Ric De Vos

Wageningen University & Research | WUR · Bioscience - Wageningen Plant Research

Post-introduction evolution of plant defense traits is fundamental to several important theories for plant invasiveness. Research on chemical defense traits of invasive plants has focused mostly on targeted chemical analysis, however, such analyses restrict novel insights to known compounds. Here, we provide an untargeted metabolomic analysis of na...

Not only leaves but also other plant organs and structures typically considered as carbon sinks, including stems, roots, flowers, fruits and seeds, may exhibit photosynthetic activity. There is still a lack of a coherent and systematized body of knowledge and consensus on the role(s) of photosynthesis in these “sink” organs. With regard to fruits,...

Lipids and oils determine the quality and industrial value of grape seeds. Studies with legume seeds demonstrated the influence of light on lipid metabolism and its association with seed photosynthesis. Grape berry seeds are photosynthetically active till mature stage, but mostly during the green stage and veraison. The objective of this work was t...

Seed aging during storage results in loss of vigor and germination ability due to the accumulation of damage by oxidation reactions. Experimental aging tests, for instance to study genetic variation, aim to mimic natural aging in a shorter timeframe. As the oxidation rate is increased by elevating the temperature, moisture, and oxygen levels, this...

Belgian endive is grown in a two-step cultivation process that involves growing of the plants in the field, cold storage of the taproots, and a second growth period in dark conditions called forcing to yield the witloof heads. In this study, the changes in the carbohydrate content and the secondary metabolite composition were studied in different t...

Drying fruits and vegetables is a long-established preservation method. For tomatoes, sun-drying is preferred. Semi-drying is a new application aimed to preserve better the original tomato properties. We have assessed the effects of different drying methods on the phytochemical variation in tomato products using untargeted metabolomics and targeted...

Products for food and feed derived from genetically modified (GM) crops are only allowed on the market when they are deemed to be safe for human health and the environment. The European Food Safety Authority (EFSA) performs safety assessment including a comparative approach: the compositional characteristics of a GM genotype are compared to those o...

To reveal the mechanisms underlying how light affects flavonoid metabolism and the potential role of flavonoids in protecting against photooxidative stress in tea leaves, tea plants adapted to low light conditions were exposed to full sunlight over 48 h. There was an increase in the activities of catalase and superoxide dismutase as well as greater...

Gamma-aminobutyric acid (GABA) and its precursor glutamate play signaling roles in a range of tissues. Both function as neurotransmitters in the central nervous system, but they also modulate pancreatic and...

Various root‐colonizing bacterial species can promote plant growth and trigger systemic resistance against aboveground leaf pathogens and herbivore insects. To date, the underlying metabolic signatures of these rhizobacteria‐induced plant phenotypes are poorly understood. To identify core metabolic pathways that are targeted by growth‐promoting rhi...

Peanuts are transported by ship from production regions to all across the globe. Quality problems are frequently encountered due to increased levels of free fatty acids (FFAs) and a decline in organoleptic quality through lipid oxidation occurring during transport and storage. We studied the role of moisture (water activityaw) in interaction with 8...

Various root-colonizing bacterial species can promote plant growth and trigger systemic resistance against aboveground leaf pathogens and herbivore insects. To date, the underlying metabolic signatures of these rhizobacteria-induced plant phenotypes are poorly understood. To identify core metabolic pathways that are targeted by growth-promoting rhi...

Genome-wide analysis of plant-growth-promoting Pseudomonas fluorescens strain SS101 (Pf SS101) followed by site-directed mutagenesis previously suggested that sulfur assimilation may play an important role in growth promotion and induced systemic resistance in Arabidopsis. Here, we investigated the effects of sulfur metabolism in Pf SS101 on growth...

Coffee cup quality is primarily determined by the type and variety of green beans chosen and the roasting regime used. Furthermore, green coffee beans are not only the starting point for the production of all coffee beverages but also are a major source of revenue for many sub-tropical countries. Green bean quality is directly related to its bioche...

Green and white asparagus are quite different crops but can be harvested from the same plant. They have distinct morphological differences due to their mode of cultivation and they are characterised by having contrasting appearance and flavour. Significant chemical differences are therefore expected. Spears from three varieties of both green and wh...

The biosynthesis, structure and accumulation of secondary metabolites in plants are largely controlled by genetic factors, which can vary substantially among genotypes within a species. Here we studied a global population of Arabidopsis thaliana accessions for qualitative and quantitative variation in volatile and non-volatile secondary metabolites...

Viticulture practices that change the light distribution in the grapevine canopy can interfere with several physiological mechanisms, such as grape berry photosynthesis and other metabolic pathways, and consequently impact the berry biochemical composition, which is key to the final wine quality. We previously showed that the photosynthetic activit...

One-class modelling is a useful approach in metabolomics for the untargeted detection of abnormal metabolite profiles, when information from a set of reference observations is available to model “normal” or baseline metabolite profiles. Such outlying profiles are typically identified by comparing the distance between an observation and the referenc...

A variety of secondary metabolites are formed and compounds released during the bioconversion of lignocellulosic biomass by white-rot fungi that can affect the nutritional value and acceptance of the biomass by ruminants. Changes in pH, ergosterol content, fibre and metabolites composition of wheat straw (WS) incubated with either Ceriporiopsis sub...

The effects of climate change are becoming a real concern for the viticulture sector, with impacts on both grapevine physiology and the quality of the fresh berries and wine. Short-term mitigation strategies, like foliar kaolin application and smart irrigation regimes, have been implemented to overcome these problems. We previously showed that thes...

Key message A major thrips resistance QTL in Capsicum was fine-mapped to a region of 0.4 Mbp, and a multidisciplinary approach has been used to study putative underlying mechanisms. Abstract Resistance to thrips is an important trait for pepper growers. These insects can cause extensive damage to fruits, flowers and leaves on field and greenhouse...

Background: Tomatoes are important fruits in the Mediterranean diet and are considered to reduce the risk of different human diseases due to their antioxidative powers. Objective: The purpose of the present study was to investigate the biodiversity within a set of 50 tomato fruit accessions collected across Turkey concerning their antioxidant capac...

Several root-colonizing bacterial species can simultaneously promote plant growth and induce systemic resistance. How these rhizobacteria modulate plant metabolism to accommodate the carbon and energy demand from these two competing processes is largely unknown. Here, we show that strains of three Paraburkholderia species, P. graminis PHS1 ( Pbg ),...

The increased usage of alternative Ayurvedic treatments as potential health-beneficial therapies emphasizes the importance of studying its efficacy in sound placebo-controlled intervention trials. An example of such a traditional Ayurvedic herbal preparation is Mohana Choorna, a mixture composed of 20 different herbs and used to prevent and treat t...

Degradation of lignocellulose by selective white-rot fungi can significantly improve the nutritional value of high lignocellulose containing biomass by affecting the access of rumen microbes to structural carbohydrates. To determine if such treated biomass is stable in time to allow it to be conserved for subsequent feeding to ruminant animals, whe...

It is well known that green tea made from fully developed leaves located at the base of young shoots is of lower quality than that made from the still developing leaves located on the top of the shoot. It has additionally been shown that plant shading can significantly improve green tea quality. Here, we aimed to get more insight into the effects o...

Questions about in vivo substrates for proanthocyanidin (PA) biosynthesis and condensation have not been resolved and wide gaps in the understanding of transport and biogenesis in ‘tannosomes’ persist. Here we examined the evolution of PA biosynthesis in ferns not previously reported, asking what PAs are synthesised and how. Chemical and gene‐expre...

The improvement and promotion of leafy vegetables, used for both food and medicine, benefits greatly from detailed knowledge of their health-promoting specialised metabolites. In the present study, we investigated the global metabolite variation in the leaves of 48 accessions of the leafy vegetable Gynandropsis gynandra using two complementary anal...

Metabolic profiles of tomatoes change during ripening and light can modulate the activity of relevant biochemical pathways. We investigated the effects of light directly supplied to the fruits on the metabolome of the fruit pericarp during ripening. Mature green tomatoes were exposed to well-controlled conditions with light as the only varying fact...

The fruit of the pomegranate (Punica granatum L.) is an important nutraceutical food rich in polyphenolic compounds, including hydrolysable tannins, anthocyanins and flavonols. Their composition varies according to cultivar, tissue and fruit development stage and is probably regulated by a combination of MYB and bHLH type transcription factors (TFs...

The broad variability of Cucumis melo (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within C. melo, we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotypin...

In this study, 50 tomato landraces grown in Turkey were investigated in terms of their secondary metabolite profiles. Each accession was planted in 2016 and 2017 in 3 replicates in an open field. In this study, color, pH and brix of the fruit samples were measured and an unbiased LCMS-based metabolomics approach was applied. Based on Principal Comp...

Asparagus (Asparagus officinalis) is one of the world’s top 20 vegetable crops. Both green and white shoots (spears) are produced; the latter being harvested before becoming exposed to light. The crop is grown in nearly all areas of the world, with the largest production regions being China, Western Europe, North America and Peru. Successful produc...

Mulberries are consumed either freshly or as processed fruits and are traditionally used to tackle several diseases, especially type II diabetes. Here, we investigated the metabolite compositions of ripe fruits of both white (Morus alba) and black (Morus nigra) mulberries, using reversed-phase HPLC coupled to high resolution mass spectrometry (LC-M...

Objective Plants produce a plethora of specialized metabolites to defend themselves against pathogens and insects, to attract pollinators and to communicate with other organisms. Many of these are also applied in the clinic and in agriculture. Genes encoding the enzymes that drive the biosynthesis of these metabolites are sometimes physically group...

BACKGROUND Greater proportions of purple tea buds and leaves usually appear in the summer, which seriously affects the color and taste quality of green tea products, yet the metabolism of purple tea shoots in summer remains unclear. Here, the metabolomic profiles and gene expression of related flavonoid metabolic pathways in the purple and normal g...

Climate changes may cause severe impacts both on grapevine and berry development. Foliar application of kaolin has been suggested as a mitigation strategy to cope with stress caused by excessive heat/radiation absorbed by leaves and grape berry clusters. However, its effect on the light micro-environment inside the canopy and clusters, as well as o...

Main conclusion The variability in nutrient content and morphology in Gynandropsis gynandra is associated with the geographic origin of the accessions and provides a basis for breeding for higher levels of vitamin C, carotenoids or tocopherols in higher-yielding cultivars. We examined the variation in carotenoids, tocopherols and ascorbic acid as w...

Turnip (Brassica rapa spp. rapa) is an important vegetable species, with a unique physiology. Several plant parts, including both the turnip tubers and leaves, are important for human consumption. During the development of turnip plants, the leaves function as metabolic source tissues, while the tuber first functions as a sink, while later the tube...

The development of pesticide resistance in insects and recent bans on pesticides call for the identification of natural sources of resistance in crops. Here, we used natural variation in pepper (Capsicum spp.) resistance combined with an untargeted metabolomics approach to detect secondary metabolites related to thrips (Frankliniella occidentalis)...

L-ascorbate (ASC) is essential for human health. Therefore, there is interest in increasing the ASC content of crops like tomato. High irradiance induces accumulation of ASC in green tomato fruits. The D-mannose/L-galactose biosynthetic pathway accounts for the most ASC in plants. The myo-inositol and galacturonate pathways have been proposed to ex...

In the natural pesticides known as pyrethrins, which are esters produced in flowers of Tanacetum cinerariifolium (Asteraceae), the monoterpenoid acyl moiety is pyrethric acid or chrysanthemic acid. We show here that pyrethric acid is produced from chrysanthemol in six steps catalyzed by four enzymes, the first five steps occurring in the trichomes...

Phytochemicals not only determine the taste and smell of plants and their products, they also play a crucial role in resistance against pests and pathogens. In previous work, we identified a form of resistance to thrips (Frankliniella occidentalis) expressed in leaves of pepper (Capsicum annuum). In the current study, we characterized leaves of an...

Key message QTLs for insect resistance parameters, trichome type IV development, and more than 200 non-volatile metabolites, including 76 acyl sugars, all co-locate at the end of Chromosome 2 of Solanum galapagense. Abstract Host plant resistance is gaining importance as more and more insecticides are being banned due to environmental concerns. In...

Introduction Untargeted metabolomics is a powerful tool to detect hundreds of metabolites within a given tissue and to compare the metabolite composition of samples in a comprehensive manner. However, with regard to pollen research such comprehensive metabolomics approaches are yet not well developed. To enable isolation of pollen that is tightly e...

The microalga Nannochloropsis gaditana is known for accumulating fatty acids, including the commercially interesting eicosapentaenoic acid (EPA) within the polar lipids (PL) and neutral lipids (NL). During microalgal growth EPA is mainly present in the PL. Upon nitrogen starvation N. gaditana accumulates large amounts of TAG in lipid bodies. The ne...

Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In t...

Guaianolides are an important class of sesquiterpene lactones with unique biological and pharmaceutical properties. They have been postulated to be derived from germacranolides, but for years no progress has been made in the elucidation of their biosynthesis that requires an unknown cyclization mechanism. Here we demonstrate the isolation and chara...

Introduction Lettuce (Lactuca sativa L.) is generally not specifically acknowledged for its taste and nutritional value, while its cultivation suffers from limited resistance against several pests and diseases. Such key traits are known to be largely dependent on the ability of varieties to produce specific phytochemicals. Objectives We aimed to i...

There is increasing demand to bring the level of metabolomics analyses down to the tissue or cell level. Significant progress has been made involving the use of in situ metabolomics imaging techniques where no tissue collection or extraction is needed prior to analysis. In this chapter we describe a relatively new method which is simple and easy to...

Figure S1. Chromatograms profiling of different species of eucalyptus Comparison of the liquid chromatography mass spectrometry (LC‐MS) profiles of E. dunnii (A), E. grandis (B) and E. pellita (C) exposed to the same temperature (20°C) for 7 d. Figure S2. Chromatograms profiling of different temperature treatments Comparison of the liquid chromato...

Table S2. Gas chromatography mass spectrometry (GC‐MS) raw dataset ClusterID refers to a unique number used in the data processing, retention time (RT) in minutes and retention index (RI) are also shown. In the last two columns is showed a mass list and its relative intensity for Eucalyptus dunnii (DU), E. grandis (GR) and E. pellita (PE). Sample n...

Table S3. Fifty‐five metabolites that appeared to be discriminatory for the genotype

Table S4. Thirty‐two metabolites that appeared to be discriminatory for the temperature treatments

Table S1. Liquid chromatography mass spectrometry (LC‐MS) raw dataset ClusterID refers to a unique number used in the data processing, retention time (RT) in minutes and m/z information (M‐H)‐ related to the most intense ion of the cluster. In the last two columns is showed a mass list (µDA) and its relative intensity, for E. dunnii (DU), E. grandi...

Tomato has quickly become a favoured species for metabolomics research. Tomato fills a niche that cannot be occupied by Arabidopsis, particularly regarding studies on fleshy fruit. Variations in genotype and phenotype have been broadly exploited using metabolomics approaches in order to gain a better understanding of fundamental aspects of plant ph...

Wild relatives of tomato possess effective means to deal with several pests, among which are a variety of insects. Here we studied the presence of resistance components against Trialeurodes vaporariorum, Myzus persicae, Frankliniella occidentalis, and Spodoptera exigua in the Lycopersicon group of Solanum section Lycopersicon by means of bioassays...

p>Nitrogen deprivation increases the triacylglycerol (TAG) content in microalgae but also severely decreases the growth rate. Most approaches that attempted to increase TAG productivity by overexpression or knockdown of specific genes related to the regulation of the lipid synthesis have reported only little success. More insight into the molecular...

Species and hybrids of Eucalyptus are the world's most widely planted hardwood trees. They are cultivated across a wide range of latitudes and therefore environmental conditions. In this context, comprehensive metabolomics approaches have been used to assess how different temperature regimes may affect the metabolism of three species of Eucalyptus,...

Metabolomics is a proven tool to obtain information about differences in food stuffs and to select biochemical markers for sensory quality of food products. A valuable application of untargeted metabolomics is the selection of metabolites that are (highly) predictive for sensory or phenotypical traits for use as (bio) markers. This chapter demonstr...

Both physical barriers and reactive phytochemicals represent two important components of a plant’s defence system against environmental stress. However, these two defence systems have generally been studied independently. Here, we have taken an exclusive opportunity to investigate the connection between a chemical-based plant defence system, repres...

Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Numbers of animals used in animal trials, however, need to be minimalized. Therefore, we explored the applicability of in vitro (human Caco-2 cells) and ex vivo intestine models (rat precision cut intestine slices and the pig in-situ s...

Caco2_429 genes_linked_to 339 genes in the rat_Hierarchically clustered. Comparison of the effects of digested onion extracts on mRNA expression between Caco-2 cells in vitro and rat small intestine slices ex vivo. A heatmap of these data is given in Fig 2. (XLSX)

Caco2_WOd_YOd_affected_genes. Effects of digested onion extracts on mRNA expression in human Caco-2 cells. A heatmap of these data is given in Fig 1A. (XLSX)

Rat_Intest_WOd_YOd_affected_genes. Effects of digested onion extracts on mRNA expression in rat intestine slices ex vivo. A heatmap of these data is given in Fig 1B. (XLSX)

Pig_Intest_WOd_YOd_affected_genes. Effects of digested onion extracts on mRNA expression in the pig SISP model. A heatmap of these data is given in Fig 1C. (XLSX)

Significantly differential expressed genes were selected for each of the three models (Rat, Caco2 and Pig-SISP) on a p-value <0.05 and a Fold Change (FC; Yod or Wod over Sd) of < 1.5 (up) or < 0.66 (down). For SISP arrays, the FC of all individual test-pigs (denoted by a number) are presented. For all three species/arrays official human gene-symbol...

Semi-polar metabolites such as flavonoids, phenolic acids, and alkaloids are very important health-related compounds in tomato. As a first step to identify genes responsible for the synthesis of semi-polar metabolites, quantitative trait loci (QTLs) that influence the semi-polar metabolite content in red-ripe tomato fruit were identified, by charac...

Introduction: Metabolomics has become a valuable tool in many research areas. However, generating metabolomics-based biochemical profiles without any related bioactivity is only of indirect value in understanding a biological process. Therefore, metabolomics research could greatly benefit from tools that directly determine the bioactivity of the d...

An ethnopharmacological survey indicates that the genus Byrsonima has some medicinal species that are commonly found in the Brazilian Cerrado and has been used as an anti-inflammatory and for gastroduodenal disorders. The aim of this study was to evaluate the anti-inflammatory and antioxidant activity along with qualitative chemical characterizatio...