The identification of metabolites in biochemical studies is a major bottleneck in the proliferating field of metabolomics. In particular in plant metabolomics, given the diversity and abundance of endogenous secondary metabolites in plants, the identification of these is not only challenging but also essential to understanding their biological role in the plant, and their value to quality and nutritional attributes as food crops.
P. Krumpochova, S. Sapthu, J.F. Brouwers, M. de Haas, R.C.H. de Vos, P. Borst, K. van de Wetering
The ATP-binding cassette (ABC) genes encode the largest family of transmembrane proteins. ABC transporters translocate a wide variety of substrates across membranes, but their physiological function is often incompletely understood. We describe a new method to study the substrate spectrum of ABC transporters: We incubate extracts of mouse urine with membrane vesicles prepared from Spodoptera frugiperda Sf9 insect cells overproducing an ABC transporter and determine the compounds transported into the vesicles by LC/MS-based metabolomics.
H.A. Verhoeven, H. Jonker, R.C.H. de Vos, R.D. Hall
The natural fragrance compounds produced by plants play key roles in the long-term fitness and survival of these plants as well as being of direct/indirect benefit to man. Almost all plant fragrances, either pleasant or unpleasant, comprise many different compounds, from different chemical classes and can indeed be highly complex in composition involving several hundred types of volatile molecule. Analyzing these mixtures and identifying their main (bio)active components is of importance in both fundamental and applied science.
Y.M. Tikunov, S. Laptenok, R.D. Hall, A. Bovy, R.C.H. de Vos
Mass peak alignment (ion-wise alignment) has recently become a popular method for unsupervised data analysis in untargeted metabolic profiling. Here we present MSClust-a software tool for analysis GC-MS and LC-MS datasets derived from untargeted profiling. MSClust performs data reduction using unsupervised clustering and extraction of putative metabolite mass spectra from ion-wise chromatographic alignment data.
The Brassicaceae family comprises a variety of plant species that are of high economic importance as -vegetables or industrial crops. This includes crops such as Brassica rapa (turnip, Bok Choi), B. oleracea (cabbages, broccoli, cauliflower, etc.), and B. napus (oil seed rape), and also includes the famous genetic model of plant research, Arabidopsis thaliana (thale cress). Brassicaceae plants contain a large variety of interesting secondary metabolites, including glucosinolates, hydroxycinnamic acids, and flavonoids.
S.A. Khan, P.Y. Chibon, R.C.H. de Vos, B.A. Schipper, E. Walraven, J. Beekwilder, T. van Dijk, R. Finkers, R.G. Visser, E.W. van de Weg, A. Bovy, A. Cestaro, R. Velasco, E. Jacobsen, H.J. Schouten
Apple (Malus×domestica Borkh) is among the main sources of phenolic compounds in the human diet. The genetic basis of the quantitative variations of these potentially beneficial phenolic compounds was investigated. A segregating F₁ population was used to map metabolite quantitative trait loci (mQTLs). Untargeted metabolic profiling of peel and flesh tissues of ripe fruits was performed using liquid chromatography-mass spectrometry (LC-MS), resulting in the detection of 418 metabolites in peel and 254 in flesh.
M.N. Calingacion, C. Boualaphanh, V. D. Daygon, R. Anacleto, R. Sackville Hamilton, B. Biais, C. Deborde, M. Maucourt, A. Moing, R. Mumm, R.C.H. de Vos, A. Erban, J. Kopka, T. H. Hansen, K.H. Laursen, J.K. Schjoerring, R.D. Hall, M.A. Fitzgerald
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).
J.E. van de Mortel, R.C.H. de Vos, E. Dekkers, A. Pineda, L. Guillod, K. Bouwmeester, J.J.A. van Loon, M. Dicke, J.M. Raaijmakers
Systemic resistance induced in plants by nonpathogenic rhizobacteria is typically effective against multiple pathogens. Here, we show that root-colonizing Pseudomonas fluorescens strain SS101 (Pf.SS101) enhanced resistance in Arabidopsis (Arabidopsis thaliana) against several bacterial pathogens, including Pseudomonas syringae pv tomato (Pst) and the insect pest Spodoptera exigua.
The Netherlands Metabolomics Centre focusses on the development of metabolomics based technologies and instrumentation to address the current and future challenges in biology, biotechnology and biomedical research in order to improve personalised health and quality of life.