Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies
Ulaszewska, Marynka M. ; Weinert, Christoph H. ; Trimigno, Alessia ; Portmann, Reto ; Andres Lacueva, Cristina ; Badertscher, René ; Brennan, Lorraine ; Brunius, Carl ; Bub, Achim ; Capozzi, Francesco ; Cialiè Rosso, Marta ; Cordero, Chiara E. ; Daniel, Hannelore ; Durand, Stéphanie ; Egert, Bjoern ; Ferrario, Paola G. ; Feskens, Edith J.M. ; Franceschi, Pietro ; Garcia-Aloy, Mar ; Giacomoni, Franck ; Giesbertz, Pieter ; González-Domínguez, Raúl ; Hanhineva, Kati ; Hemeryck, Lieselot Y. ; Kopka, Joachim ; Kulling, Sabine E. ; Llorach, Rafael ; Manach, Claudine ; Mattivi, Fulvio ; Migné, Carole ; Münger, Linda H. ; Ott, Beate ; Picone, Gianfranco ; Pimentel, Grégory ; Pujos-Guillot, Estelle ; Riccadonna, Samantha ; Rist, Manuela J. ; Rombouts, Caroline ; Rubert, Josep ; Skurk, Thomas ; Sri Harsha, Pedapati S.C. ; Meulebroek, Lieven Van; Vanhaecke, Lynn ; Vázquez-Fresno, Rosa ; Wishart, David ; Vergères, Guy - \ 2018
Molecular Nutrition & Food Research 63 (2018)1. - ISSN 1613-4125
GC–MS - LC–MS - metabolomics - NMR - nutrition
The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful “tips and tricks” along the analytical workflow.
Multi-platform metabolomics analyses of a broad collection of fragrant and non-fragrant rice varieties reveals the high complexity of grain quality characteristics
Mumm, R. ; Hageman, J.A. ; Calingacion, M.N. ; Vos, C.H. de; Jonker, H.H. ; Erban, A. ; Kopka, J. ; Hansen, T.H. ; Laursen, K.H. ; Schjoerring, J.K. ; Ward, J.L. ; Beale, M.H. ; Jongee, S. ; Rauf, A. ; Habibi, F. ; Indrasari, S.D. ; Sakhan, S. ; Ramli, A. ; Romero, M. ; Reinke, R. ; Ohtsubo, K. ; Boualaphanh, C. ; Fitzgerald, M.A. ; Hall, R.D. - \ 2016
Metabolomics 12 (2016)2. - ISSN 1573-3882 - 19 p.
The quality of rice in terms not only of its nutritional value but also in terms of its aroma and flavour is becoming increasingly important in modern rice breeding
where global targets are focused on both yield stability and grain quality. In the present paper we have exploited advanced, multi-platform metabolomics approaches to determine the biochemical differences in 31 rice varieties from a diverse range of genetic backgrounds and origin. All were grown under the specific local conditions for which they have been bred and all aspects of varietal identification and sample purity have been guaranteed by local experts from each country. Metabolomics analyses using 6 platforms have revealed the extent of biochemical differences (and similarities) between the chosen rice genotypes.
Comparison of fragrant rice varieties showed a difference in the metabolic profiles of jasmine and basmati varieties. However with no consistent separation of the germplasm class. Storage of grains had a significant effect on the
metabolome of both basmati and jasmine rice varieties but changes were different for the two rice types. This shows how metabolic changes may help prove a causal relationship with developing good quality in basmati rice or
incurring quality loss in jasmine rice in aged grains. Such metabolomics approaches are leading to hypotheses on the potential links between grain quality attributes, biochemical composition and genotype in the context of breeding for improvement. With this knowledge we shall establish a
stronger, evidence-based foundation upon which to build targeted strategies to support breeders in their quest for improved rice varieties.
A genomics and multi-platform metabolomics approach to identify new traits of rice quality in traditional and improved varieties
Callingacion, M.N. ; Boualaphanh, C. ; Daygon, V.D. ; Anacleto, R. ; Sackville Hamilton, R. ; Biais, B. ; Deborde, C. ; Maucourt, M. ; Moing, A. ; Mumm, R. ; Vos, C.H. de; Erban, A. ; Kopka, J. ; Hansen, T.H. ; Laursen, K.H. ; Schjoerring, J.K. ; Hall, R.D. ; Fitzgerald, M.A. - \ 2012
Metabolomics 8 (2012)5. - ISSN 1573-3882 - p. 771 - 783.
plant metabolomics - metabolite - components - nutrition - issues - bread - grain - acid - bran
Using a novel approach combining four complementary metabolomic and mineral platforms with genome-wide genotyping at 1536 single nucleotide polymorphism (SNP) loci, we have investigated the extent of biochemical and genetic diversity in three commercially-relevant waxy rice cultivars important to food production in the Lao People’s Democratic Republic (PDR). Following cultivation with different nitrogen fertiliser regimes, multiple metabolomic data sets, including minerals, were produced and analysed using multivariate statistical methods to reveal the degree of similarity between the genotypes and to identify discriminatory compounds supported by multiple technology platforms. Results revealed little effect of nitrogen supply on metabolites related to quality, despite known yield differences. All platforms revealed unique metabolic signatures for each variety and many discriminatory compounds could be identified as being relevant to consumers in terms of nutritional value and taste or flavour. For each platform, metabolomic diversity was highly associated with genetic distance between the varieties. This study demonstrates that multiple metabolomic platforms have potential as phenotyping tools to assist breeders in their quest to combine key yield and quality characteristics. This better enables rice improvement programs to meet different consumer and farmer needs, and to address food security in rice-consuming countries.
Plant Metabolomics and Its Potential for Systems Biology Research: Background Concepts, Technology, and Methodology
Allwood, J.W. ; Vos, C.H. de; Moing, A. ; Deborde, C. ; Erban, A. ; Kopka, J. ; Goodacre, R. ; Hall, R.D. - \ 2011
In: Methods in Systems Biology / Jameson, D., Verma, M., Westerhoff, H. V., - p. 299 - 336.
chromatography-mass-spectrometry - minimum reporting standards - arabidopsis-thaliana - gas-chromatography - liquid-chromatography - functional genomics - tomato fruit - metabolite profiles - magnetic-resonance - sample preparation
The "metabolome" comprises the entire complement of small molecules in a plant or any other organism. It represents the ultimate phenotype of cells, deduced from the perturbation of gene expression and the modulation of protein function, as well as environmental cues. Extensive advances over the past decade, regarding the high-throughput (HTP) nature of "omics" research, have given birth to the expectation that a type of "systems level" overview may soon be possible. Having such a global overview of the molecular organization of a plant in the context of a particular set of genetic or environmental conditions, be it at cell, organ, or whole plant level, would clearly be very powerful. Currently, we are far from achieving this goal; however, within our hands, plant metabolomics is an HTP and informative "omics" approach to both sample generation and data generation, as well as raw data preprocessing, statistical analysis, and biological interpretation. Within this chapter, we aim to describe the great attention given to experimental design to ensure that the correct sample set and control are included and to, thereby, enable reliable statistical analysis of the data. For as comprehensive metabolite coverage as possible, we advocate the use of multiparallel approaches; thus, we describe a step-by-step standardized method for Nuclear magnetic resonance spectroscopy, as well as discussing with reference to standardized methodologies the techniques of gas chromatography-time of flight/mass spectrometry, and liquid chromatography mass spectrometry.
Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics
Moing, A. ; Aharoni, A. ; Biais, B. ; Rogachev, I. ; Meir, S. ; Brodsky, L. ; Allwood, J.W. ; Erban, A. ; Dunn, W.B. ; Kay, S. ; Koning, S. ; Vos, C.H. de; Jonker, H.H. ; Mumm, R. ; Deborde, C. ; Maucourt, M. ; Bernillon, S. ; Gibon, Y. ; Hansen, T.H. ; Husted, S. ; Goodacre, R. ; Kopka, J. ; Schjoerring, J.K. ; Rolin, D. ; Hall, R.D. - \ 2011
New Phytologist 190 (2011)3. - ISSN 0028-646X - p. 683 - 696.
mass-spectrometry data - cucumis-melo - gas-chromatography - network analysis - aroma volatiles - gene-expression - tomato - plants - l. - identification
Celiac disease (CD) is a chronic inflammatory disease affecting the small intestinal mucosa. The causative agents have been identified as gluten proteins from wheat, barley and rye, and the only available treatment for CD patients is a lifelong gluten-free diet. Non-gluten containing cereals would be a valuable contribution to the gluten-free diet. In this respect, oats are a good choice. However, commercial lots of oat flakes and flour frequently are contaminated with wheat, barley and rye, and two studies have reported that some peptides derived from the gluten-like avenin storage proteins of oat can trigger an immune response in some CD patients. In the present study we have initiated the investigation whether all oat varieties contain similar amounts of potentially harmful sequences by biochemical and immunological methods. We confirm that commercial oat preparations are contaminated with other cereals that contain gluten or gluten-like proteins. Moreover, our results demonstrate that contamination-free oat varieties differ in their capacity to stimulate an avenin-sensitive gamma-gliadin specific T cell line derived from a patient with CD, indicative for differences in the two known avenin epitopes among oat varieties, implying that selection and breeding of completely safe oat varieties for all CD patients may be a realistic possibility.
Inter-laboratory reproducibility of fast gas chromatography-electron impact-time of flight mass spectrometry (GC-EI-TOF/MS) based plant metabolomics
Allwood, J.W. ; Erban, A. ; Koning, S. ; Dun, W.B. ; Luedemann, A. ; Lommen, A. ; Kay, L. ; Löscher, R. ; Kopka, J. ; Goodacre, R. - \ 2009
Metabolomics 5 (2009)4. - ISSN 1573-3882 - p. 479 - 496.
minimum reporting standards - independent component analysis - liquid-chromatography - chemical-analysis - cucumis-melo - transcriptomics - toxicogenomics - hepatotoxicity - identification - metabolites
The application of gas chromatography¿mass spectrometry (GC¿MS) to the `global¿ analysis of metabolites in complex samples (i.e. metabolomics) has now become routine. The generation of these data-rich profiles demands new strategies in data mining and standardisation of experimental and reporting aspects across laboratories. As part of the META-PHOR project¿s (METAbolomics for Plants Health and OutReach: http://www.meta-phor.eu/) priorities towards robust technology development, a GC¿MS ring experiment based upon three complex matrices (melon, broccoli and rice) was launched. All sample preparation, data processing, multivariate analyses and comparisons of major metabolite features followed standardised protocols, identical models of GC (Agilent 6890N) and TOF/MS (Leco Pegasus III) were also employed. In addition comprehensive GC×GC¿TOF/MS was compared with 1 dimensional GC¿TOF/MS. Comparisons of the paired data from the various laboratories were made with a single data processing and analysis method providing an unbiased assessment of analytical method variants and inter-laboratory reproducibility. A range of processing and statistical methods were also assessed with a single exemplary dataset revealing near equal performance between them. Further investigations of long-term reproducibility are required, though the future generation of global and valid metabolomics databases offers much promise
A proposed framework for the description of plant metabolomics experiments and their results
Jenkens, H. ; Hardy, N. ; Beckmann, M. ; Draper, J. ; Smith, A.R. ; Taylor, J. ; Fiehn, O. ; Goodacre, R. ; Bino, R.J. ; Hall, R.D. ; Kopka, J. ; Lane, G.A. ; Lange, B.M. ; Liu, J.R. ; Mendes, P. ; Nikolau, B.J. ; Oliver, S.G. ; Paton, I.R. ; Roessner-Tunali, U. ; Saito, K. ; Smedsgaard, J. ; Sumner, L.W. ; Wang, T. ; Walsh, S. ; Wurtele, E.S. ; Kell, D.B. - \ 2004
Nature Biotechnology 22 (2004)12. - ISSN 1087-0156 - p. 1601 - 1606.
mass-spectrometry - miame standards - systems biology - genomics - database - microarray - identification - algorithms - networks - extracts
The study of the metabolite complement of biological samples, known as metabolomics, is creating large amounts of data, and support for handling these data sets is required to facilitate meaningful analyses that will answer biological questions. We present a data model for plant metabolomics known as ArMet (architecture for metabolomics). It encompasses the entire experimental time line from experiment definition and description of biological source material, through sample growth and preparation to the results of chemical analysis. Such formal data descriptions, which specify the full experimental context, enable principled comparison of data sets, allow proper interpretation of experimental results, permit the repetition of experiments and provide a basis for the design of systems for data storage and transmission. The current design and example implementations are freely available (http://www.armet.org/). We seek to advance discussion and community adoption of a standard for metabolomics, which would promote principled collection, storage and transmission of experiment data.
Potential of metabolomics as a functional genomics tool
Bino, R.J. ; Hall, R.D. ; Fiehn, O. ; Kopka, J. ; Saito, K. ; Draper, J. ; Nikolau, B.J. ; Mendes, P. ; Roessner-Tunali, U. ; Beale, M. ; Trethewey, R.N. ; Lange, B.M. ; Wurtele, E.S. ; Sumner, L.W. - \ 2004
Trends in Plant Science 9 (2004)9. - ISSN 1360-1385 - p. 418 - 424.
mass-spectrometry - systems biology - secondary metabolites - arabidopsis-thaliana - plant metabolomics - potato-tuber - database - chromatography - information - proteomics
Metabolomics is developing as an important functional genomics tool; however, there is still room for technical improvements in both the large-scale determination of metabolites from complex plant tissues and the dissemination of metabolomics research data. For the continued maturation of metabolomics, the following three objectives need to be achieved: (i) improvement in the comprehensive coverage of the plant metabolome, (ii) facilitation of comparison of results between laboratories and experiments, and (iii) enhancement of the integration of metabolomic data with other functional genomic information. Because these challenges are widely recognized and endorsed, we propose community-based efforts to define common criteria and to initiate concerted actions directed towards the release of standard reference materials, construction of consolidated metabolite libraries, and development of metabolite-specific data-management systems.
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