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.

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    Application of apigeninidin-rich red sorghum biocolorant in a fermented food improves product quality
    Akogou, Folachodé U.G. ; Canoy, Tessa S. ; Kayodé, Adéchola P.P. ; Besten, Heidy M.W. den; Linnemann, Anita R. ; Fogliano, Vincenzo - \ 2019
    Journal of the Science of Food and Agriculture 99 (2019)4. - ISSN 0022-5142 - p. 2014 - 2020.
    antioxidant activity - apigeninidin - fermentation - maize dough - nutritional quality - volatile compounds

    BACKGROUND: The ‘clean label’ trend is pushing the food industry to replace synthetic colorants with plant-based colorants. However, technological efficacy and undesirable side effects restrict the use of plant-based colorants in industrial applications. This research studied the production of fermented maize dough coloured by apigeninidin-rich red sorghum biocolorant, as practised for centuries in West Africa, as a model to assess the impact of the biocolorant on nutritional and sensorial quality of foods. RESULTS: A 3-day fermentation of a dyed maize dough (containing 327 µg g−1 dry matter of apigeninidin) by Pichia kudriavzevii and Lactobacillus fermentum led to a degradation of 69% of the apigeninidin content, causing a clearly visible colour difference (ΔE*00 17.4). The antioxidant activity of fermented dyed dough (DD) increased by 51% compared to fermented non-dyed dough (NDD). However, the phytate dephosphorylation and volatile organic compound concentrations were lower in DD than in NDD. This suggests a lower mineral solubility and change in the sensory quality of fermented DD. CONCLUSION: Apigeninidin extract from sorghum leaf sheaths proved to be a bioactive red biocolorant with potential in fermented foods. The formation of new antioxidant compounds needs further investigation, as does the impact on the development of volatile compounds.

    Volatile-mediated interactions in the rhizosphere
    Cordovez da Cunha, Viviane - \ 2016
    Wageningen University. Promotor(en): Francine Govers; Jos Raaijmakers, co-promotor(en): V.J. Carrion. - Wageningen : Wageningen University - ISBN 9789462579019 - 219
    rhizosphere bacteria - rhizosphere fungi - microbial interactions - volatile compounds - suppressive soils - actinobacteria - streptomyces - microbacterium - thanatephorus cucumeris - growth stimulators - biological control - defence mechanisms - genomics - transcriptomics - rizosfeerbacteriën - rizosfeerschimmels - microbiële interacties - vluchtige verbindingen - ziektewerende gronden - actinobacteria - streptomyces - microbacterium - thanatephorus cucumeris - groeistimulatoren - biologische bestrijding - verdedigingsmechanismen - genomica - transcriptomica

    Plants and microorganisms are constantly engaged in highly dynamic interactions both above- and belowground. Several of these interactions are mediated by volatile organic compounds (VOCs), small carbon-based compounds with high vapor pressure at ambient temperature. In the rhizosphere, VOCs have an advantage in intra- and interorganismal signaling since they can diffuse through soil pores over longer distances than other metabolites and are not dependent on water availability. The research described in this PhD thesis explored how beneficial and pathogenic microorganisms that live in the rhizosphere and endosphere modulate plant growth, development and resistance via the production of VOCs. In vitro and in vivo bioassays as well as different ‘omic’ approaches, such as volatomics, transcriptomics and genomics, were employed to investigate underlying mechanisms of VOC-mediated microbe-microbe and microbe-plant interactions.

    To investigate the diversity and functions of microbial VOCs, a disease-suppressive soil was used as the source of the VOC-producing microorganisms. Previous metagenomics studies reported Actinobacteria, in particular Streptomyces and Microbacterium species, as the most abundant bacterial genera found in a soil naturally suppressive to the fungal root pathogen Rhizoctonia solani. VOCs of several Streptomyces isolates inhibited hyphal growth of R. solani and in addition, promoted plant growth. Coupling the Streptomyces VOC profiles with their effects on fungal growth pinpointed methyl 2-methylpentanoate and 1,3,5-trichloro-2-methoxy benzene as antifungal VOCs. Also Microbacterium isolates showed VOC-mediated antifungal activity and plant growth promotion. VOC profiling of Microbacterium sp. EC8 revealed several sulfur-containing compounds and ketones such as dimethyl disulfide, trimethyl trisulfide and 3,3,6-trimethylhepta-1,5-dien-4-one (also known as Artemisia ketone). Genome analysis of strain EC8 revealed genes involved in sulfur metabolism. Resolving the role of the identified compounds and genes in VOC-mediated plant growth promotion and induced resistance will be subject of future studies. VOC-mediated chemical warfare underground has been proposed as a key mechanism of natural disease-suppressive soils. The results presented in this thesis indeed point in that direction. However, to more conclusively determine the role of the identified Actinobacterial VOCs in soil suppressiveness to R. solani, it will be important to demonstrate that the fungicidal VOCs are actually produced in situ at the right place and at sufficient concentrations to suppress plant infection by the pathogenic fungus.

    In agriculture, VOCs and VOC-producing microorganisms provide a potential alternative to the use of pesticides to protect plants and to improve crop production. In the past decades, several in vitro studies have described the effects of microbial VOCs on other (micro)organisms. However, little is still known on the potential of VOCs in large-scale agriculture and horticulture. The results described in this thesis show that VOCs from Microbacterium sp. EC8 stimulate the growth of Arabidopsis, lettuce and tomato, but do not control damping-off disease of lettuce caused by R. solani. Significant biomass increases were also observed for plants exposed only shortly to the bacterial VOCs prior to transplantation of the seedlings to soil. These results indicate that VOCs from strain EC8 can prime plants for growth promotion without direct contact and prolonged colonization. Furthermore, the induction of the plant growth-promoting effects appeared to be plant tissue specific. Root exposure to the bacterial VOCs led to a significant increase in plant biomass whereas shoot exposure did not result in significant biomass increase of lettuce and tomato seedlings. Genome-wide transcriptome analysis of Arabidopsis seedlings exposed to VOCs from this bacterium showed an up-regulation of genes involved in sulfur and nitrogen metabolism and in ethylene and jasmonic acid signaling. These results suggest that the blend of VOCs of strain EC8 favors, in part, the plant’s assimilation of sulfate and nitrogen, essential nutrients for plant growth, development and also resistance.

    Similar to beneficial microorganisms, plant pathogenic microorganisms have also evolved strategies to modulate growth and defense of their hosts. For instance, compounds secreted by pathogens may suppress or interfere with plant defense. In this thesis I show that R. solani produces an array of VOCs that promote growth, accelerate development, change VOC emission and reduce insect resistance of plants. Plant growth-promoting effects induced by the fungal VOCs were not transgenerational. Genome-wide transcriptome analysis of Arabidopsis seedlings revealed that exposure to fungal VOCs caused up-regulation of genes involved in auxin signaling, but down-regulation of genes involved in ethylene and jasmonic acid signaling. These findings suggest that this soil-borne pathogen uses VOCs to predispose plants for infection by stimulating lateral root formation and enhancing root biomass while suppressing defense mechanisms. Alternatively, upon perception of VOCs from soil-borne pathogens, plants may invest in root biomass while minimizing investments in defense, a trade-off that helps them to speed up growth and reproduction and to survive pathogen attack.

    In conclusion, the research presented in this thesis shows that both plants and microorganisms engage via VOCs in long-distance interactions and that beneficial and pathogenic soil microorganisms can alter plant physiology in different ways. Here, I provided a first step in identifying microbial genes involved in the regulation of biologically active VOCs as well as candidate plant genes involved in VOC perception and signal transduction. How plants sense and differentiate among VOCs from beneficial and pathogenic soil microorganisms will be an intriguing subject for future studies.

    Non-destructive sensing of the freshness of packed cod fish using conductivity and pH electrodes
    Heising, J.K. ; Bartels, P.V. ; Boekel, M.A.J.S. van; Dekker, M. - \ 2014
    Journal of Food Engineering 124 (2014). - ISSN 0260-8774 - p. 80 - 85.
    volatile compounds - spoilage - quality
    The use of pH and conductivity electrodes as non-destructive methods for monitoring changes in the freshness status of packed fish is explored. The electrodes monitor changes in the electrical properties of an aqueous phase positioned in the headspace of the fish package. Volatile compounds produced in/ on the packed fish and released in the headspace dissolve into this aqueous phase. Several compounds affect the electrode signals. The signals of the electrodes were compared with the volatile amines content of fresh cod fillets stored at 0–15 degrees C. The changes in the pH signal were strongly temperature dependent and not suitable as quality indication for practical storage temperatures. The conductivity signal showed a characteristic pattern, that correlated with the increasing volatile amines content at all temperatures. The non-destructive measurement of conductivity establishes the proof of principles for monitoring the freshness of packed fish and paths the way towards new developments of intelligent packaging concepts.
    Influence of different proteolytic strains of Streptococcus thermophilus in co-culture with Lactobacillus delbrueckii subsp. bulgaricus on the metabolite profile of set-yoghurt
    Settachaimongkon, S. ; Nout, M.J.R. ; Antunes Fernandes, E.C. ; Hettinga, K.A. ; Vervoort, J.J.M. ; Hooijdonk, A.C.M. van; Zwietering, M.H. ; Smid, E.J. ; Valenberg, H.J.F. van - \ 2014
    International Journal of Food Microbiology 177 (2014). - ISSN 0168-1605 - p. 29 - 36.
    lactic-acid bacteria - nuclear-magnetic-resonance - food fermentations - volatile compounds - functional foods - flavor formation - fermented milks - dairy-cows - shelf-life - metabolomics
    Proto-cooperation between Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus is one of the key factors that determine the fermentation process and final quality of yoghurt. In this study, the interaction between different proteolytic strains of S. thermophilus and L. delbrueckii subsp. bulgaricuswas investigated in terms of microbial growth, acidification and changes in the biochemical composition of milk during set-yoghurt fermentation. A complementary metabolomics approach was applied for global characterization of volatile and non-volatile polar metabolite profiles of yoghurt associated with proteolytic activity of the individual strains in the starter cultures. The results demonstrated that only non-proteolytic S. thermophilus (Prt-) strain performed proto-cooperation with L. delbrueckii subsp. bulgaricus. The proto-cooperation resulted in significant higher populations of the two species, faster milk acidification, significant abundance of aroma volatiles and non-volatile metabolites desirable for a good organoleptic quality of yoghurt. Headspace SPME-GC/MS and 1H NMR resulted in the identification of 35 volatiles and 43 non-volatile polar metabolites, respectively. Furthermore, multivariate statistical analysis allows discriminating set-yoghurts fermented by different types of starter cultures according to their metabolite profiles. Our finding underlines that selection of suitable strain combinations in yoghurt starters is important for achieving the best technological performance regarding the quality of product.
    Capturing flavors from Capsicum baccatum by introgression in sweet pepper
    Eggink, P.M. ; Tikunov, Y.M. ; Maliepaard, C.A. ; Haanstra, J.P.W. ; Rooij, H. de; Vogelaar, A. ; Gutteling, E.W. ; Freymark, G. ; Bovy, A.G. ; Visser, R.G.F. - \ 2014
    Theoretical and Applied Genetics 127 (2014)2. - ISSN 0040-5752 - p. 373 - 390.
    plastid compartment size - lycopersicon-esculentum - volatile compounds - anthracnose resistance - chemical-composition - gas-chromatography - sensory evaluation - mass-spectrometry - candidate gene - essential oils
    The species Capsicum baccatum includes the most common hot peppers of the Andean cuisine, known for their rich variation in flavors and aromas. So far the C. baccatum genetic variation remained merely concealed for Capsicum annuum breeding, due to post-fertilization genetic barriers encountered in interspecific hybridization. However, to exploit the potential flavor wealth of C. baccatum we combined interspecific crossing with embryo rescue, resulting in a multi-parent BC2S1 population. Volatile and non-volatile compounds plus some physical characters were measured in mature fruits, in combination with taste evaluation by a sensory panel. An enormous variation in biochemical composition and sensory attributes was found, with almost all traits showing transgression. A population-specific genetic linkage map was developed for QTL mapping. BC2S1 QTLs were validated in an experiment with near-isogenic lines, resulting in confirmed genetic effects for physical, biochemical and sensory traits. Three findings are described in more detail: (1) A small C. baccatum LG3 introgression caused an extraordinary effect on flavor, resulting in significantly higher scores for the attributes aroma, flowers, spices, celery and chives. In an attempt to identify the responsible biochemical compounds few consistently up- and down-regulated metabolites were detected. (2) Two introgressions (LG10.1 and LG1) had major effects on terpenoid content of mature fruits, affecting at least 15 different monoterpenes. (3) A second LG3 fragment resulted in a strong increase in Brix without negative effects on fruit size. The mapping strategy, the potential application of studied traits and perspectives for breeding are discussed.
    Fermentation characteristics of yeasts isolated from traditionally fermented masau (Ziziphus mauritiana) fruits
    Nyanga, L.K. ; Nout, M.J.R. ; Smid, E.J. ; Boekhout, C. ; Zwietering, M.H. - \ 2013
    International Journal of Food Microbiology 166 (2013)3. - ISSN 0168-1605 - p. 426 - 432.
    saccharomyces-cerevisiae - volatile compounds - wine yeasts - immobilized cells - grape varieties - zimbabwe - strains - metabolism - acid - evolution
    Yeast strains were characterized to select potential starter cultures for the production of masau fermented beverages. The yeast species originally isolated from Ziziphus mauritiana (masau) fruits and their traditionally fermented fruit pulp in Zimbabwe were examined for their ability to ferment glucose and fructose using standard broth under aerated and non-aerated conditions. Most Saccharomyces cerevisiae strains were superior to other species in ethanol production. The best ethanol producing S. cerevisiae strains, and strains of the species Pichia kudriavzevii, Pichia fabianii and Saccharomycopsis fibuligera were tested for production of flavor compounds during fermentation of masau fruit juice. Significant differences in the production of ethanol and other volatile compounds during fermentation of masau juice were observed among and within the four tested species. Alcohols and esters were the major volatiles detected in the fermented juice. Trace amounts of organic acids and carbonyl compounds were detected. Ethyl hexanoate and ethyl octanoate were produced in highest amounts as compared to the other volatile compounds. S. cerevisiae strains produced higher amounts of ethanol and flavor compounds as compared to the other species, especially fatty acid ethyl esters that provide the major aroma impact of freshly fermented wines. The developed library of characteristics can help in the design of mixtures of strains to obtain a specific melange of product functionalities. Keywords: Masau juice; Fermentation; Yeast; Volatile compounds; Flavor; Wine
    Biosynthesis of monoterpene alcohols, derivatives and conjugates in plants : roles in resistance to western flower thrips
    Yang, T. - \ 2013
    Wageningen University. Promotor(en): Marcel Dicke; Harro Bouwmeester, co-promotor(en): Maarten Jongsma. - S.l. : s.n. - ISBN 9789461735317 - 116
    planten - plaagresistentie - verdedigingsmechanismen - insectenplagen - frankliniella occidentalis - monoterpenen - vluchtige verbindingen - biosynthese - pyrethrinen - plants - pest resistance - defence mechanisms - insect pests - frankliniella occidentalis - monoterpenes - volatile compounds - biosynthesis - pyrethrins

    Western flower thrips (WFT), Frankliniella occidentalis, is one of the most serious pests in several vegetable and flower crops worldwide. It is a highly polyphagous insect and a vector of several plant viruses of which the Tomato Spotted Wilt Virus and the Impatiens Necrotic Spot Virus are the most important. Feeding by WFT causes light coloured patches on leaves, petals and fruits, stunted plant growth, and flower and fruit deformation. Synthetic pesticides has been widely used to control WFT. However, the frequent use of these pesticides leads to rapid resistance in WFT, and they are a threat to the environment. Therefore, it is desirable to identify natural sources of resistance effective against WFT to allow breeders to improve resistance in crop species.

    Monoterpenes, as constituents of floral scents and plant resins, play an important role in pollinator attraction and in direct and indirect plant defence against pest insects and pathogens. For example, linalool is a common floral scent constituent and found to be emitted from the leaves by many plant species after herbivore attack. In earlier work, linalool-overexpressing Arabidopsis has been tested for resistance to the pest aphid, Myzus persicae, in dual-choice assays, and transgenic plants significantly repelled or deterred the aphids. A linalool synthase (LIS) was overexpressed in chrysanthemum plants and studied the effect of transgenic plants on WFT (Chapter 2). The volatiles from leaves of transgenic plants were significantly attractive to WFT, however, WFT were significantly deterred by the content of leaf discs from transgenic plants. The headspace analysis showed that the volatiles of LIS chrysanthemum leaves were strongly dominated by linalool,but, they also emitted small amounts of the C11-homoterpene, (3E)-4,8-dimethyl-1,3,7-nonatriene, a derivative of nerolidol. In addition, LC-MS analysis showed that several non-volatile linalool glycosides were significantly increased in the leaves of LIS chrysanthemum compared with leaves of wild-type plants. A geraniol synthase (GES) was overexpressed in maize to see whether WFT could be affected by geraniol or its derivatives (Chapter 3). However, geraniol produced in transgenic maize was all efficiently converted to non-volatile glycoside, geranoyl-6-O-malonyl-β-D-glucopyranoside, and GES maize had no effect on WFT behaviour. These studies demonstrate complex effects of terpene engineering on the metabolic changes in transgenic plants. These results suggest that the release/glycosylation of terpenes should be controlled to improve plant resistance against WFT upon metabolic engineering with terpene synthases.

    The research subsequently focused on a well-known natural pesticide—pyrethrins. Pyrethrins comprise a group of six closely related esters, derived from the monoterpene alcohol chrysanthemol. Pyrethrins are the economically most important natural insecticide with broad uses in homes, agriculture and stored products for more than 150 years. The effect of pyrethrins against WFT was evaluated on its survival, feeding behaviour, and reproduction both in vitro and in planta (infiltrated chrysanthemum leaves) (Chapter 4). Pyrethrins at 0.1% (w/v) and 1% (w/v) exhibited a significantly negative effect on feeding, and the effects of natural concentrations of pyrethrins in pyrethrum leaves can explain the observed high mortality of WFT feeding on pyrethrum leaves. After the finding of this strong effect of pyrethrins on WFT, the study on the biosynthetic pathway of pyrethrins was continued in order to introduce pyrethrin biosynthesis in transgenic plants. A second function of the published enzyme, chrysanthemyl diphosphate synthase (CDS) was identified (Chapter 5). CDS has been reported to catalyse the formation of chrysanthemyl diphosphate (CPP). However, CDS was demonstrated to also catalyse the next step of CPP into chrysanthemol both in vitro and in vivo. CDS was proposed to be renamed as a chrysanthemol synthase (CHS) using DMAPP as substrate. The gene involved in the next step converting chrysanthemol to chrysanthemic acid has also been characterized (Ramirez, 2013). A chrysanthemic acid:CoA

    ligase, which is involved in the final stage of pyrethrin biosynthesis was also studied (Chapter 6). The function of this enzyme was confirmed in vitro and the encoding gene showed a similar expression pattern as CHS in several different tissues and flower developmental stages. The gene responsible for making the final esters is a GDSL-lipase-like acyltransferase (Kikuta et al., 2012). We assume still three to four enzymes are required for the biosynthesis of the basic one of the six pyrethrin esters, jasmolin I, from the precursors DMAPP and jasmonic acid which are universal in plants. And four to five extra genes are required for the complete biosynthesis of all six pyrethrin esters.

    In this study, new insights were gained for the biosynthesis of monoterpenes and their derivatives and conjugates, as well as for plant resistance to WFT mediated by these compounds. The characterization of genes involved in pyrethrin biosynthesis paves the way for metabolic engineering of this natural pesticide in other crops.

    Prediction of sweet pepper (Capsicum annuum) flavour over different harvests
    Eggink, P.M. ; Maliepaard, C.A. ; Tikunov, Y.M. ; Haanstra, J.P.W. ; Pohu-Flament, L.M.M. ; Wit-Maljaars, S.C. de; Willeboordse-Vos, F. ; Bos, S. ; Benning-de Waard, C. ; Grauw-van Leeuwen, P.J. de; Freymark, G. ; Bovy, A.G. ; Visser, R.G.F. - \ 2012
    Euphytica 187 (2012)1. - ISSN 0014-2336 - p. 117 - 131.
    lycopersicon-esculentum - chemical-composition - volatile compounds - metabolomics - tomatoes
    To better understand and predict the complex multifactorial trait flavor, volatile and non-volatile components were measured in fresh sweet pepper (Capsicum annuum) fruits throughout the growing season in a diverse panel of 24 breeding lines, hybrids, several cultivated genotypes and one gene bank accession. Biochemical profiles were linked to individual flavor attributes, that were objectively quantified by a trained descriptive expert panel. We used a Random Forest regression approach for prediction of the flavor attributes within and between harvests. Predictions of texture related attributes (juiciness, toughness, crunchiness and stickiness of the skin) and sweetness were good (around 60–65 %in the analyses with the three harvests combined). The predictions of the attributes aroma intensity, sourness and fruity/apple were somewhat lower and more variable between harvests. (E)-2-hexen-1-ol, neopentane, p-menth-1-en-9-al, 3-hepten-2-one, (Z)-b-ocimene, (Z)-2-penten-1-ol, 1-methyl-1,4-cyclohexadiene, glucose, fructose and three unknown volatile compounds were identified as key-metabolites involved in the flavor differences between both genotypes and harvests. The complex nature of flavor is exemplified by the observed masking effect of fructose and other sugars on sourness and sourness related metabolites, like citrate. The knowledge obtained from the overall biochemical, sensory and prediction analyses forms a basis for targeted flavor improvement by breeding.
    Transport and biodegradation of volatile organic compounds : influence on vapor intrusion into buildings
    Picone, S. - \ 2012
    Wageningen University. Promotor(en): Huub Rijnaarts, co-promotor(en): Tim Grotenhuis; P.F.M. van Gaans. - S.l. : s.n. - ISBN 9789461732767 - 149
    vluchtige verbindingen - organische verbindingen - biodegradatie - biochemisch transport - gebouwen - grondwaterverontreiniging - binnenklimaat - volatile compounds - organic compounds - biodegradation - biochemical transport - buildings - groundwater pollution - indoor climate

    Vapor intrusion occurs when volatile subsurface contaminants, migrating from the saturated zone through the unsaturated zone, accumulate in buildings. It is often the most relevant pathway for human health risks at contaminated sites, especially in urban areas; yet its assessment is controversial. Field assessment of vapor intrusion risk is complicated by two interrelated main factors that are controlled by the contaminant’s properties: transport processes in the unsaturated zone and biodegradation in the unsaturated zone. Commonly available vapor intrusion models either overlook significant properties at the field scale or, conversely, are too complex to be applicable at this scale. Specifically, moisture variation, liquid diffusion, dynamic processes such as water table variations, and biodegradation are not adequately accounted for. As a result, the soil gas and indoor air concentrations predicted by existing models frequently overestimate measured concentrations by several orders of magnitude.
    This thesis addressed transport and biodegradation processes of volatile organic compounds, focusing on aerobic unsaturated zones. The main aims were to i) characterize significant transport processes influencing vapor intrusion and ii) quantify and mechanistically describe biodegradation in unsaturated soils. Field experience, numerical modeling and laboratory experiments with toluene and vinyl chloride as reference compounds were combined to separate out the relevant processes influencing vapor intrusion.
    The main conclusions from this thesis indicate that soil moisture variations and aerobic biodegradation are crucial aspects to be jointly considered for the assessment of vapor intrusion. These may contribute to a significant reduction in the risk associated with dissolved volatile organic contaminants. Specific and relevant implications for modeling and monitoring vapor intrusion can be derived. With respect to vapor intrusion modeling, when including unsaturated zone biodegradation, the use of liquid phase biodegradation rates as derived from liquid mixed batches may underestimate by several orders of magnitude the liquid degradation rates in the unsaturated system. Therefore, biodegradation rates derived from unsaturated system appear more appropriate. With respect to monitoring, vertical soil moisture variations and contaminant/oxygen concentration profiles need to be measured in the field, in order to account for the above processes.

    Multitrophic effects of plant resistance: from basic ecology to application in transgenic crops
    Kos, M. - \ 2012
    Wageningen University. Promotor(en): Marcel Dicke; Louise Vet, co-promotor(en): Joop van Loon. - S.l. : s.n. - ISBN 9789461732064 - 303
    brassicaceae - verdedigingsmechanismen - insectenplagen - multitrofe interacties - parasitoïden - predatoren - glucosinolaten - vluchtige verbindingen - transgene planten - niet-doelorganismen - ecologische risicoschatting - brassicaceae - defence mechanisms - insect pests - multitrophic interactions - parasitoids - predators - glucosinolates - volatile compounds - transgenic plants - nontarget organisms - ecological risk assessment

    Plants have evolved a wide array of direct and indirect resistance traits that prevent or reduce herbivory by insects. The aim of this thesis was to study the effects of direct and indirect plant resistance traits on the multitrophic interactions between brassicaceous plants, leaf-chewing and phloem-sucking aboveground herbivores and their natural enemies, parasitoids and predators. Brassica oleracea cultivars and Arabidopsis thaliana ecotypes were used that differ in production of glucosinolates or emission of volatiles, secondary plant chemicals acting in direct and indirect resistance respectively. There was a considerable intraspecific variation in the multitrophic effects of plant resistance traits in both plant species. In the field, bottom-up forces (plant chemistry and morphology) appeared more important for herbivore abundance than plant-mediated top-down forces (attraction and arrestment of natural enemies). Under greenhouse conditions, glucosinolates affected the performance of herbivores and that of their natural enemies. The performance of both a generalist and a specialist caterpillar was negatively correlated with glucosinolates in the plant, whereas that of a parasitoid of the specialist caterpillar was positively correlated with glucosinolates. Performance of a specialist aphid was positively correlated with phloem glucosinolates, and the aphid selectively sequestered these glucosinolates. Glucosinolates and their volatile hydrolytic products correlated negatively with the performance and behaviour of one of the predators of this aphid, but positively with that of one of its parasitoids. These results suggest that direct and indirect resistance traits can be in conflict, but they can also work in concert to enhance resistance to herbivores, depending on the biology of the herbivore and carnivore involved. Transgenic A. thaliana plants engineered to emit larger amounts of volatile terpenoids repelled the aphid, attracted the parasitoid, but did not affect predator behaviour.

    These fundamental ecological results provided the background information required to strengthen ecological risk analysis for transgenicplants in the framework of the programme ‘Ecology Regarding Genetically modified Organisms’ funded by the Dutch government. The effects of transgenic plants on non-target organisms were compared with the baseline variation in the effects on non-target organisms that exists among conventional varieties or, in the case of A. thaliana, wild ecotypes. Four B. oleracea cultivars and three A. thaliana ecotypes were selected to represent the baseline variation. The baseline variation in effects on target and non-target organisms was relatively consistent over different environments, soil types and time. The effects of transgenic A. thaliana plants altered in direct and indirect resistance on non-target organisms were mostly within the baseline variation in these effects. Finally, the knowledge gained was applied to develop guidelines for governmental regulators that can be used to assess the potential ecological effects of transgenic crops on non-target organisms, in relation to baseline variation.

    Microbiota of Tayohounta, a fermented baobab flavour food of Benin
    Chadare, F.J. ; Jonkman, J. ; Wolkers-Rooijackers, J.C.M. ; Nout, M.J.R. ; Hounhouigan, J.D. ; Zwietering, M.H. - \ 2011
    African journal of biotechnology 10 (2011)69. - ISSN 1684-5315 - p. 15607 - 15615.
    adansonia-digitata l. - bean parkia-biglobosa - bacillus-subtilis - volatile compounds - west-africa - natural fermentation - heat-treatment - products - condiments - diversity
    The present work provides data on the microbial composition of Tayohounta, a product of natural fermentation of baobab seed kernels. Samples were collected from 3 different small scale producers from Benin at the end of the fermentation process. Microorganisms were enumerated and identified using phenotypic and molecular approaches. Tayohounta was also investigated using culture independent techniques, direct DNA extraction, polymerase chain reaction - denaturing gradient gel electrophoresis (PCR-DGGE) and cloning. Isolated microorganisms were tested for their functionality in baobab seed kernels fermentation. Total viable counts were around 9 log cfu/g representing mainly Bacillus spp., whereas lactic acid bacteria (LAB) (8 log cfu/g), yeasts and moulds represent a smaller part of the total flora in all Tayohounta samples. Sequencing of clones of polymerase chain reaction (PCR) products of bacterial DNA directly extracted from Tayohounta revealed large differences between the products made by different producers. In all products, Bacillus licheniformis, B. pumilus, B. subtilis, B. thermoamylovorans and Lactobacillus fermentum were present. Other microorganisms (B. thuringiensis, Brevibacterium borstelensis, Enterococcus casseliflavus, E. durans, Lb. agilis, Pediococcus pentosaceus, Streptococcus equinus and Weissella confusa) were present occasionally. In experimental pure culture fermentations, B. subtilis showed little effect on pH, but degraded protein and caused a typical pungent smell typical of Tayohounta.
    Sweaty skin: an invitation to bite?
    Smallegange, R.C. ; Verhulst, N.O. ; Takken, W. - \ 2011
    Trends in Parasitology 27 (2011)4. - ISSN 1471-4922 - p. 143 - 148.
    gas chromatography/mass spectrometry - mosquito anopheles-gambiae - human kin recognition - human-body odor - l-lactic acid - aedes-aegypti - malaria mosquito - candidate attractants - pattern-recognition - volatile compounds
    Anopheles gambiae sensu stricto and Aedes aegypti have a preference for human blood, which determines their importance as vectors of pathogens responsible for human diseases. Volatile organic chemicals are the principal cues by which humans are being located. Human sweat contains components that are attractive to anthropophilic mosquito species, and variation in sweat composition causes differential attractiveness to mosquitoes within and between individuals and also between humans and other mammals. Characteristics of skin glands and skin microbiota define the odorous organic compounds emitted by sweat, thereby the degree of attractiveness of the host to mosquitoes. Carboxylic acids in particular appear to characterize humans. Thus sweat-associated human volatiles are probably the primary determinant factor in the host preference of anthropophilic mosquitoes
    The role of skin microbiota in the attractiveness of humans to the malaria mosquito Anopheles gambiae Giles
    Verhulst, N.O. - \ 2010
    Wageningen University. Promotor(en): Willem Takken; Marcel Dicke. - S.l. : s.n. - ISBN 9789085858300 - 236
    anopheles gambiae - mens - geurstoffen - bacteriën - lokstoffen - gedrag bij zoeken van een gastheer - vluchtige verbindingen - in vitro - in vivo experimenten - anopheles gambiae - man - odours - bacteria - attractants - host-seeking behaviour - volatile compounds - in vitro - in vivo experimentation
    Malaria is one of the most serious infectious diseases in the world. The African mosquito Anopheles gambiae sensu stricto (henceforth termed An. gambiae) is highly competent for malaria parasites and preferably feeds on humans inside houses, which make it one of the most effective vectors of the disease. Human body odours are presumably the most important cues that enable An. gambiae to find its host. Knowledge on the odours that mediate the host-seeking behaviour of malaria vectors is expected to contribute to novel intervention methods for disease control.
    The skin microbiota plays an important role in the production of human body odours and the human microbial and chemical signature displays a qualitative and quantitative correlation. Several studies have indicated a possible role of skin bacteria in the production of volatiles attractive to mosquitoes. The principle goal of this thesis was to understand the role of the human skin microbiota in mosquito-host interactions and to identify which compounds produced by these micro-organisms are involved in the attraction of An. gambiae to humans.
    Skin bacteria isolated from human feet and grown in vitro on agar plates attracted An. gambiae and this attraction was affected by incubation time and dilution of the skin microbiota. Semi-field experiments showed similar results and field experiments in Kenya suggested that skin bacterial volatiles also attract other disease vectors. Volatiles produced by five bacterial species common on the human skin showed that volatile blends produced by some species, including Staphylococcus epidermidis, were more attractive than blends produced by other species. Volatiles produced by Pseudomonas aeruginosa did not affect the behaviour of An. gambiae.
    Analysis of the volatiles produced by human skin microbiota grown in vitro led to the identification of 16 compounds, the majority of which had an effect on An. gambiae behaviour. 3-Methyl-1-butanol enhanced the attractiveness of a synthetic blend by a factor of three, and could be used to increase mosquito trap catches for monitoring or vector control purposes. 2-Phenylethanol decreased mosquito catches of a synthetic blend and may act as a spatial repellent.
    In order to examine the interaction between the microbiota on the skin and human attractiveness to mosquitoes, skin emanation and skin microbiota samples were taken from 48 individuals. The skin emanations from the individuals varied significantly in attractiveness to An. gambiae and several compounds originating from the skin were associated with individuals that were highly attractive or less attractive to mosquitoes. Individuals with a higher abundance of bacteria on their skin were more attractive to An. gambiae, whereas individuals with a higher diversity of skin microbiota were less attractive. Staphylococcus spp. were associated with individuals that were highly attractive and Pseudomonas spp. with individuals that were less attractive to mosquitoes. Human Leukocyte Antigens (HLA) genes are considered to influence the human body odour profile and HLA profile analysis of the 48 human individuals indicated that these genes may also affect the attractiveness of humans to mosquitoes.
    The studies described in this thesis show that volatiles produced by the human skin microbiota play an important role in the host-seeking behaviour of An. gambiae and the abundance and composition of the skin microbiota determine an individual’s attractiveness to mosquitoes. Optimised blends of the compounds identified can be used in push-pull strategies for the manipulation of mosquitoes, thereby reducing the number of malaria mosquitoes, the human-biting frequency, and the intensity of Plasmodium transmission. Research on the role of skin microbiota in the host-seeking behaviour and host preference of biting insects may lead to a better understanding of vector-host interactions and contribute to the fight against vector-borne diseases.

    Detection of pathogen infection at greenhouse scale through plant emitted volatiles
    Jansen, R.M.C. - \ 2009
    Wageningen University. Promotor(en): Eldert van Henten; Harro Bouwmeester; J. Wildt, co-promotor(en): Jan Willem Hofstee. - [S.l. : S.n. - ISBN 9789085854449 - 177
    kasgewassen - oogstschade - vluchtige verbindingen - plantenziekteverwekkers - botrytis cinerea - gezondheid - monitoring - solanum lycopersicum - tomaten - detectie - greenhouse crops - crop damage - volatile compounds - plant pathogens - botrytis cinerea - health - monitoring - solanum lycopersicum - tomatoes - detection
    Induced plant volatiles allow sensitive monitoring of plant health status in greenhouses
    Jansen, R.M.C. ; Hofstee, J.W. ; Wildt, J. ; Verstappen, F.W.A. ; Bouwmeester, H.J. ; Henten, E.J. van - \ 2009
    Plant Signaling & Behavior 4 (2009)9. - ISSN 1559-2316 - p. 1 - 6.
    gewasbescherming - plantenziekteverwekkers - vluchtige verbindingen - botrytis cinerea - schimmelziekten - tomaten - solanum lycopersicum - glastuinbouw - overlevingsstrategieën van planten - gewasmonitoring - plant protection - plant pathogens - volatile compounds - botrytis cinerea - fungal diseases - tomatoes - solanum lycopersicum - greenhouse horticulture - plant strategies - crop monitoring
    This paper provides a synthesis of our research on the use of induced plant volatiles for sensitive monitoring of plant health status in greenhouses. The main research objective of this research was to investigate whether plant-emitted volatiles can be used to detect a Botrytis cinerea infection in a large-scale greenhouse. The pathogenic fungus B. cinerea and the plant species tomato (Lycopersicon esculentum) were selected as model organisms. Based on this choice, three main research questions were formulated: (1) What is the effect of a B. cinerea infection on the emission of volatiles from tomato? (2) Are B. cinerea induced emissions of tomato specific for the infection with this pathogen? (3) Are B. cinerea induced concentrations of volatiles detectable in large-scale greenhouses?
    Health monitoring of plants by their emitted volatiles: trichome damage and cell membrane damage are detectable at greenhouse scale
    Jansen, R.M.C. ; Hofstee, J.W. ; Wildt, J. ; Verstappen, F.W.A. ; Bouwmeester, H.J. ; Posthumus, M.A. ; Henten, E.J. van - \ 2009
    Annals of Applied Biology 154 (2009)3. - ISSN 0003-4746 - p. 441 - 452.
    gewasbescherming - monitoring - vluchtige verbindingen - gaschromatografie - massaspectrometrie - solanum lycopersicum - tomaten - gewasmonitoring - glastuinbouw - plant protection - monitoring - volatile compounds - gas chromatography - mass spectrometry - solanum lycopersicum - tomatoes - crop monitoring - greenhouse horticulture - reaction mass-spectrometry - organic-compounds - gas-chromatography - methyl salicylate - leaf volatiles - cotton plants - voc emissions - jasmonic acid - tomato - herbivory
    Pathogen attack and herbivore infestation have a major impact on plant health. In a model study, these two plant health issues were simulated to study whether plant health can be monitored at greenhouse scale through the analysis of volatile organic compounds (VOCs) in greenhouse atmosphere. To simulate pathogen attack and herbivore infestation, we repeatedly stroked the stems of tomato plants (Lycopersicon esculentum) and repeatedly removed their side shoots. In addition, we studied the effect of fruit picking on the concentration of plant-emitted VOCs in greenhouse atmosphere. Analysis of air samples obtained before these treatments revealed up to 17 VOCs that are known to be released from tomato plants, of which the most dominant one was the monoterpene ß-phellandrene. When plants were 7 weeks old, the concentration of this VOC was approximately 0.06 ppbv before treatment. When plants were 12 weeks old, this concentration was raised to approximately 0.14 ppbv. Stroking of the stems, removing the side shoots and fruit picking resulted in an increase in the concentrations of all mono- and most sesquiterpenes up to 60-fold, which was expected because these VOCs are well-known constituents of trichomes. The treatments did not result in substantially increased concentrations of the stress-related compounds ¿-copaene, methyl salicylate and (E,E)-4,8,12-trimethyl-1,3,7,11-tridecatetraene. In contrast to stroking and fruit picking, shoot removal resulted in the emission of the lipoxygenase-derived product (Z)-3-hexenol in greenhouse atmosphere expressing cell membrane degradation. The findings presented in this paper focus on the feasibility of monitoring plant health through the analysis of VOCs in greenhouse air, but findings might also be relevant for atmospheric chemistry.
    Bayesian networks for omics data analysis
    Gavai, A.K. - \ 2009
    Wageningen University. Promotor(en): Jack Leunissen; Michael Muller, co-promotor(en): Guido Hooiveld; P.J.F. Lucas. - [S.l.] : S.n. - ISBN 9789085853909 - 98
    bio-informatica - waarschijnlijkheidsmodellen - bayesiaanse theorie - netwerkanalyse - genexpressie - roken - vluchtige verbindingen - biochemische omzettingen - voedingsonderzoek bij de mens - genexpressieanalyse - microarrays - netwerken - nutrigenomica - bioinformatics - probabilistic models - bayesian theory - network analysis - gene expression - smoking - volatile compounds - biochemical pathways - human nutrition research - genomics - microarrays - networks - nutrigenomics
    This thesis focuses on two aspects of high throughput technologies, i.e. data storage and data analysis, in particular in transcriptomics and metabolomics. Both technologies are part of a research field that is generally called ‘omics’ (or ‘-omics’, with a leading hyphen), which refers to genomics, transcriptomics, proteomics, or metabolomics. Although these techniques study different entities (genes, gene expression, proteins, or metabolites), they all have in common that they use high-throughput technologies such as microarrays and mass spectrometry, and thus generate huge amounts of data. Experiments conducted using these technologies allow one to compare different states of a living cell, for example a healthy cell versus a cancer cell or the effect of food on cell condition, and at different levels.
    The tools needed to apply omics technologies, in particular microarrays, are often manufactured by different vendors and require separate storage and analysis software for the data generated by them. Moreover experiments conducted using different technologies cannot be analyzed simultaneously to answer a biological question. Chapter 3 presents MADMAX, our software system which supports storage and analysis of data from multiple microarray platforms. It consists of a vendor-independent database which is tightly coupled with vendor-specific analysis tools. Upcoming technologies like metabolomics, proteomics and high-throughput sequencing can easily be incorporated in this system.
    Once the data are stored in this system, one obviously wants to deduce a biological relevant meaning from these data and here statistical and machine learning techniques play a key role. The aim of such analysis is to search for relationships between entities of interest, such as genes, metabolites or proteins. One of the major goals of these techniques is to search for causal relationships rather than mere correlations. It is often emphasized in the literature that "correlation is not causation" because people tend to jump to conclusions by making inferences about causal relationships when they actually only see correlations. Statistics are often good in finding these correlations; techniques called linear regression and analysis of variance form the core of applied multivariate statistics. However, these techniques cannot find causal relationships, neither are they able to incorporate prior knowledge of the biological domain. Graphical models, a machine learning technique, on the other hand do not suffer from these limitations.
    Graphical models, a combination of graph theory, statistics and information science, are one of the most exciting things happening today in the field of machine learning applied to biological problems (see chapter 2 for a general introduction). This thesis deals with a special type of graphical models known as probabilistic graphical models, belief networks or Bayesian networks. The advantage of Bayesian networks over classical statistical techniques is that they allow the incorporation of background knowledge from a biological domain, and that analysis of data is intuitive as it is represented in the form of graphs (nodes and edges). Standard statistical techniques are good in describing the data but are not able to find non-linear relations whereas Bayesian networks allow future prediction and discovering nonlinear relations. Moreover, Bayesian networks allow hierarchical representation of data, which makes them particularly useful for representing biological data, since most biological processes are hierarchical by nature. Once we have such a causal graph made either by a computer program or constructed manually we can predict the effects of a certain entity by manipulating the state of other entities, or make backward inferences from effects to causes. Of course, if the graph is big, doing the necessary calculations can be very difficult and CPU-expensive, and in such cases approximate methods are used.
    Chapter 4 demonstrates the use of Bayesian networks to determine the metabolic state of feeding and fasting mice to determine the effect of a high fat diet on gene expression. This chapter also shows how selection of genes based on key biological processes generates more informative results than standard statistical tests. In chapter 5 the use of Bayesian networks is shown on the combination of gene expression data and clinical parameters, to determine the effect of smoking on gene expression and which genes are responsible for the DNA damage and the raise in plasma cotinine levels of blood of a smoking population. This study was conducted at Maastricht University where 22 twin smokers were profiled. Chapter 6 presents the reconstruction of a key metabolic pathway which plays an important role in ripening of tomatoes, thus showing the versatility of the use of Bayesian networks in metabolomics data analysis.
    The general trend in research shows a flood of data emerging from sequencing and metabolomics experiments. This means that to perform data mining on these data one requires intelligent techniques that are computationally feasible and able to take the knowledge of experts into account to generate relevant results. Graphical models fit this paradigm well and we expect them to play a key role in mining the data generated from omics experiments.
    Quality control of raw cows' milk by headspace analysis : a new approach to mastitis diagnosis
    Hettinga, K.A. - \ 2009
    Wageningen University. Promotor(en): Toon van Hooijdonk, co-promotor(en): T.J.G.M. Lam. - [S.l.] : S.n. - ISBN 9789085853008 - 127
    rauwe melk - kwaliteitscontroles - rundermastitis - vluchtige verbindingen - analytische methoden - raw milk - quality controls - bovine mastitis - volatile compounds - analytical methods
    In de levensmiddelenindustrie wordt veelvuldig de kwaliteit van levensmiddelen getest met behulp van apparaten die aan het voedsel ruiken. Dit is ook op melk toegepast. Hierbij bleek dat melk van goede kwaliteit slechts zeven verschillende geurstoffen bevat (ter vergelijking, in kaas worden meer dan honderd verschillende geurstoffen aangetroffen). Na analyse van de geurpatronen in melk met verschillende gebreken bleek dat in melk onder andere residuen van reinigingsmiddelen en de mate van vetafbraak gedetecteerd konden worden. Vervolgens is onderzoek gedaan naar melk van koeien met uierontsteking (mastitis), één van de belangrijkste ziekten bij melkkoeien. In een eerste experiment bleek dat de geurstoffen in mastitis melkmonsters een bijzonder patroon vertoonden, waarbij een statistisch model op basis van het patroon aan geurstoffen kon voorspellen welke bacterie de veroorzaker van de uierontsteking was. Vervolgens is bepaald dat de geurstoffen gevormd werden door de bacterie zelf. Uit het laatste experiment bleek dat 4 tot 8 uur incubatietijd nodig was voorafgaand aan de identificatie van geurstoffen.
    Risk assessment of nickel, mineral oils, polycyclic aromatic hydrocarbons and volatile organic compounds in animal feed materials
    Bulder, A.S. ; Hoogenboom, L.A.P. ; Kan, C.A. ; Raamsdonk, L.W.D. van; Traag, W.A. ; Bouwmeester, H. - \ 2008
    Wageningen : RIKILT (Report / RIKILT 2007.020) - 102
    voer - besmetting - nikkel - mineraaloliën - vluchtige verbindingen - risicoschatting - polycyclische aromatische koolwaterstoffen - feeds - contamination - nickel - mineral oils - volatile compounds - risk assessment - polycyclic aromatic hydrocarbons
    Butter and butter oil classification by PTR-MS
    Ruth, S.M. van; Koot, A.H. ; Akkermans, W. ; Araghipour, N. ; Rozijn, M. ; Baltussen, M.A.H. ; Wisthaler, A. ; Mark, T.D. ; Frankhuizen, R. - \ 2008
    European Food Research and Technology 227 (2008)1. - ISSN 1438-2377 - p. 307 - 317.
    reaction-mass-spectrometry - sweet cream butter - trace gas-analysis - volatile compounds - food authenticity - dairy-products - flavor - quality - aroma
    The potential of proton transfer reaction mass spectrometry (PTR-MS) as a tool for classification of milk fats was evaluated in relation to quality and authentication issues. Butters and butter oils were subjected to heat and off-flavouring treatments in order to create sensorially defective samples. The effect of the treatments was evaluated by means of PTR-MS analysis, sensory analysis and classical chemical analysis. Subsequently, partial least square-discriminant analysis models (PLS-DA) were fitted to predict the matrix (butter/butter oil) and the sensory grades of the samples from their PTR-MS data. Using a 10-fold cross-validation scheme, 84% of the samples were successfully classified into butter and butter oil classes. Regarding sensory quality, 89% of the samples were correctly classified. As the milk fats were fairly successfully classified by the combination of PTR-MS and PLS-DA, this combination seems a promising approach with potential applications in quality control and control of regulations.
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