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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Covariances Simultaneous Component Analysis: a new method within a framework for modeling covariances
Smilde, A.K. ; Timmerman, M.E. ; Saccenti, E. ; Jansen, J.J. ; Hoefsloot, H.C.J. - \ 2015
Journal of Chemometrics 29 (2015)5. - ISSN 0886-9383 - p. 277 - 288.
metabolomics data - phenotypes - algorithm
In modern omics research, it is more rule than exception that multiple data sets are collected in a study pertaining to the same biological organism. In such cases, it is worthwhile to analyze all data tables simultaneously to arrive at global information of the biological system. This is the area of data fusion or multi-set analysis, which is a lively research topic in chemometrics, bioinformatics, and biostatistics. Most methods of analyzing such complex data focus on group means, treatment effects, or time courses. There is also information present in the covariances among variables within a group, because this relates directly to individual differences, heterogeneity of responses, and changes of regulation in the biological system. We present a framework for analyzing covariance matrices and a new method that fits nicely in this framework. This new method is based on combining covariance prototypes using simultaneous components and is, therefore, coined Covariances Simultaneous Component Analysis (COVSCA). We present the framework and our new method in mathematical terms, thereby explaining the (dis)similarities of the methods. Systems biology models based on differential equations illustrate the type of variation generated in real-life biological systems and how this type of variation can be modeled within the framework and with COVSCA. The method is subsequently applied to two real-life data sets from human and plant metabolomics studies showing biologically meaningful results
Safety assessment of plant varieties using transcriptomics profiling and a one-class classifier
Dijk, J.P. van; Mello, C.S. de; Voorthuijzen, M.M. ; Hutten, R.C.B. ; Maisonnave Arisi, A.C. ; Jansen, J.J. ; Buydens, L.M.C. ; Voet, H. van der; Kok, E.J. - \ 2014
Regulatory Toxicology and Pharmacology 70 (2014)1. - ISSN 0273-2300 - p. 297 - 303.
potato-tubers - microarray data - risk-assessment - food - identification - components - gene
An important part of the current hazard identification of novel plant varieties is comparative targeted analysis of the novel and reference varieties. Comparative analysis will become much more informative with unbiased analytical approaches, e.g. omics profiling. Data analysis estimating the similarity of new varieties to a reference baseline class of known safe varieties would subsequently greatly facilitate hazard identification. Further biological and eventually toxicological analysis would then only be necessary for varieties that fall outside this reference class. For this purpose, a one-class classifier tool was explored to assess and classify transcriptome profiles of potato (Solanum tuberosum) varieties in a model study. Profiles of six different varieties, two locations of growth, two year of harvest and including biological and technical replication were used to build the model. Two scenarios were applied representing evaluation of a ’different’ variety and a ‘similar’ variety. Within the model higher class distances resulted for the ‘different’ test set compared with the ‘similar’ test set. The present study may contribute to a more global hazard identification of novel plant varieties
An ecogenomic analysis of herbivore-induced plant volatiles in Brassica juncea
Mathur, V. ; Tytgat, T.O.G. ; Hordijk, C.A. ; Harhangi, H.R. ; Jansen, J.J. ; Reddy, A.S. ; Harvey, J.A. ; Vet, L.E.M. ; Dam, N.M. van - \ 2013
Molecular Ecology 22 (2013)24. - ISSN 0962-1083 - p. 6179 - 6196.
parasitoids cotesia-glomerata - brussels-sprouts plants - green leaf volatiles - arabidopsis-thaliana - glucosinolate hydrolysis - secondary metabolism - nicotiana-attenuata - insect herbivores - natural enemies - jasmonic acid
Upon herbivore feeding, plants emit complex bouquets of induced volatiles that may repel insect herbivores as well as attract parasitoids or predators. Due to differences in the temporal dynamics of individual components, the composition of the herbivore-induced plant volatile (HIPV) blend changes with time. Consequently, the response of insects associated with plants is not constant either. Using Brassica juncea as the model plant and generalist Spodoptera spp. larvae as the inducing herbivore, we investigated herbivore and parasitoid preference as well as the molecular mechanisms behind the temporal dynamics in HIPV emissions at 24, 48 and 72 h after damage. In choice tests, Spodoptera litura moth preferred undamaged plants, whereas its parasitoid Cotesia marginiventris favoured plants induced for 48 h. In contrast, the specialist Plutella xylostella and its parasitoid C. vestalis preferred plants induced for 72 h. These preferences matched the dynamic changes in HIPV blends over time. Gene expression analysis suggested that the induced response after Spodoptera feeding is mainly controlled by the jasmonic acid pathway in both damaged and systemic leaves. Several genes involved in sulphide and green leaf volatile synthesis were clearly up-regulated. This study thus shows that HIPV blends vary considerably over a short period of time, and these changes are actively regulated at the gene expression level. Moreover, temporal changes in HIPVs elicit differential preferences of herbivores and their natural enemies. We argue that the temporal dynamics of HIPVs may play a key role in shaping the response of insects associated with plants.
Birds exploit herbivore-induced plant volatiles to locate herbivorous prey
Amo, L. ; Jansen, J.J. ; Dam, N.M. van; Dicke, M. ; Visser, M.E. - \ 2013
Ecology Letters 16 (2013)11. - ISSN 1461-023X - p. 1348 - 1355.
dimethyl sulfide - insectivorous birds - neotropical forest - great tits - trees - food - attraction - insects - defense - attack
Arthropod herbivory induces plant volatiles that can be used by natural enemies of the herbivores to find their prey. This has been studied mainly for arthropods that prey upon or parasitise herbivorous arthropods but rarely for insectivorous birds, one of the main groups of predators of herbivorous insects such as lepidopteran larvae. Here, we show that great tits (Parus major) discriminate between caterpillar-infested and uninfested trees. Birds were attracted to infested trees, even when they could not see the larvae or their feeding damage. We furthermore show that infested and uninfested trees differ in volatile emissions and visual characteristics. Finally, we show, for the first time, that birds smell which tree is infested with their prey based on differences in volatile profiles emitted by infested and uninfested trees. Volatiles emitted by plants in response to herbivory by lepidopteran larvae thus not only attract predatory insects but also vertebrate predators.
A tritrophic approach to the preference-performance hypothesis involving an exotic and a native plant
Fortuna, T.F.M. ; Woelke, J.B. ; Hordijk, C.A. ; Jansen, J.J. ; Dam, N.M. van; Vet, L.E.M. ; Harvey, J.A. - \ 2013
Biological Invasions 15 (2013)11. - ISSN 1387-3547 - p. 2387 - 2401.
parasitoids cotesia-glomerata - phytophagous insects - oviposition preference - invasive plant - c-rubecula - specialist herbivore - bunias orientalis - natural enemies - host - butterflies
Exotic plants often generate physical and chemical changes in native plant communities where they become established. A major challenge is to understand how novel plants may affect trophic interactions in their new habitats, and how native herbivores and their natural enemies might respond to them. We compared the oviposition preference and offspring performance of the crucifer specialist, Pieris brassicae, on an exotic plant, Bunias orientalis, and on a related native plant, Sinapis arvensis. Additionally, we studied the response of the parasitoid, Cotesia glomerata to herbivore-induced plant volatiles (HIPV) and determined the volatile blend composition to elucidate which compound(s) might be involved in parasitoid attraction. On both host plants we also compared the parasitism rate of P. brassicae by C. glomerata. Female butterflies preferred to oviposit on the native plant and their offspring survival and performance was higher on the native plant compared to the exotic. Although, headspace analysis revealed qualitative and quantitative differences in the volatile blends of both plant species, C. glomerata did not discriminate between the HIPV blends in flight-tent bioassays. Nevertheless, parasitism rate of P. brassicae larvae was higher on the native plant under semi-field conditions. Overall, P. brassicae oviposition preference may be more influenced by bottom-up effects of the host plant on larval performance than by top-down pressure exerted by its parasitoid. The potential for dietary breadth expansion of P. brassicae to include the exotic B. orientalis and the role of top-down processes played by parasitoids in shaping herbivore host shifts are further discussed
One-class classification for safety evaluation of novel foods using transcriptomics data
Dijk, J.P. van; Souza de Mello, C. ; Voorhuijzen, M.M. ; Hutten, R.C.B. ; Arisi, A.C.M. ; Jansen, J.J. ; Buydens, L.M.C. ; Voet, H. van der; Kok, E.J. - \ 2012
Identification of Biologically Relevant Compounds in Aboveground and Belowground Induced Volatile Blends
Dam, N.M. van; Qiu, B.L. ; Hordijk, C.A. ; Vet, L.E.M. ; Jansen, J.J. - \ 2010
Journal of Chemical Ecology 36 (2010)9. - ISSN 0098-0331 - p. 1006 - 1016.
herbivore-induced volatiles - partial least-squares - jasmonic acid - specialist herbivore - cotesia-glomerata - parasitic wasps - natural enemies - plants - root - performance
Plants under attack by aboveground herbivores emit complex blends of volatile organic compounds (VOCs). Specific compounds in these blends are used by parasitic wasps to find their hosts. Belowground induction causes shifts in the composition of aboveground induced VOC blends, which affect the preference of parasitic wasps. To identify which of the many volatiles in the complex VOC blends may explain parasitoid preference poses a challenge to ecologists. Here, we present a case study in which we use a novel bioinformatics approach to identify biologically relevant differences between VOC blends of feral cabbage (Brassica oleracea L.). The plants were induced aboveground or belowground with jasmonic acid (JA) and shoot feeding caterpillars (Pieris brassicae or P. rapae). We used Partial Least Squares--Discriminant Analysis (PLSDA) to integrate and visualize the relation between plant-emitted VOCs and the preference of female Cotesia glomerata. Overall, female wasps preferred JA-induced plants over controls, but they strongly preferred aboveground JA-induced plants over belowground JA-induced plants. PLSDA revealed that the emission of several monoterpenes was enhanced similarly in all JA-treated plants, whereas homoterpenes and sesquiterpenes increased exclusively in aboveground JA-induced plants. Wasps may use the ratio between these two classes of terpenes to discriminate between aboveground and belowground induced plants. Additionally, it shows that aboveground applied JA induces different VOC biosynthetic pathways than JA applied to the root. Our bioinformatic approach, thus, successfully identified which VOCs matched the preferences of the wasps in the various choice tests. Additionally, the analysis generated novel hypotheses about the role of JA as a signaling compound in aboveground and belowground induced responses in plants
Stress-induced DNA methylation changes and their heritability in asexual dandelions
Verhoeven, K.J.F. ; Jansen, J.J. ; Dijk, P.J. ; Biere, A. - \ 2010
New Phytologist 185 (2010)4. - ISSN 0028-646X - p. 1108 - 1118.
transposable elements - arabidopsis-thaliana - epigenetic inheritance - phenotypic plasticity - disease resistance - plant evolution - gene-expression - tobacco plants - genome - hypomethylation
DNA methylation can cause heritable phenotypic modifications in the absence of changes in DNA sequence. Environmental stresses can trigger methylation changes and this may have evolutionary consequences, even in the absence of sequence variation. However, it remains largely unknown to what extent environmentally induced methylation changes are transmitted to offspring, and whether observed methylation variation is truly independent or a downstream consequence of genetic variation between individuals.•Genetically identical apomictic dandelion (Taraxacum officinale) plants were exposed to different ecological stresses, and apomictic offspring were raised in a common unstressed environment. We used methylation-sensitive amplified fragment length polymorphism markers to screen genome-wide methylation alterations triggered by stress treatments and to assess the heritability of induced changes.•Various stresses, most notably chemical induction of herbivore and pathogen defenses, triggered considerable methylation variation throughout the genome. Many modifications were faithfully transmitted to offspring. Stresses caused some epigenetic divergence between treatment and controls, but also increased epigenetic variation among plants within treatments.•These results show the following. First, stress-induced methylation changes are common and are mostly heritable. Second, sequence-independent, autonomous methylation variation is readily generated. This highlights the potential of epigenetic inheritance to play an independent role in evolutionary processes, which is superimposed on the system of genetic inheritance.
Metabolomic analysis of the interaction between plants and herbivores
Jansen, J.J. ; Allwood, J.W. ; Marsden-Edwards, E. ; Putten, W.H. van der; Goodacre, R. ; Dam, M. van - \ 2009
Metabolomics 5 (2009)1. - ISSN 1573-3882 - p. 150 - 161.
magnetic-resonance-spectroscopy - brassica-rapa leaves - jasmonic acid - pieris-rapae - induced resistance - induced responses - cell-cultures - defense - sequestration - insect
Insect herbivores by necessity have to deal with a large arsenal of plant defence metabolites. The levels of defence compounds may be increased by insect damage. These induced plant responses may also affect the metabolism and performance of successive insect herbivores. As the chemical nature of induced responses is largely unknown, global metabolomic analyses are a valuable tool to gain more insight into the metabolites possibly involved in such interactions. This study analyzed the interaction between feral cabbage (Brassica oleracea) and small cabbage white caterpillars (Pieris rapae) and how previous attacks to the plant affect the caterpillar metabolism. Because plants may be induced by shoot and root herbivory, we compared shoot and root induction by treating the plants on either plant part with jasmonic acid. Extracts of the plants and the caterpillars were chemically analysed using Ultra Performance Liquid Chromatography/Time of Flight Mass Spectrometry (UPLCT/MS). The study revealed that the levels of three structurally related coumaroylquinic acids were elevated in plants treated on the shoot. The levels of these compounds in plants and caterpillars were highly correlated: these compounds were defined as the ‘metabolic interface’. The role of these metabolites could only be discovered using simultaneous analysis of the plant and caterpillar metabolomes. We conclude that a metabolomics approach is useful in discovering unexpected bioactive compounds involved in ecological interactions between plants and their herbivores and higher trophic levels
Field parasitism rates of caterpillars on Brassica oleracea plants are reliably predicted by diffential attraction of Cotesia parasitoids
Poelman, E.H. ; Oduor, A.M.O. ; Broekgaarden, C. ; Hordijk, C.A. ; Jansen, J.J. ; Loon, J.J.A. van; Dam, N.M. van; Vet, L.E.M. ; Dicke, M. - \ 2009
Functional Ecology 23 (2009)5. - ISSN 0269-8463 - p. 951 - 962.
natural enemies - rubecula hymenoptera - methyl salicylate - abiotic factors - damaged plants - herbivore - volatiles - defense - host - specialist
1. Herbivore-induced plant volatiles (HIPVs) play an important role in host location of parasitoid wasps and may benefit the plant by top–down control of its herbivorous attackers. Although many studies have shown that accessions of plants differ in attractiveness to parasitoid wasps under controlled laboratory studies, few studies have confirmed that the most attractive accessions also sustain highest parasitism rates in the field. Here, we tested whether in-flight preference of parasitoids for HIPVs from cultivars of Brassica oleracea in the laboratory reliably predicts the parasitism rates of herbivores feeding on these cultivars in the field. 2. In wind tunnel tests in the laboratory, we ranked cultivars of B. oleracea for the preference of two congeneric parasitoids (Cotesia glomerata and C. rubecula) for their HIPVs. The cultivars were then compared for their relative parasitism rates of caterpillars in the field. Throughout the growth season in the field, we infested the different cultivars with Pieris caterpillars on a weekly basis. The caterpillars were recollected after 3 days, dissected and scored for the rate of parasitism. 3. Cultivars of B. oleracea that we identified as most attractive to parasitoids in the laboratory also sustained highest proportions of parasitism in the field. The composition of the headspace of the B. oleracea cultivars damaged by P. rapae differs among these cultivars in the amounts of terpenoids and methyl salicylate emitted, which may be responsible for the differential attraction of parasitoids to the cultivars. 4. Our results show that intraspecific variation in HIPVs of plants is paralleled by differential parasitism of caterpillars in the field. The widely used laboratory assays on HIPV-based preferences of parasitoids provided reliable information on relative parasitism differences of herbivores as found in the field. 5. Thereby, our work confirms that through HIPVs plants attract parasitoids that effectively parasitize herbivores even under the complex and variable abiotic and biotic conditions in (agro-) ecosystems
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