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Metabolomic Analysis (metabolomic + analysis)

Distribution by Scientific Domains

Chemistry	62%
Life Sciences	37%

Selected Abstracts

Metabolomic analysis of Echinacea spp. by 1H nuclear magnetic resonance spectrometry and multivariate data analysis technique,

PHYTOCHEMICAL ANALYSIS, Issue 1 2010
Michel Frédérich
Abstract Introduction , The genus Echinacea (Asteraceae) comprises about 10 species originally distributed in North America. Three species are very well known as they are used worldwide as medicinal plants: Echinacea purpurea, E. pallida, E. angustifolia. Objective , To discriminate between these three Echinacea species and E. simulata by 1H NMR-based metabolomics. Methodology , 1H NMR and multivariate analysis techniques were applied to diverse Echinacea plants including roots and aerial parts, authentic plants, commercial plants and commercial dry extracts. Results , Using the 1H NMR metabolomics, it was possible, without previous evaporation or separation steps, to obtain a metabolic fingerprint to distinguish between species. Conclusion , A clear distinction between the three pharmaceutical species was possible and some useful metabolites were identified. Copyright © 2009 John Wiley & Sons, Ltd. [source]

Metabolomic analysis of host plant resistance to thrips in wild and cultivated tomatoes,

PHYTOCHEMICAL ANALYSIS, Issue 1 2010
Mohammad Mirnezhad
Abstract Introduction , Western flower thrips (Frankliniella occidentalis) are among the most serious crop pests worldwide. Control of thrips mainly depends on pesticides, excessive use of which leads to human health risks and environmental contamination. As an alternative, we study host plant resistance to thrips. Objective , To apply nuclear magnetic resonance spectroscopy (NMR) metabolomics to study host plant resistance to thrips in wild and cultivated tomatoes. Methodology , Ten wild species and 10 cultivated tomato lines were compared. Five replicates of each species and lines were used for a thrips bioassay while another five replicates were used for the metabolomic analysis. The three most resistant and susceptible wild species, and cultivated lines, as identified by the thrips bioassay, were used for the metabolomics, performed by 1H NMR spectroscopy followed by principal component analysis. Results , Wild and cultivated tomatoes differed significantly in thrips resistance. Only wild tomatoes were thrips-resistant, among which Lycopersicon pennellii and L. hirsutum exhibited the lowest thrips damage. Their 1H NMR-based metabolomic profiles were significantly different from those of thrips-susceptible tomatoes. Thrips-resistant tomatoes contained acylsugars, which are known for their negative effect on herbivores. Conclusion , The identification of acylsugars as a resistance factor for thrips in tomato proves that NMR-based metabolomics an important tool to study plant defences, providing fundamental information for the development and realisation of herbivore resistance breeding programmes in agricultural crops. Copyright © 2009 John Wiley & Sons, Ltd. [source]

The nucleotidase/phosphatase SAL1 is a negative regulator of drought tolerance in Arabidopsis

THE PLANT JOURNAL, Issue 2 2009
Pip B. Wilson
Summary An Arabidopsis thaliana drought-tolerant mutant, altered expression of APX2 (alx8), has constitutively increased abscisic acid (ABA) content, increased expression of genes responsive to high light stress and is reported to be drought tolerant. We have identified alx8 as a mutation in SAL1, an enzyme that can dephosphorylate dinucleotide phosphates or inositol phosphates. Previously identified mutations in SAL1, including fiery (fry1-1), were reported as being more sensitive to drought imposed by detachment of rosettes. Here we demonstrate that alx8, fry1-1 and a T-DNA insertional knockout allele all have markedly increased resistance to drought when water is withheld from soil-grown intact plants. Microarray analysis revealed constitutively altered expression of more than 1800 genes in both alx8 and fry1-1. The up-regulated genes included some characterized stress response genes, but few are inducible by ABA. Metabolomic analysis revealed that both mutants exhibit a similar, dramatic reprogramming of metabolism, including increased levels of the polyamine putrescine implicated in stress tolerance, and the accumulation of a number of unknown, potential osmoprotectant carbohydrate derivatives. Under well-watered conditions, there was no substantial difference between alx8 and Col-0 in biomass at maturity; plant water use efficiency (WUE) as measured by carbon isotope discrimination; or stomatal index, morphology or aperture. Thus, SAL1 acts as a negative regulator of predominantly ABA-independent and also ABA-dependent stress response pathways, such that its inactivation results in altered osmoprotectants, higher leaf relative water content and maintenance of viable tissues during prolonged water stress. [source]

Walls are thin 1 (WAT1), an Arabidopsis homolog of Medicago truncatula NODULIN21, is a tonoplast-localized protein required for secondary wall formation in fibers

THE PLANT JOURNAL, Issue 3 2010
Philippe Ranocha
Summary By combining Zinnia elegans in vitro tracheary element genomics with reverse genetics in Arabidopsis, we have identified a new upstream component of secondary wall formation in xylary and interfascicular fibers. Walls are thin 1 (WAT1), an Arabidopsis thaliana homolog of Medicago truncatula NODULIN 21 (MtN21), encodes a plant-specific, predicted integral membrane protein, and is a member of the plant drug/metabolite exporter (P-DME) family (transporter classification number: TC 2.A.7.3). Although WAT1 is ubiquitously expressed throughout the plant, its expression is preferentially associated with vascular tissues, including developing xylem vessels and fibers. WAT1:GFP fusion protein analysis demonstrated that WAT1 is localized to the tonoplast. Analysis of wat1 mutants revealed two cell wall-related phenotypes in stems: a defect in cell elongation, resulting in a dwarfed habit and little to no secondary cell walls in fibers. Secondary walls of vessel elements were unaffected by the mutation. The secondary wall phenotype was supported by comparative transcriptomic and metabolomic analyses of wat1 and wild-type stems, as many transcripts and metabolites involved in secondary wall formation were reduced in abundance. Unexpectedly, these experiments also revealed a modification in tryptophan (Trp) and auxin metabolism that might contribute to the wat1 phenotype. Together, our data demonstrate an essential role for the WAT1 tonoplast protein in the control of secondary cell wall formation in fibers. [source]

Abiotic stress and plant responses from the whole vine to the genes

AUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH, Issue 2010
G.R. CRAMER
Abstract Drought, salinity and extreme temperatures significantly limit the distribution of grapes around the world. In this review, the literature of grape responses to abiotic stress with particular reference to whole plant and molecular responses observed in recent studies is discussed. A number of short-term and long-term studies on grapevine shoots and berries have been conducted using a systems biology approach. Transcripts, proteins and metabolites were profiled. Water deficit, salinity and chilling altered the steady-state abundance of a large number of transcripts. Common responses to these stresses included changes in hormone metabolism, particularly abscisic acid (ABA), photosynthesis, growth, transcription, protein synthesis, signalling and cellular defences. Some of the transcriptional changes induced by stress were confirmed by proteomic and metabolomic analyses. More than 2000 genes were identified whose transcript abundance was altered by both water deficit and ABA. Different gene sets were used to map molecular pathways regulated by ABA, water deficit, salinity and chilling in grapevine. This work supports the hypothesis that ABA is a central regulator of abiotic stress tolerance mechanisms. ABA affects signalling pathways that trigger important molecular activities involving metabolism, transcription, protein synthesis, and cellular defence and also regulates important physiological responses such as stomatal conductance, photoprotection and growth. Systems biology approaches are providing more comprehensive understanding of the complex plant responses to abiotic stress. The molecular sets generated from mapping the ABA-inducible stress responses provide numerous targets for genetic and cultural manipulation for improved plant protection and grape quality. [source]

Time-series integrated "omic" analyses to elucidate short-term stress-induced responses in plant liquid cultures,

BIOTECHNOLOGY & BIOENGINEERING, Issue 1 2009
Bhaskar Dutta
Abstract The research that aims at furthering our understanding of plant primary metabolism has intensified during the last decade. The presented study validated a systems biology methodological framework for the analysis of stress-induced molecular interaction networks in the context of plant primary metabolism, as these are expressed during the first hours of the stress treatment. The framework involves the application of time-series integrated full-genome transcriptomic and polar metabolomic analyses on plant liquid cultures. The latter were selected as the model system for this type of analysis, because they provide a well-controlled growth environment, ensuring that the observed plant response is due only to the applied perturbation. An enhanced gas chromatography,mass spectrometry (GC,MS) metabolomic data correction strategy and a new algorithm for the significance analysis of time-series "omic" data are used to extract information about the plant's transcriptional and metabolic response to the applied stress from the acquired datasets; in this article, it is the first time that these are applied for the analysis of a large biological dataset from a complex eukaryotic system. The case-study involved Arabidopsis thaliana liquid cultures subjected for 30 h to elevated (1%) CO2 stress. The advantages and validity of the methodological framework are discussed in the context of the known A. thaliana or plant, in general, physiology under the particular stress. Of note, the ability of the methodology to capture dynamic aspects of the observed molecular response allowed for 9 and 24 h of treatment to be indicated as corresponding to shifts in both the transcriptional and metabolic activity; analysis of the pathways through which these activity changes are manifested provides insight to regulatory processes. Biotechnol. Bioeng. 2009;102: 264,279. © 2008 Wiley Periodicals, Inc. [source]

Metabolomic analysis of host plant resistance to thrips in wild and cultivated tomatoes,

Phosphonium labeling for increasing metabolomic coverage of neutral lipids using electrospray ionization mass spectrometry,

RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 12 2009
Hin-Koon Woo
Mass spectrometry has become an indispensable tool for the global study of metabolites (metabolomics), primarily using electrospray ionization mass spectrometry (ESI-MS). However, many important classes of molecules such as neutral lipids do not ionize well by ESI and go undetected. Chemical derivatization of metabolites can enhance ionization for increased sensitivity and metabolomic coverage. Here we describe the use of tris(2,4,6,-trimethoxyphenyl)phosphonium acetic acid (TMPP-AA) to improve liquid chromatography (LC)/ESI-MS detection of hydroxylated metabolites (i.e. lipids) from serum extracts. Cholesterol which is not normally detected from serum using ESI is observed with attomole sensitivity. This approach was applied to identify four endogenous lipids (hexadecanoyl-sn-glycerol, dihydrotachysterol, octadecanol, and alpha-tocopherol) from human serum. Overall, this approach extends the types of metabolites which can be detected using standard ESI-MS instrumentation and demonstrates the potential for targeted metabolomics analysis. Published in 2009 by John Wiley & Sons, Ltd. [source]