Use of NMR for metabolic profiling in plant systems

Colquhoun, Ian J.

doi:10.1584/jpestics.r07-03

Cited by 59 publications

(37 citation statements)

References 58 publications

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“…In any case where aqueous or part-aqueous solvents were employed, a 100 mM deuterated ammonium acetate buffer was introduced to reduce variance in the chemical shifts of pH-sensitive metabolites, as recommended by Colquhoun. [30] Additionally, 0.5 mM sodium azide was added as a bacteriostat [31,32] and 100 µM trimethylsilylpropionate-d 4 (TMSP-d 4 ) was utilized as a chemical shift reference. Following perchloric acid treatment (method 5), extracts were titrated to a pH meter reading of 4.76.…”

Section: Resultsmentioning

confidence: 99%

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

Kaiser

Barding

Larive

2009

Magnetic Reson in Chemistry

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Metabolite analysis is recognized as an important facet of systems biology, however complete metabolome characterization has not been realized due to challenges in sample preparation, inherent instrumental limitations and the labor intensive task of data interpretation. This work aims to compare several commonly used metabolite extraction strategies for their effect on the (1)H nuclear magnetic resonance (NMR) metabolic profile of extracts of the model plant Arabidopsis thaliana. Extractions were carried out on aliquots from a pool of homogenized plant tissue using CD(3)CN/D(2)O, buffered D(2)O, perchloric acid in D(2)O, CD(3)OD/D(2)O and CD(3)OD/D(2)O/CDCl(3) as the extraction solvents. The effects of lyophilization as a sample pretreatment, solvent evaporation and extract fractionation for removal of interfering species were studied. Representative spectra are presented for qualitative interpretation. Analytical reproducibility was evaluated by principal components analysis. Perchloric acid facilitated acid-catalyzed cleavage of sucrose, further complicating biological interpretation of the resulting metabolite profile. The solvent system CD(3)OD/D(2)O/CDCl(3) gave the least reproducible results in our hands. D(2)O extracts suffered from poor stability probably due to contamination by soluble enzymes, which were not denatured in this solvent. CD(3)CN/D(2)O extracts showed greater stability than D(2)O alone, but problems were encountered due to degradation of (1)H NMR spectral resolution during lengthy acquisitions due to partial phase separation. In addition, this solvent system produced spectra with significant contamination by lipids that obscured spectral regions containing the resonances of the aliphatic amino acids. These problems were solved by speedvacuuming the CD(3)CN/D(2)O extract and reconstituting in D(2)O solution.

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Section: Resultsmentioning

confidence: 99%

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

Kaiser

Barding

Larive

2009

Magnetic Reson in Chemistry

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“…In this review we found that environmental metabolomics has been mostly applied in the study of soil health, pesticide in soil and pesticide residues using earthworm models (62,66) and metabolomics as a tool to study plant defenses and profiling (67,69). Thirty-one percent of the articles reviewed used the worm as an organism of study and 10% in plants, Figure 5b.…”

Section: Environmental Metabolomics and Bioavailabilitymentioning

confidence: 99%

Metabolómica y Pesticidas: Revisión sistemática de literatura usando teoría de grafos para el análisis de referencias

Zuluaga

Robledo

Osorio-Zuluaga

et al. 2016

nova

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The systematic literature review presented here is designed to illustrate the role of metabonomics and metabolomics in pesticide exposure studies. The search was conducted in Thomson Reuters Web of Science (ISI Web of Knowledge) database. The references and citations for each article were downloaded for analysis. Graph theory was used to determine relevant articles and distinct relationships between classic and current research in this field through its structural characteristics. The initial network included 4423 nodes and 4978 links, from which indegree, outdegree and betweenness indicators were extracted. After preprocessing the data, the network was reduced to 415 nodes and 974 links. From this network, 80 articles with the highest score between the three indicators were extracted for review. This methodology allowed for the identification of different perspectives of metabolomic and metabonomic pesticide studies that included the mode and mechanism of action, toxicological and biological monitoring, environmental metabolomics, metabolism, dose response and biomarkers and its role in pesticide exposure.Keywords: Metabonomics; metabolomics; pesticides. ResumenLa revisión sistemática de literatura presentada a continuación tiene como objetivo dar a conocer el rol que han tenido la metabolómica en el estudio de la exposición a plaguicidas. La búsqueda se llevó a cabo en la base de datos Thomson Reuters Web of Science (ISI Web of Knowledge). Posteriormente, se descargaron todos los registros producto de resultado de la búsqueda y cada citación dentro de cada artículo. Estas referencias fueron analizadas mediante la teoría de grafos con el fin de identificar los artículos más relevantes, los artículos clásicos y recientes y los que presentan mayor intermediación en el tema de investigación. La red de citaciones fue construida con inicialmente con 4423 nodos (artículos) y 4978 enlaces (citaciones) a los cuales se les determinó los indicadores de grado de entrada, grado de salida y centralidad en el grafo. Posteriormente, esta red de citaciones fue procesada eliminando los artículos desconectados, reduciendo la red a 415 nodos y 974 enlaces. De esta red ya procesada se extrajeron 80 artículos que presentaron mayores indicadores de grado y centralidad. Finalmente, esta metodología permitió la identificación de diferentes perspectivas de los estudios metabolómicos y metabonómicos en la exposición a plaguicidas que incluyen estudios de modo de acción, mecanismos de acción, monitoreo biológico y toxicológico, metabolómica ambiental, metabolismo, dosis respuesta e identificación de biomarcadores.Palabras clave: Metabolómica, metabonómica, pesticidas.

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“…As shown in the literature research above, this is a very well documented and widely used approach. To test the feasibility of this approach, it is subjected to a detailed review:  Analytical-scale separation and determination of molecular structure is a very well-researched area in the scientific field of substance discovery in plant extracts [40][41][42][43][44][45][46]. Nevertheless, these techniques are optimized with the focus being to identify one or at least a few substances.…”

Section: Solid-liquid-extractionmentioning

confidence: 99%

Characterization of Feed Properties for Conceptual Process Design Involving Complex Mixtures, Such as Natural Extracts

Josch¹,

Both²,

Strube³

2012

FNS

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The number of products used as agro-chemicals, food additives, flavors, aromas, pharmaceuticals and nutraceuticals which are made by fermentation or extraction from plants has increased significantly. Despite this growth, initial predictions for a potential product purification process for these complex mixtures remains entirely experimentally based. The present work represents an initial study to demonstrate the benefits of a systematic approach. For process development of chemically well-studied systems model based process design methods are already available. Therefore the proposed approach focuses on a method for the efficient characterization of the physical properties of the key components. Once this is adequately defined, unit operations and their potential to separate the feed components can be modeled. The current state of research is discussed. Based on this evaluation the most efficient method for conceptual process development has been identified and further developed. The resulting methodology consists of model-based cost accounting accompanied by experimental model-parameter determination. The latter is carried out at in miniaturized laboratory-scale measurement cells for each unit operation using the complete original feed. The model-based modelparameter determination from these experiments is accompanied by a comprehensive error analysis. The experimental plan currently includes the determination of thermodynamic equilibrium conditions in the mixture directly from the raw material mixture. Transport kinetics and fluid dynamic parameters are first estimated from known correlations or preexisting knowledge. Later on these parameters are determined exactly in mini-plant experiments. Furthermore, biological and botanical-based guidelines are developed to identify thermodynamically favored basic operations. Finally, the developed approaches are successfully validated using two plant extracts. Firstly, it could be proven that the botanical pre-selection can reduce the experimental plan significantly. Secondly, it was shown that the experimental equilibrium data of the kinetics and fluid dynamics can have a significant impact on the separation costs. Therefore, detailed rigorous modeling approaches have to be chosen instead of short-cut methods in order to make any valid process development conclusions or to further optimize the system.

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Use of NMR for metabolic profiling in plant systems

Cited by 59 publications

References 58 publications

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

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

Metabolómica y Pesticidas: Revisión sistemática de literatura usando teoría de grafos para el análisis de referencias

Characterization of Feed Properties for Conceptual Process Design Involving Complex Mixtures, Such as Natural Extracts

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Use of NMR for metabolic profiling in plant systems

Cited by 59 publications

References 58 publications

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

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

Metabolómica y Pesticidas: Revisión sistemática de literatura usando teoría de grafos para el análisis de referencias

Characterization of Feed Properties for Conceptual Process Design Involving Complex Mixtures, Such as Natural Extracts

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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

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