniques that are most useful in metabolomics when combined with computational approaches in data analyses. Using cases from Arabidopsis and other selected plant systems, this review highlights how information can be integrated from metabolomics and other functional genomics platforms to obtain a global picture of plant cellular responses. We discuss how metabolomics is enabling large-scale and parallel interrogation of cell states under different stages of development and defined environmental conditions to uncover novel interactions among various pathways. Finally, we discuss selected applications of metabolomics.

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Year:  2005        PMID: 16220342     DOI: 10.1007/s00299-005-0054-9

Source DB:  PubMed          Journal:  Plant Cell Rep        ISSN: 0721-7714            Impact factor:   4.570


  44 in total

Review 1.  Metabolomics--the link between genotypes and phenotypes.

Authors:  Oliver Fiehn
Journal:  Plant Mol Biol       Date:  2002-01       Impact factor: 4.076

2.  Plant metabolomics: the missing link in functional genomics strategies.

Authors:  Robert Hall; Mike Beale; Oliver Fiehn; Nigel Hardy; Lloyd Sumner; Raoul Bino
Journal:  Plant Cell       Date:  2002-07       Impact factor: 11.277

3.  Metabolomic strategy for the classification and quality control of phytomedicine: a case study of chamomile flower (Matricaria recutita L.).

Authors:  Yulan Wang; Huiru Tang; Jeremy K Nicholson; Peter J Hylands; Julia Sampson; Ian Whitcombe; Christopher G Stewart; Steve Caiger; Isaac Oru; Elaine Holmes
Journal:  Planta Med       Date:  2004-03       Impact factor: 3.352

4.  Analysis of longitudinal metabolomics data.

Authors:  Jeroen J Jansen; Huub C J Hoefsloot; Hans F M Boelens; Jan van der Greef; Age K Smilde
Journal:  Bioinformatics       Date:  2004-04-15       Impact factor: 6.937

5.  Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics.

Authors:  Masami Yokota Hirai; Marion Klein; Yuuta Fujikawa; Mitsuru Yano; Dayan B Goodenowe; Yasuyo Yamazaki; Shigehiko Kanaya; Yukiko Nakamura; Masahiko Kitayama; Hideyuki Suzuki; Nozomu Sakurai; Daisuke Shibata; Jim Tokuhisa; Michael Reichelt; Jonathan Gershenzon; Jutta Papenbrock; Kazuki Saito
Journal:  J Biol Chem       Date:  2005-05-02       Impact factor: 5.157

6.  Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry.

Authors:  O Fiehn; J Kopka; R N Trethewey; L Willmitzer
Journal:  Anal Chem       Date:  2000-08-01       Impact factor: 6.986

7.  Comparative quantitative trait loci mapping of aliphatic, indolic and benzylic glucosinolate production in Arabidopsis thaliana leaves and seeds.

Authors:  D J Kliebenstein; J Gershenzon; T Mitchell-Olds
Journal:  Genetics       Date:  2001-09       Impact factor: 4.562

8.  Regulation of floral scent production in petunia revealed by targeted metabolomics.

Authors:  Julian C Verdonk; C H Ric de Vos; Harrie A Verhoeven; Michel A Haring; Arjen J van Tunen; Robert C Schuurink
Journal:  Phytochemistry       Date:  2003-03       Impact factor: 4.072

9.  A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis.

Authors:  Daniel Cook; Sarah Fowler; Oliver Fiehn; Michael F Thomashow
Journal:  Proc Natl Acad Sci U S A       Date:  2004-09-21       Impact factor: 11.205

10.  Metabolite profiling of tomato (Lycopersicon esculentum) using 1H NMR spectroscopy as a tool to detect potential unintended effects following a genetic modification.

Authors:  Gwénaëlle Le Gall; Ian J Colquhoun; Adrienne L Davis; Geoff J Collins; Martine E Verhoeyen
Journal:  J Agric Food Chem       Date:  2003-04-23       Impact factor: 5.279

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  13 in total

1.  Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds.

Authors:  Fangping Mu; Clifford J Unkefer; Pat J Unkefer; William S Hlavacek
Journal:  Bioinformatics       Date:  2011-04-08       Impact factor: 6.937

2.  Metabolic Profiling of Human Blood by High Resolution Ion Mobility Mass Spectrometry (IM-MS).

Authors:  Prabha Dwivedi; Albert J Schultz; Herbert H Hill
Journal:  Int J Mass Spectrom       Date:  2010-12       Impact factor: 1.986

3.  Metabolic profiling of Escherichia coli by ion mobility-mass spectrometry with MALDI ion source.

Authors:  Prabha Dwivedi; Geoffery Puzon; Maggie Tam; Denis Langlais; Shelley Jackson; Kimberly Kaplan; William F Siems; Albert J Schultz; Luying Xun; Amina Woods; Herbert H Hill
Journal:  J Mass Spectrom       Date:  2010-12       Impact factor: 1.982

4.  Root metabolic response of rice (Oryza sativa L.) genotypes with contrasting tolerance to zinc deficiency and bicarbonate excess.

Authors:  Michael T Rose; Terry J Rose; Juan Pariasca-Tanaka; Tadashi Yoshihashi; Heiko Neuweger; Alexander Goesmann; Michael Frei; Matthias Wissuwa
Journal:  Planta       Date:  2012-04-24       Impact factor: 4.116

Review 5.  Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes.

Authors:  Uday Chand Jha; Abhishek Bohra; Rintu Jha; Swarup Kumar Parida
Journal:  Plant Cell Rep       Date:  2019-01-12       Impact factor: 4.570

6.  Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork.

Authors:  Arnis Druka; Ilze Druka; Arthur G Centeno; Hongqiang Li; Zhaohui Sun; William T B Thomas; Nicola Bonar; Brian J Steffenson; Steven E Ullrich; Andris Kleinhofs; Roger P Wise; Timothy J Close; Elena Potokina; Zewei Luo; Carola Wagner; Günther F Schweizer; David F Marshall; Michael J Kearsey; Robert W Williams; Robbie Waugh
Journal:  BMC Genet       Date:  2008-11-18       Impact factor: 2.797

7.  Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps.

Authors:  Peter Meinicke; Thomas Lingner; Alexander Kaever; Kirstin Feussner; Cornelia Göbel; Ivo Feussner; Petr Karlovsky; Burkhard Morgenstern
Journal:  Algorithms Mol Biol       Date:  2008-06-26       Impact factor: 1.405

Review 8.  Metabolomics in plants and humans: applications in the prevention and diagnosis of diseases.

Authors:  Diego F Gomez-Casati; Maria I Zanor; María V Busi
Journal:  Biomed Res Int       Date:  2013-08-06       Impact factor: 3.411

9.  Multi-platform metabolomic analyses of ergosterol-induced dynamic changes in Nicotiana tabacum cells.

Authors:  Fidele Tugizimana; Paul A Steenkamp; Lizelle A Piater; Ian A Dubery
Journal:  PLoS One       Date:  2014-01-31       Impact factor: 3.240

Review 10.  Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement.

Authors:  Abirami Ramalingam; Himabindu Kudapa; Lekha T Pazhamala; Wolfram Weckwerth; Rajeev K Varshney
Journal:  Front Plant Sci       Date:  2015-12-24       Impact factor: 5.753

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