A comparison of metabolite extraction strategies for <sup>1</sup>H‐NMR‐based metabolic profiling using mature leaf tissue from the model plant <i>Arabidopsis thaliana</i>

Kaiser, Kayla A.; Barding, Gregory A.; Larive, Cynthia K.

doi:10.1002/mrc.2457

Cited by 53 publications

(32 citation statements)

References 40 publications

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“…The use of a two-phase solvent system, composed of a mixture of chloroform, methanol and water (2:1:1, v/v), has proven to be the most advisable method (Choi et al 2004). For detailed information about the different extraction properties, see Kim and Verpoorte (2010) and Kaiser et al (2009).…”

Section: Analytical Techniquesmentioning

confidence: 99%

Ecological metabolomics: overview of current developments and future challenges

2011

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Ecometabolomics, which aims to analyze the metabolome, the total number of metabolites and its shifts in response to environmental changes, is gaining importance in ecological studies because of the increasing use of new technical advances, such as modern HNMR spectrometers and GC-MS coupled to bioinformatic advances. We review here the state of the art and the perspectives of ecometabolomics. The studies available demonstrate ecometabolomic techniques have great sensitivity in detecting the phenotypic mechanisms and key molecules underlying organism responses to abiotic environmental changes to biotic interactions. But such studies are still scarce, and in most cases they are limited to the direct effects of a single abiotic factor or of biotic interactions between two trophic levels under controlled conditions. Several exciting challenges remain to be achieved through the use of ecometabolomics in field conditions, involving more than two trophic levels, or combining the effects of abiotic gradients with intra-and inter-specific relationships. The coupling of ecometabolomic studies with genomics, transcriptomics, ecosystem stoichiometry, community biology and biogeochemistry may provide a further step forward in many areas of ecological sciences, including stress responses, species lifestyle, life history variation, population structure, trophic interaction, nutrient cycling, ecological niche and global change.

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Section: Analytical Techniquesmentioning

confidence: 99%

Ecological metabolomics: overview of current developments and future challenges

2011

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“…A consequence of working with whole body homogenates is that cellular compartmentalisation is lost, hence substrates become readily available to enzymes. Problems with poor stability of D 2 O extracts has been reported before (Kaiser et al 2009) and steps to denaturalise internal enzymes using high temperatures have been essayed (Kim et al 2004). The D 2 O method is therefore not suitable for the extraction of H. diversicolor metabolome unless steps to stop enzyme activity are taken.…”

Section: Discussionmentioning

confidence: 98%

Evaluation of extraction methods for use with NMR-based metabolomics in the marine polychaete ragworm, Hediste diversicolor

et al. 2010

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The sediment-dwelling polychaete, Hediste diversicolor, is commonly found in Northern temperate estuaries. Its limited mobility and tolerance to polluted conditions makes it a good candidate for biological monitoring. Moreover, its importance in the functioning of the sediment ecosystem has caused it to be described as a keystone species. Here we present the development of analytical methodology that will enable the use of H. diversicolor in environmental metabolomics studies for the biomonitoring of estuarine ecosystems. Polar and nonpolar extraction solvents have been used to solubilise a wide range of metabolites. Extraction solvents assessed include: aqueous phosphate buffer solution, methanol:chloroform:water (1:1:0.9), methanol:water (1:1 and 2:1) and chloroform. The metabolites were analysed using 1-dimensional (1D) 1 H nuclear magnetic resonance (NMR) spectroscopy. Using the methanol:water (1:1) method, previous freezing to aid cell rupture did not result in an enhanced extraction. Removal of methanol with a speed vacuum resulted in reduction in yield. Methanol:water (1:1) and chloroform extractions proved to be the most appropriate techniques based on the sample yield and repeatability. NMR-based metabolomics in the ragworm can now be used to understand the ecophysiology of this important estuarine organism and has applications in biomonitoring, biomarker development and ecotoxicological studies.

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“…Furthermore, these techniques have been successfully applied to deciphering gene function in plant functional genomics (Roessner et al 2001;Sumner et al 2003;Krishnan et al 2005;Saito and Matsuda 2010). Recently, to increase the robustness and reproducibility of 1 H NMR based metabolic profiling, the protocol for sample preparation, metabolite extraction and chemometric analysis has standardized (Beckonert et al 2007;Kaiser et al 2009;Kim et al 2010). Therefore, 1 H NMR fingerprinting is the ideal technique for large scale plant metabolomics (Ward et al 2010).…”

Section: Introductionmentioning

confidence: 99%

Metabolic evaluation of cellular differentiation of tobacco leaf explants in response to plant growth regulators in tissue cultures using 1H NMR spectroscopy and multivariate analysis

Kim

Ahn

et al. 2011

Plant Cell Tiss Organ Cult

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To investigate the metabolic changes that precede visible organogenesis in tissue culture, tobacco leaf explants were cultured on media supplemented with various plant growth regulators (PGRs) and analyzed with proton nuclear magnetic resonance ( 1 H NMR) spectroscopy. Principal component analysis (PCA) of 1 H NMR spectral data was unable to differentiate between leaf explants cultured with a-naphthaleneacetic acid and those cultured with 6-benzyladenine after 4 days of culture; however, a difference was evident after 8 days of culture. A hierarchical dendrogram from PCA analysis could be grouping leaf explants cultured with various auxins separately from those treated by various cytokinins. However, leaf explants cultured with thidiazuron (TDZ) were identified as an outlier group; TDZ appeared to produce pleiotropic metabolic effects that differed from those induced by other PGRs. These results show that dedifferentiation can be initiated by either auxins or cytokinins, which is reflected by similar metabolic changes produced by the two distinct PGRs during the initial incubation period. The subsequent redifferentiation differs according to the PGR treatment, which is reflected by differential metabolic changes, depending on the fate of cells in organogenesis. Glutamine and glutamate levels increased approximately twofold in cytokinin-treated leaf explants compared with auxin-treated explants; however, changes in the levels of sugar compounds did not differ between the two treatments, demonstrating auxin regulation of the carbon/nitrogen ratio in favor of rooting. Taken together, our results suggest that 1 H-NMR spectroscopy combined with multivariate analysis is a promising means for the metabolic evaluation of plant growth and differentiation.

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A comparison of metabolite extraction strategies for ¹H‐NMR‐based metabolic profiling using mature leaf tissue from the model plant Arabidopsis thaliana

Cited by 53 publications

References 40 publications

Ecological metabolomics: overview of current developments and future challenges

Ecological metabolomics: overview of current developments and future challenges

Evaluation of extraction methods for use with NMR-based metabolomics in the marine polychaete ragworm, Hediste diversicolor

Metabolic evaluation of cellular differentiation of tobacco leaf explants in response to plant growth regulators in tissue cultures using 1H NMR spectroscopy and multivariate analysis

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A comparison of metabolite extraction strategies for 1H‐NMR‐based metabolic profiling using mature leaf tissue from the model plant Arabidopsis thaliana

Cited by 53 publications

References 40 publications

Ecological metabolomics: overview of current developments and future challenges

Ecological metabolomics: overview of current developments and future challenges

Evaluation of extraction methods for use with NMR-based metabolomics in the marine polychaete ragworm, Hediste diversicolor

Metabolic evaluation of cellular differentiation of tobacco leaf explants in response to plant growth regulators in tissue cultures using 1H NMR spectroscopy and multivariate analysis

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A comparison of metabolite extraction strategies for ¹H‐NMR‐based metabolic profiling using mature leaf tissue from the model plant Arabidopsis thaliana